diff --git a/README.md b/README.md
index b36447b266276e1d14d582ca37f11b88b0940a0d..cfb0bb098f004ff6bb307f4e6d24454ab489540e 100755
--- a/README.md
+++ b/README.md
@@ -10,21 +10,16 @@ Determining cellular heterogeneity in the human prostate with single-cell RNA se
* PI: Douglas W. Strand, PhD
* <a href="https://orcid.org/0000-0002-0746-927X" target="orcid.widget" rel="noopener noreferrer" style="vertical-align:top;"><img src="https://orcid.org/sites/default/files/images/orcid_16x16.png" style="width:1em;margin-right:.5em;" alt="ORCID iD icon">orcid.org/0000-0002-0746-927X</a>
* PI Email: [douglas.strand@utsouthwestern.edu](mailto:douglas.strand@utsouthwestern.edu)
+* **ANALYZED DATA FOR QUERYING AT: [StrandLab.net](http://strandlab.net/analysis.php)**
+* **Raw data at: [GEO (scRNA-Seq)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117403) & [GEO (popRNA-Seq)](https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE117271) & [GenitoUrinary Development Molecular Anatomy Project (GUDMAP)]("https://doi.org/10.25548/W-R8CM")**
+* **Publication at: PENDING**
Data Analysis
-------------
* **Requirements:**
- * /analysis/DATA/D17PrF/
- * D17PrF-demultiplex.csv
- * 10x/
- * aggregation_csv.csv
- * GRCh38/
- * "barcodes.tsv"
- * "genes.tsv"
- * "matrix.mtx"
- * /analysis/DATA/D27PrF/
- * D27PrF-demultiplex.csv
+ * /analysis/DATA/
+ * Pd-demultiplex.csv
* 10x/
* aggregation_csv.csv
* GRCh38/
@@ -46,12 +41,15 @@ Data Analysis
* RColorBrewer (v1.1-2)
* monocle (v2.6.3)
* dplyr (v0.7.6)
+ * viridis (v0.5.1)
* *and all dependencies*
* **HOW TO RUN**
- * 1 Patient D17PrF
- * run bash script sc_TissueMapper-D17PrF.sh
- * 2 Patients D17PrF and D27PrF
- * run bash script sc_TissueMapper-DPrF2.sh
+ * 1 Run on 3 patient aggregate
+ * run bash script [sc\_TissueMapper\-Pr.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-Pd.sh)
+ * 2 Run on 1st patent FACS samples
+ * run bash script [sc\_TissueMapper\-D17\_FACS.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-D17_FACS.sh)
+ * 3 Run on 2nd patient FACS samples
+ * run bash script [sc\_TissueMapper\-D27\_FACS.sh](https://git.biohpc.swmed.edu/StrandLab/sc-TissueMapper_Pr/blob/master/bash.scripts/sc_TissueMapper-D27_FACS.sh)
* **Pipeline:**
* Link cellranger count/aggr output to analysis
* Create demultiplex file to add custom sample groups
@@ -61,8 +59,8 @@ Data Analysis
* Load cellranger data into R/Seurat
* Label cells based on their cell cycle stated using Seurat based method
* QC and filter cells/genes
- * *If combining multiple experiments:* Align experiments using canonical correlation analysis (CCA)
- * Perform principle component analysis (PCA) using most highly variable genes (HVG) for downstream clustering etc
+ * *If analyzing samples from multiple patients:* Align experiments using canonical correlation analysis (CCA)
+ * *If analyzing samples from one patient:* Perform principle component analysis (PCA) using most highly variable genes (HVG) for downstream clustering etc
* Perform initial "over" clustering
* Identify "highly stressed" cells using custom PCA based analysis, remove stressed clusters/cells, and re-cluster
* Correlate cluster gene expression using Quantitative Set Analysis for Gene Expression (QuSAGE) on lineage genesets for identification (epithelia, and stroma)
@@ -82,36 +80,40 @@ Data Analysis
* "regev\_lab\_cell\_cycle\_genes.txt" G2M and S phase genes from [*Genome Res. 2015 Dec; 25(12): 1860–1872*](https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4665007/)
* Stress:
* "DEG\_C2.CGP.M10970.txt" MSigDB C2 Chemical and Genetic Perturbations M10970 [**CHUANG\_OXIDATIVE\_STRESS\_RESPONSE\_UP**](http://software.broadinstitute.org/gsea/msigdb/cards/CHUANG_OXIDATIVE_STRESS_RESPONSE_UP.html)
- * "genes.deg.Stress.csv" DWS generated DEGs of stressed cells from scRNA-Seq of patient D17 only
- * "" DWS generated DEGs of stressed cells from scRNA-Seq of an aggregation of patient D17 and D27
+ * "genes.deg.Stress.csv" DWS generated DEGs of stressed cells from scRNA-Seq of 3 patient aggregate
* Lineage:
* "DEG\_Epi_5FC.txt" DWS generated DEGs of epithelia from FACS population (bulk) RNA-sequencing
* "DEG\_FMSt_5FC.txt" DWS generated DEGs of fibromuscular stroma from FACS population (bulk) RNA-sequencing
- * "genes.deg.Epi.csv" DWS generated DEGs of epithelial cells from scRNA-Seq of patient D17 only
- * "genes.deg.St.csv" DWS generated DEGs of stromal cells from scRNA-Seq of patient D17 only
- * "" DWS generated DEGs of epithelial cells from from scRNA-Seq of an aggregation of patient D17 and D27
- * "" DWS generated DEGs of stromal cells from scRNA-Seq of an aggregation of patient D17 and D27
+ * "genes.deg.Epi.csv" DWS generated DEGs of epithelial cells from scRNA-Seq of 3 patient aggregate
+ * "genes.deg.St.csv" DWS generated DEGs of stromal cells from scRNA-Seq of 3 patient aggregate
* Epithelia:
* "DEG\_BE_5FC.txt" DWS generated DEGs of basal epithelia from FACS population (bulk) RNA-sequencing
* "DEG\_LE_5FC.txt" DWS generated DEGs of luminal epithelia from FACS population (bulk) RNA-sequencing
* "DEG\_OE_5FC.txt" DWS generated DEGs of "other" epithelia from FACS population (bulk) RNA-sequencing
- * "genes.deg.BE.csv" DWS generated DEGs of basal epithelial cells from scRNA-Seq of patient D17 only
- * "genes.deg.LE.csv" DWS generated DEGs of luminal epithelial cells from scRNA-Seq of patient D17 only
- * "genes.deg.OE1.csv" DWS generated DEGs of "other" epithelia cluster 1 cells from scRNA-Seq of patient D17 only
- * "genes.deg.OE2.csv" DWS generated DEGs of "other" epithelia cluster 2 cells from scRNA-Seq of patient D17 only
+ * "genes.deg.BE.csv" DWS generated DEGs of basal epithelial cells from scRNA-Seq of 3 patient aggregate
+ * "genes.deg.LE.csv" DWS generated DEGs of luminal epithelial cells from scRNA-Seq of 3 patient aggregate
+ * "genes.deg.OE1.csv" DWS generated DEGs of "other" epithelia cluster 1 cells from scRNA-Seq of 3 patient aggregate
+ * "genes.deg.OE2.csv" DWS generated DEGs of "other" epithelia cluster 2 cells from scRNA-Seq of 3 patient aggregate
* Stroma:
* "DEG\_C5.BP.M11704.txt" MSigDB C5 GO Biological Processes M11704 [**GO\_ENDOTHELIAL\_CELL\_DIFFERENTIATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_ENDOTHELIAL_CELL_DIFFERENTIATION.html)
* "DEG\_C5.BP.M10794.txt" MSigDB C5 GO Biological Processes M10794 [**GO\_SMOOTH\_MUSCLE\_CELL\_DIFFERENTIATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_SMOOTH_MUSCLE_CELL_DIFFERENTIATION.html)
* "DEG\_C5.BP.M13024.txt" MSigDB C5 GO Biological Processes M13024 [**GO\_REGULATION\_OF\_FIBROBLAST\_PROLIFERATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_REGULATION_OF_FIBROBLAST_PROLIFERATION.html)
* "DEG\_C5.BP.M10124.txt" MSigDB C5 GO Biological Processes M10124 [**GO\_LEUKOCYTE\_ACTIVATION**](http://software.broadinstitute.org/gsea/msigdb/cards/GO_LEUKOCYTE_ACTIVATION.html)
+ * "genes.deg.Fib.csv" DWS generated DEGs of fibroblast cells from scRNA-Seq of 3 patient aggregate
+ * "genes.deg.SM.csv" DWS generated DEGs of smooth muscle cells from scRNA-Seq of 3 patient aggregate
+ * "genes.deg.Endo.csv" DWS generated DEGs of endothelial ccells from scRNA-Seq of 3 patient aggregate
+ * "genes.deg.Leu.csv" DWS generated DEGs of leukocyte cells from scRNA-Seq of 3 patient aggregate
* Neuroendocrine:
* "EurUrol.2005.NE.txt" Neuroendocrine markers from Table 1 of [*Eur Urol. 2005 Feb;47(2):147-55*](https://www.ncbi.nlm.nih.gov/pubmed/15661408)
- * "genes.deg.NE.csv" DWS generated DEGs of neuroendocrine epithelial cells from scRNA-Seq of patient D17 only
- * "" DWS generated DEGs of neuroendocrine epithelial cells from scRNA-Seq of patient D17 only
+ * "genes.deg.NE.csv" DWS generated DEGs of neuroendocrine epithelial cells from scRNA-Seq of 3 patient aggregate
* Lung epithelia from [Lung Gene Expression Analysis (LGEA) Web Portal](https://research.cchmc.org/pbge/lunggens/mainportal.html):
* "Basal cells-signature-genes.csv" scRNA-Seq LGEA generated top 20 DEGs for [human lung Basal Cells] (https://research.cchmc.org/pbge/lunggens/lungDisease/celltype_IPF.html?cid=3)
* "Normal AT2 cells-signature-genes.csv" scRNA-Sequecing LGEA generated top 20 DEGs for [human lung Alveolar Type 2 Cells](https://research.cchmc.org/pbge/lunggens/lungDisease/celltype_IPF.html?cid=1)
* "Club\_Goblet cells-signature-genes.csv" scRNA-Sequencing LGEA generated top 20 DEGs for [human lung Club/Goblet Cells](https://research.cchmc.org/pbge/lunggens/lungDisease/celltype_IPF.html?cid=4)
+ * Lung epithelia from [*Nature 2018 Aug;560(7718):319*](https://doi.org/10.1038/s41586-018-0393-7)
+ * "SupTab3\_Consensus\_Sigs.csv" scRNA-Sequencing DEGs of mouse basal, club, ciliated, tuft, neuroendocrine, ionocyte cells (Supplementary Tables, SupTab3\_Consensus\_Sigs)
+ * "SupTab6\_Krt13\_Hillock.csv" scRNA-Sequencing DEGs of mouse Krt13+ hillock cells (Supplementary Tables, SupTab6\_Krt13\_Hillock)
+ * "Ensemble.mus-hum.txt" Ensemble export of mouse (GRCm38.p6) to human ortholog mapping
* General MSigDb
* "c2.all.v6.1.symbols.gmt" MSigDB C2 Curated Gene Sets [**MSigDB C2**](http://software.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=C2)
* "c2.cp.kegg.v6.1.symbols" MSigDB C2 KEGG Gene Subsets [**KEGG**](http://software.broadinstitute.org/gsea/msigdb/genesets.jsp?collection=CP:KEGG)
diff --git a/bash.scripts/sc_TissueMapper-D17_FACS.sh b/bash.scripts/sc_TissueMapper-D17_FACS.sh
new file mode 100644
index 0000000000000000000000000000000000000000..a1b9e80f4b3ce0e426aa055443adfa3bf91f95cd
--- /dev/null
+++ b/bash.scripts/sc_TissueMapper-D17_FACS.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+#SBATCH --job-name R_FullAnalysis
+#SBATCH -p 256GB,256GBv1,384GB
+#SBATCH -N 1
+#SBATCH -t 7-0:0:0
+#SBATCH -o job_%j.out
+#SBATCH -e job_%j.out
+#SBATCH --mail-type ALL
+#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
+
+module load R/3.4.1-gccmkl
+
+Rscript ../r.scripts/sc-TissueMapper_RUN.D17_FACS.R
diff --git a/bash.scripts/sc_TissueMapper-D27_FACS.sh b/bash.scripts/sc_TissueMapper-D27_FACS.sh
new file mode 100644
index 0000000000000000000000000000000000000000..492d870914d32d72cbfe82f9a201fee8df210ae4
--- /dev/null
+++ b/bash.scripts/sc_TissueMapper-D27_FACS.sh
@@ -0,0 +1,13 @@
+#!/bin/bash
+#SBATCH --job-name R_FullAnalysis
+#SBATCH -p 256GB,256GBv1,384GB
+#SBATCH -N 1
+#SBATCH -t 7-0:0:0
+#SBATCH -o job_%j.out
+#SBATCH -e job_%j.out
+#SBATCH --mail-type ALL
+#SBATCH --mail-user gervaise.henry@utsouthwestern.edu
+
+module load R/3.4.1-gccmkl
+
+Rscript ../r.scripts/sc-TissueMapper_RUN.D27_FACS.R
diff --git a/genesets/DEG_C2.CGP.M10970.txt b/genesets/DEG_C2.CGP.M10970.txt
index cf19e5894e208ba53d22f4caff433554740f7836..2c11eacf33be93632fb1aaf802774540ff38c79e 100755
--- a/genesets/DEG_C2.CGP.M10970.txt
+++ b/genesets/DEG_C2.CGP.M10970.txt
@@ -1,5 +1,4 @@
CHUANG_OXIDATIVE_STRESS_RESPONSE_UP
-> Genes up-regulated in MCF7 cells (breast cancer) after treatment with the oxydants: hydrogen peroxyde, menadione, and t-butyl hydroperoxyde [PubChem=784;4055;6410].
CTAGE5
CYP1B1
DDIT3
@@ -27,4 +26,4 @@ PSMD3
RCBTB1
RPL38
SLC35B3
-ZBTB4
\ No newline at end of file
+ZBTB4
diff --git a/genesets/SupTab3_Consensus_Sigs.csv b/genesets/SupTab3_Consensus_Sigs.csv
new file mode 100644
index 0000000000000000000000000000000000000000..4470e84bda5bc86370ace0c03784830b9731ebcb
--- /dev/null
+++ b/genesets/SupTab3_Consensus_Sigs.csv
@@ -0,0 +1,288 @@
+Supplementary Table 3,,,,,
+"Consensus marker genes for cell-type clusters from both initial 3' droplet-based and full-length plate-based scRNA-seq data (7,193 + 301 cells, in Sup. Tabs 1 and 2, respectively)",,,,,
+"Thresholds: Fisher's combined FDR: 0.001 for plate-based and maximum FDR: 0.05 for droplet-based, Minimum log2 fold-change:0.25",,,,,
+,,,,,
+,,,,,
+,,,,,
+Basal,Club,Ciliated,Tuft,Neuroendocrine,Ionocyte
+Aqp3,Scgb1a1,AU040972,Lrmp,Chga,Stap1
+Icam1,Bpifa1,Tmem212,Gnat3,Calca,Gm933
+Krt17,Scgb3a2,Dynlrb2,Gnb3,Cxcl13,Ascl3
+Krt5,Sftpd,Ccdc153,Plac8,Scg2,Foxi1
+Krt15,Alox15,Tppp3,Trpm5,Nov,Atp6v0d2
+Sfn,Pon1,1110017D15Rik,Gng13,Scg5,Moxd1
+Perp,Cyp4a12b,Fam183b,Ltc4s,Pcsk1,Gnas
+Fxyd3,Wfdc1,Sec14l3,Rgs13,Dnajc12,Ldhb
+Sdc1,Mgst1,Pltp,Hck,Uchl1,Rasd1
+Gstm2,Akr1c18,Rsph1,Alox5ap,Ddc,P2ry14
+F3,Sftpa1,Mlf1,Avil,Snca,Tfcp2l1
+Epas1,Lypd2,2410004P03Rik,Alox5,Snap25,Cd81
+Abi3bp,Ces1f,Tekt1,Ptpn6,Cib3,Cftr
+Adh7,Gsto1,Cdh26,Atp2a3,Bex2,Slc12a2
+Id1,Tst,Cdhr3,Plk2,Guk1,Asgr1
+Upk1b,Ffar4,Nme5,Zfp428,Chgb,Parm1
+Hspa1a,Hp,Ccdc17,Ethe1,Ascl1,Atp6v1e1
+Dapl1,Chad,Adam8,Mctp1,Ngf,Iqgap1
+Hspb1,Selenbp1,Cyp2s1,Fxyd6,Cplx2,Rbpms
+Zfp296,Mgat3,1700007K13Rik,1810046K07Rik,Igfbp5,
+Dcn,Gabrp,Tm4sf1,Pik3r5,Pkib,
+Rplp0,,Elof1,Cd300lf,Lrp11,
+Fam107b,,Ly6a,Rassf6,Tcerg1l,
+Tacstd2,,Sntn,Dclk1,Rbp4,
+Rpl13,,Ppil6,Spib,Mthfd2,
+Sat1,,Ifitm1,Pik3cg,Cd9,
+Sult1d1,,Tctex1d4,Pde2a,Meis2,
+Hpgd,,Aldh3b1,Matk,Ly6h,
+S100a14,,Lrrc48,Vav1,Tmem158,
+Rps18,,Foxj1,Sh2d7,Cacna2d1,
+Emp1,,1700026L06Rik,Bmx,Syt7,
+Sgk1,,Csrp2,Fyb,Ptp4a3,
+Gsta4,,Pifo,Ccdc28b,,
+Rps4x,,Acot1,Ptpn18,,
+Rps5,,Dnali1,Bpgm,,
+Oat,,Ccdc113,Itgb7,,
+Rps8,,Pcp4l1,Ccdc109b,,
+S100a16,,Spag6,Anxa4,,
+Phlda3,,Capsl,Rgs2,,
+Dusp1,,Lrrc51,Tspan6,,
+Crlf1,,2610028H24Rik,Prss53,,
+Sh3bgrl3,,Ldlrad1,Ly6g6f,,
+Rps2,,Stmnd1,Inpp5d,,
+Junb,,1700024G13Rik,Ivns1abp,,
+Pcolce,,Dmkn,Nkd1,,
+Cotl1,,Ccdc78,Sh3bgrl,,
+Sord,,Chchd6,Pou2f3,,
+Igfbp7,,1700016K19Rik,Sox9,,
+Rpl8,,Calml4,Chn2,,
+Rpl4,,Vpreb3,Krt18,,
+,,Odf3b,Calm2,,
+,,Ak7,Kctd12,,
+,,1700003M02Rik,Etv1,,
+,,1700026D08Rik,Coprs,,
+,,Lrrc23,Cd47,,
+,,BC051019,Espn,,
+,,Tubb4b,Tmem245,,
+,,Enkur,Pitpnc1,,
+,,Bphl,Hap1,,
+,,Spata18,Reep5,,
+,,Fam216b,H2afj,,
+,,Riiad1,Selm,,
+,,1700088E04Rik,NA,,
+,,1700007G11Rik,NA,,
+,,Rsph4a,NA,,
+,,Fam47e,NA,,
+,,Agr3,NA,,
+,,Fbxo36,NA,,
+,,1700001C02Rik,NA,,
+,,Cmbl,NA,,
+,,Spag16,NA,,
+,,Bok,NA,,
+,,Ift43,NA,,
+,,Ubxn10,NA,,
+,,Tekt4,NA,,
+,,Ccdc108,NA,,
+,,Erich2,NA,,
+,,6820408C15Rik,NA,,
+,,Prdx5,NA,,
+,,Fam92b,NA,,
+,,Smim5,NA,,
+,,Hdc,NA,,
+,,Serpina9,NA,,
+,,Ly6c1,NA,,
+,,Aldh1a1,NA,,
+,,Fhl1,NA,,
+,,4833427G06Rik,NA,,
+,,Rfk,NA,,
+,,Dnaic2,NA,,
+,,Ppp1r36,NA,,
+,,Ak8,NA,,
+,,B9d1,NA,,
+,,Chchd10,NA,,
+,,Zmynd10,NA,,
+,,Rsph9,NA,,
+,,Nek5,NA,,
+,,Gm973,NA,,
+,,Ccdc39,NA,,
+,,Efhc1,NA,,
+,,Hsph1,NA,,
+,,Tuba1b,NA,,
+,,Ubxn11,NA,,
+,,Slc23a2,NA,,
+,,Spa17,NA,,
+,,Nat9,NA,,
+,,Efcab10,NA,,
+,,Cd177,NA,,
+,,Hsp90aa1,NA,,
+,,Iqca,NA,,
+,,Dync2li1,NA,,
+,,Ruvbl1,NA,,
+,,Ppp1r32,NA,,
+,,Spef1,NA,,
+,,Ccdc81,NA,,
+,,Dnajb13,NA,,
+,,Acox2,NA,,
+,,Fhad1,NA,,
+,,Spag8,NA,,
+,,Nudc,NA,,
+,,Ccdc146,NA,,
+,,Pih1d2,NA,,
+,,Vwa3a,NA,,
+,,Fam179a,NA,,
+,,Fth1,NA,,
+,,Ccdc151,NA,,
+,,Lrrc36,NA,,
+,,Cxcl17,NA,,
+,,Kif9,NA,,
+,,Ccdc37,NA,,
+,,Mapk15,NA,,
+,,Lhb,NA,,
+,,Cd82,NA,,
+,,Fam161a,NA,,
+,,Rabl2,NA,,
+,,Fank1,NA,,
+,,Wdr63,NA,,
+,,Glipr1,NA,,
+,,Zfp474,NA,,
+,,Lgals3bp,NA,,
+,,Dpcd,NA,,
+,,Ttc29,NA,,
+,,Ttc16,NA,,
+,,Mdh1b,NA,,
+,,Ruvbl2,NA,,
+,,Gipc2,NA,,
+,,Arc,NA,,
+,,Mak,NA,,
+,,Dcdc2b,NA,,
+,,Ccdc30,NA,,
+,,1700028P14Rik,NA,,
+,,Mycbp,NA,,
+,,Oscp1,NA,,
+,,Morn5,NA,,
+,,Iqcg,NA,,
+,,Eno4,NA,,
+,,Ift74,NA,,
+,,Lrrc34,NA,,
+,,Cetn4,NA,,
+,,Ankrd66,NA,,
+,,Dnajc15,NA,,
+,,Ulk4,NA,,
+,,Tbata,NA,,
+,,Traf3ip1,NA,,
+,,Akr1b8,NA,,
+,,6430531B16Rik,NA,,
+,,Armc4,NA,,
+,,Maats1,NA,,
+,,Plekhb1,NA,,
+,,Meig1,NA,,
+,,Morn3,NA,,
+,,Lrrc71,NA,,
+,,1110004E09Rik,NA,,
+,,Ift88,NA,,
+,,Timp4,NA,,
+,,Fam166b,NA,,
+,,Ccdc121,NA,,
+,,Usp18,NA,,
+,,Ccdc33,NA,,
+,,Slc23a1,NA,,
+,,Gm166,NA,,
+,,1810037I17Rik,NA,,
+,,Syt5,NA,,
+,,Dnaaf1,NA,,
+,,Mns1,NA,,
+,,Dusp14,NA,,
+,,Wdr78,NA,,
+,,Dynll1,NA,,
+,,Gas8,NA,,
+,,Ccdc114,NA,,
+,,Crip2,NA,,
+,,Ctxn1,NA,,
+,,1700040L02Rik,NA,,
+,,Tcp11,NA,,
+,,Kif19a,NA,,
+,,Ccdc65,NA,,
+,,Tmem107,NA,,
+,,Adgb,NA,,
+,,Cib1,NA,,
+,,Dnaic1,NA,,
+,,Odc1,NA,,
+,,Dnaaf3,NA,,
+,,Cdkl4,NA,,
+,,Mrps17,NA,,
+,,Wdr34,NA,,
+,,Slc9a3r1,NA,,
+,,Kcnmb2,NA,,
+,,Swi5,NA,,
+,,Plin5,NA,,
+,,Zc2hc1a,NA,,
+,,Jam3,NA,,
+,,Lrrc6,NA,,
+,,Sptlc3,NA,,
+,,Hydin,NA,,
+,,Fam216a,NA,,
+,,4932443I19Rik,NA,,
+,,Ankrd42,NA,,
+,,Wdr60,NA,,
+,,Lrrc45,NA,,
+,,Spef2,NA,,
+,,Ezr,NA,,
+,,Wnt11,NA,,
+,,Fam213a,NA,,
+,,Gtsf1l,NA,,
+,,Lbp,NA,,
+,,Wdr95,NA,,
+,,Syne1,NA,,
+,,Abhd3,NA,,
+,,Tctex1d2,NA,,
+,,Ttc39a,NA,,
+,,Lrrc46,NA,,
+,,Stk33,NA,,
+,,Slc2a12,NA,,
+,,Mipep,NA,,
+,,Mst1,NA,,
+,,Myl4,NA,,
+,,Oaz2,NA,,
+,,Ttc12,NA,,
+,,Ccdc176,NA,,
+,,Ift57,NA,,
+,,Wdr54,NA,,
+,,4930444P10Rik,NA,,
+,,Tuba1a,NA,,
+,,1700013F07Rik,NA,,
+,,Mxra8,NA,,
+,,D430036J16Rik,NA,,
+,,Spag17,NA,,
+,,Ddo,NA,,
+,,Sri,NA,,
+,,Ctsk,NA,,
+,,Calm1,NA,,
+,,4430402I18Rik,NA,,
+,,2310007B03Rik,NA,,
+,,Psmc3ip,NA,,
+,,Nudt4,NA,,
+,,Ttll9,NA,,
+,,Dusp18,NA,,
+,,Rfc2,NA,,
+,,1700029J07Rik,NA,,
+,,Naga,NA,,
+,,Akap14,NA,,
+,,Atp2a2,NA,,
+,,Pttg1,NA,,
+,,Casc1,NA,,
+,,Ccdc60,NA,,
+,,Dydc2,NA,,
+,,Lrrc10b,NA,,
+,,Mycbpap,NA,,
+,,1700001L19Rik,NA,,
+,,Dlec1,NA,,
+,,Kif6,NA,,
+,,Ropn1l,NA,,
+,,Eml2,NA,,
+,,Ech1,NA,,
+,,Slc1a4,NA,,
+,,Sftpc,NA,,
+,,1700101E01Rik,NA,,
+,,Efcab1,NA,,
+,,Sirt3,NA,,
+,,Pacrg,NA,,
+,,Cdc14a,NA,,
+,,Itln1,NA,,
diff --git a/genesets/SupTab6_Krt13_Hillock.csv b/genesets/SupTab6_Krt13_Hillock.csv
new file mode 100644
index 0000000000000000000000000000000000000000..1fa9fc8244896fd65a42b5a8ee323db9f1670e93
--- /dev/null
+++ b/genesets/SupTab6_Krt13_Hillock.csv
@@ -0,0 +1,5327 @@
+Supplementary Table 6,,,,
+Related to Extended Data 4g: Krt4+/Krt13+ hillock-associated genes from 3' droplet-based scRNA-seq,,,,
+Thresholds: all genes shown,,,,
+,,,,
+,,,,
+,,,,
+Gene,log2 fold-change (means),log2 fold-change (MAST),p,FDR
+Ltf,4.371203488,1.997240249,2.12E-49,2.80E-47
+Krt4,2.883475949,2.715058937,3.95E-132,6.28E-129
+Upk3bl,2.789597952,2.775599468,1.09E-119,1.15E-116
+Nupr1,2.636378961,1.374198552,1.46E-41,1.45E-39
+S100g,2.625057175,2.520313317,3.50E-77,1.13E-74
+Lyz2,2.546423323,0.614993261,0.000231006,0.000456555
+Calml3,2.475765933,2.099366701,1.19E-75,3.60E-73
+Pglyrp1,2.434081355,1.60674033,7.79E-46,8.84E-44
+Crip1,2.388405052,2.069027685,6.52E-103,3.77E-100
+Ecm1,2.357414095,2.494416786,1.79E-98,8.76E-96
+S100a6,2.340319525,1.921351835,8.96E-152,2.85E-148
+Plac8,2.248865737,2.037148508,1.30E-67,3.06E-65
+Tppp3,2.23317182,2.510407089,5.57E-91,2.53E-88
+Cyp2a5,2.17096444,0.759483717,4.25E-12,5.37E-11
+Lgals3,2.077996831,2.427323601,1.72E-143,3.65E-140
+Cxcl17,2.038171513,1.030735714,3.53E-28,1.84E-26
+Ly6a,1.837604202,1.39606292,3.87E-51,5.48E-49
+Anxa1,1.835708894,2.195120887,1.87E-156,1.19E-152
+Ly6g6c,1.787286065,2.287473681,2.38E-55,3.78E-53
+Pdzk1ip1,1.750092129,1.376609155,8.05E-64,1.71E-61
+Cldn3,1.736300069,1.47012116,3.04E-106,1.93E-103
+2200002D01Rik,1.708508705,1.594216664,6.22E-79,2.20E-76
+Gsto1,1.66989588,1.366396368,2.10E-99,1.11E-96
+Sftpd,1.627169073,0.823349108,1.12E-21,3.95E-20
+Aldh1a1,1.615581755,0.659550713,1.32E-13,2.12E-12
+Pmm1,1.600405893,1.51168239,8.49E-85,3.38E-82
+Ndufa4,1.585913199,1.03861041,5.42E-60,1.04E-57
+Aqp5,1.567800927,1.816979092,9.19E-115,7.30E-112
+Slc16a11,1.563973486,0.704549261,2.00E-23,7.71E-22
+Scgb1a1,1.548737328,-1.054654362,2.05E-11,2.24E-10
+Chchd10,1.439711453,0.907958686,1.21E-23,4.75E-22
+Mal,1.432942435,1.438213019,5.51E-67,1.25E-64
+Upk1b,1.425739123,1.855816764,1.19E-63,2.44E-61
+Serpinb2,1.363477724,1.719984036,1.76E-47,2.20E-45
+Selenbp1,1.350855341,1.163362137,6.83E-55,1.06E-52
+Wfdc2,1.300652298,0.73103849,8.70E-27,4.04E-25
+Krt13,1.297049823,1.62029367,4.89E-33,3.31E-31
+Krt7,1.290614332,1.938782188,3.15E-122,4.00E-119
+Lrrc26,1.290586953,0.789865688,1.91E-35,1.48E-33
+Gabrp,1.290280684,0.77771119,2.85E-33,1.95E-31
+Cyp2b10,1.288995542,1.023290897,1.00E-40,9.65E-39
+Muc1,1.278783396,0.72805763,2.70E-27,1.28E-25
+Ly6e,1.265519729,0.942961381,6.55E-59,1.23E-56
+Pdlim1,1.225608541,1.260436821,2.07E-56,3.65E-54
+Krt15,1.222297944,1.779374151,2.59E-66,5.67E-64
+Ttc36,1.203599663,0.980892597,1.49E-40,1.38E-38
+Igfbp5,1.203541629,1.026713226,1.08E-38,9.31E-37
+S100a11,1.194691909,1.21670117,3.29E-115,2.99E-112
+Anxa3,1.173804934,1.371011691,3.54E-77,1.13E-74
+Ffar4,1.16253494,1.055926181,2.97E-51,4.29E-49
+Cd24a,1.152102004,0.882856505,7.53E-21,2.46E-19
+Qsox1,1.151083325,0.563475343,3.41E-14,5.80E-13
+Clca3b,1.131627199,0.879408754,2.68E-54,4.05E-52
+Alox15,1.11465741,0.597393309,1.61E-21,5.57E-20
+Socs2,1.10811153,0.967715386,4.58E-43,4.94E-41
+Txn1,1.100613032,0.818346722,2.52E-32,1.65E-30
+Tspo,1.091116077,1.128067989,1.03E-68,2.52E-66
+Porcn,1.074923076,1.0537818,1.79E-36,1.50E-34
+Cldn23,1.05859618,1.045825728,4.94E-40,4.49E-38
+Tacstd2,1.053937863,1.389993294,1.42E-55,2.31E-53
+Map1lc3a,1.030562527,1.01468104,2.79E-56,4.79E-54
+Ahnak,1.019957973,0.982600986,7.70E-46,8.84E-44
+Anxa2,1.005931457,1.558051857,1.45E-109,1.03E-106
+Krt23,0.99687152,0.847909907,1.23E-28,6.68E-27
+1810037I17Rik,0.974937316,0.894585759,9.64E-36,7.57E-34
+Ces1f,0.969763476,0.345538642,7.68E-15,1.40E-13
+S100a10,0.954702046,1.770067525,4.71E-61,9.36E-59
+Muc4,0.953978097,0.812118201,5.19E-30,3.03E-28
+Mgst3,0.945952909,1.133024383,6.22E-44,6.82E-42
+Lypd2,0.937773557,0.337824172,7.49E-06,2.18E-05
+Tspan1,0.929865493,0.442746632,1.20E-08,6.90E-08
+Gsta4,0.929786044,1.190897298,1.65E-83,6.16E-81
+Cyba,0.91956081,0.620934448,2.02E-27,9.71E-26
+St3gal4,0.918893788,0.901165362,1.83E-42,1.94E-40
+Ctsh,0.910706194,0.777605097,2.34E-35,1.79E-33
+Cldn7,0.90457056,0.978312028,2.84E-50,3.85E-48
+Ypel3,0.900066516,0.789060168,2.17E-34,1.59E-32
+Adh7,0.898427476,1.128975278,7.58E-51,1.05E-48
+Tspan8,0.897599234,0.901707015,5.95E-28,3.05E-26
+Fmo3,0.896108264,0.423253268,2.00E-12,2.68E-11
+Lmo7,0.892474596,0.814248664,7.63E-26,3.35E-24
+Sub1,0.889348458,0.720605451,3.59E-31,2.26E-29
+Capg,0.879521526,1.096395228,1.48E-45,1.65E-43
+Cd44,0.870810067,0.882754332,1.68E-33,1.20E-31
+Ebp,0.869112144,0.802133586,2.88E-30,1.73E-28
+Alcam,0.86827811,0.632843245,2.41E-28,1.28E-26
+S100a14,0.866587556,1.112455256,1.36E-53,2.02E-51
+Taldo1,0.863789861,0.77983576,2.20E-39,1.97E-37
+Ifitm1,0.849831918,1.09227457,9.17E-36,7.29E-34
+Crip2,0.843335977,1.074021961,2.90E-48,3.76E-46
+Trp53inp2,0.84104974,0.789034015,2.17E-28,1.17E-26
+Cwh43,0.840379884,0.95214878,3.24E-38,2.75E-36
+Cmpk1,0.827305108,0.731710963,3.41E-27,1.61E-25
+Neat1,0.818735448,0.551991992,2.14E-15,4.20E-14
+Tmsb4x,0.807745933,1.139481666,3.44E-56,5.75E-54
+Ces1d,0.804905003,0.898131643,3.66E-30,2.16E-28
+Krt19,0.794526333,1.271993149,1.55E-89,6.59E-87
+Clic1,0.793190583,0.87935758,1.26E-46,1.51E-44
+Polr2f,0.789769521,0.577216203,2.33E-19,6.91E-18
+Clic3,0.784108248,0.787543894,6.68E-28,3.40E-26
+Mrpl14,0.769488254,0.519020512,4.77E-16,1.02E-14
+Myh14,0.768228861,0.489674501,3.07E-15,5.88E-14
+S100a1,0.76199469,0.493993847,3.70E-12,4.72E-11
+Ly6d,0.752698241,0.788240171,1.00E-15,2.03E-14
+Fth1,0.745891053,0.741920067,6.47E-46,7.62E-44
+Krt8,0.740280784,1.169984136,2.68E-69,6.82E-67
+Tst,0.738248347,0.186165823,0.002156685,0.003346308
+Spint2,0.737294865,0.690485847,1.21E-46,1.48E-44
+Kctd14,0.735383573,0.662637189,5.74E-29,3.20E-27
+Rab25,0.714352965,0.76710415,1.96E-34,1.45E-32
+Prdx5,0.711861156,0.621110872,2.81E-16,6.10E-15
+Prr13,0.707096455,0.694790969,3.55E-32,2.28E-30
+Cyb5a,0.705088238,0.604360207,3.85E-32,2.45E-30
+Pllp,0.703824059,0.692012757,1.60E-29,9.11E-28
+Agr2,0.703116433,0.273413409,0.031796216,0.038889217
+Gprc5a,0.69781096,1.015837642,1.05E-47,1.34E-45
+Emp2,0.697236819,0.746551681,9.06E-23,3.31E-21
+AU040972,0.694985987,0.730521948,6.60E-20,2.00E-18
+Cmas,0.685811921,0.574685305,6.82E-24,2.71E-22
+Pmp22,0.685275009,0.9738596,1.16E-32,7.68E-31
+Pdlim2,0.684833643,0.669799346,1.13E-29,6.51E-28
+Ctnnb1,0.681419428,0.576769625,7.40E-19,2.13E-17
+Cav1,0.680456864,1.017386127,6.87E-36,5.53E-34
+Foxq1,0.676065481,0.775778503,3.59E-24,1.47E-22
+Atp5e,0.672654135,0.153211556,0.018049813,0.023056199
+H3f3a,0.664436966,0.627378373,7.84E-25,3.33E-23
+Uqcr10,0.663129944,0.318011208,1.96E-06,6.61E-06
+Rfk,0.654888915,0.49920186,3.38E-18,8.94E-17
+Tmbim1,0.644259135,0.864612531,2.52E-30,1.52E-28
+Rpl39,0.640504176,-0.099637564,0.001190015,0.001965333
+Akr1c18,0.640483512,0.255153818,5.27E-12,6.52E-11
+Pfdn1,0.639186814,0.437057487,2.64E-20,8.32E-19
+Esd,0.633927738,0.811302872,2.57E-34,1.86E-32
+Clu,0.632531709,0.27781023,1.56E-09,1.10E-08
+Ces1h,0.630684768,0.692871044,4.44E-24,1.79E-22
+Psmb8,0.622914945,0.398876833,2.81E-17,6.68E-16
+Bace2,0.621442907,0.601131261,5.33E-23,1.99E-21
+Ndufa2,0.621255888,0.309563106,4.70E-08,2.30E-07
+Arpc3,0.6206854,0.672748222,3.05E-22,1.10E-20
+Metap2,0.603795682,0.515537533,1.32E-21,4.65E-20
+Epcam,0.603050412,0.710114043,2.82E-24,1.17E-22
+Ppap2c,0.601677288,0.554155971,1.50E-29,8.62E-28
+Chmp4b,0.601440959,0.500861167,1.79E-16,3.97E-15
+Ubl5,0.594961565,0.24664164,2.63E-10,2.23E-09
+Sf3b6,0.592306892,0.598381384,4.24E-21,1.39E-19
+Ndufa7,0.592180174,0.24533883,1.07E-11,1.25E-10
+Sptssb,0.591447344,0.82860992,1.30E-27,6.46E-26
+Rbx1,0.583128511,0.500905654,1.34E-17,3.40E-16
+Wfdc1,0.581184056,0.213030234,4.01E-11,4.15E-10
+Ccnl1,0.579586339,0.534377495,2.36E-17,5.69E-16
+2300002M23Rik,0.576712328,0.813465239,1.61E-34,1.20E-32
+Atp5j2,0.576360505,0.327417452,5.16E-11,5.20E-10
+Rnf186,0.575875474,0.323534079,9.13E-19,2.61E-17
+Gipc1,0.574048589,0.648659134,1.84E-23,7.16E-22
+Nbl1,0.572163602,0.991531819,2.32E-36,1.92E-34
+Ndufb7,0.570301638,0.231998241,1.96E-08,1.07E-07
+Ralbp1,0.569760701,0.614292855,1.39E-17,3.51E-16
+Cox6b1,0.567709456,0.331045321,2.95E-11,3.15E-10
+Alox12e,0.565593627,0.488103193,7.69E-20,2.32E-18
+Arpp19,0.56351867,0.45984153,3.30E-18,8.78E-17
+Cd82,0.558563408,0.55016776,2.10E-24,8.79E-23
+Fxyd3,0.554764106,0.743706806,4.60E-24,1.84E-22
+Tceb2,0.553063417,0.499765806,1.21E-18,3.39E-17
+Bspry,0.55145778,0.549435508,1.95E-21,6.61E-20
+Rps27l,0.549332968,0.369721039,3.75E-10,3.06E-09
+Shfm1,0.54810951,0.393344097,2.38E-13,3.76E-12
+Phlda1,0.547879941,0.966581005,2.58E-33,1.79E-31
+Fam129b,0.547474861,0.472920875,7.43E-23,2.75E-21
+Sdcbp,0.544450287,0.699628196,4.73E-22,1.69E-20
+Ptgr1,0.542823778,0.403617969,1.34E-16,3.04E-15
+Cstb,0.539113921,0.674632622,1.21E-24,5.11E-23
+Atox1,0.538694149,0.462898327,6.23E-14,1.04E-12
+Ostf1,0.537753851,0.57709475,5.39E-23,2.00E-21
+Spint1,0.534901012,0.495687351,1.57E-21,5.47E-20
+Mfge8,0.532687042,0.661997658,1.82E-26,8.19E-25
+Ezr,0.532094357,0.917072742,8.33E-42,8.41E-40
+Basp1,0.5319966,0.122200995,8.70E-07,3.20E-06
+Prr15l,0.529561703,0.352720738,2.60E-11,2.80E-10
+S100a13,0.52531881,0.346656945,1.18E-16,2.68E-15
+Gng5,0.52281917,0.423381985,8.90E-16,1.82E-14
+Plet1,0.52240226,0.436157161,4.12E-10,3.32E-09
+Vamp8,0.521309848,0.586180003,1.87E-21,6.36E-20
+Crb3,0.521152381,0.471016491,3.58E-21,1.19E-19
+H2-D1,0.519478817,0.518021152,9.54E-18,2.45E-16
+Ly6g6e,0.518579474,0.499417569,3.24E-25,1.38E-23
+2010107E04Rik,0.518122382,0.050432783,2.78E-05,6.96E-05
+Por,0.517978537,0.281771986,4.07E-05,9.73E-05
+Ddah2,0.517398495,0.523953048,1.17E-20,3.75E-19
+Tmem238,0.514138514,0.426885484,2.79E-14,4.76E-13
+Areg,0.513720861,0.743311088,9.97E-20,2.99E-18
+Anapc13,0.509834503,0.162959293,2.26E-10,1.96E-09
+Timm13,0.509718356,0.278520995,1.06E-10,1.00E-09
+Atp6v0e,0.509484396,0.513428623,6.24E-20,1.90E-18
+Vpreb3,0.508395254,0.348534312,4.44E-08,2.19E-07
+Fam32a,0.505738275,0.399461514,1.99E-15,3.92E-14
+Ptgs2,0.504346603,0.527917395,1.64E-18,4.54E-17
+Atpif1,0.501608218,0.577289791,4.48E-20,1.37E-18
+Mall,0.500862163,0.688995533,1.88E-27,9.11E-26
+Ahnak2,0.499581125,0.477213363,4.36E-17,1.02E-15
+Smim6,0.498488377,0.236298103,1.85E-12,2.50E-11
+Ptp4a2,0.495648673,0.406727777,1.03E-13,1.67E-12
+Acadl,0.495040706,0.427715916,1.15E-15,2.31E-14
+Pls3,0.491749238,0.613539064,3.29E-19,9.55E-18
+Ctnna1,0.49018073,0.477278248,9.36E-18,2.41E-16
+Sec14l3,0.490114109,0.138930084,1.40E-08,7.91E-08
+1700027J19Rik,0.489499244,0.457234245,9.71E-19,2.76E-17
+D8Ertd738e,0.488899787,0.323667139,1.52E-17,3.78E-16
+Myof,0.488314983,0.355297611,2.17E-12,2.88E-11
+Fus,0.48789346,0.483032257,6.78E-16,1.42E-14
+Cldn4,0.485955648,1.48917945,1.03E-58,1.86E-56
+Hes1,0.484457177,0.745293651,2.84E-19,8.32E-18
+Ost4,0.483554673,0.324319079,2.96E-09,1.94E-08
+Tnfrsf21,0.483117679,0.487804355,2.43E-18,6.63E-17
+Rpp21,0.480309496,0.307585766,9.69E-12,1.14E-10
+Mrpl57,0.480175459,0.27128739,6.77E-16,1.42E-14
+Gnai2,0.477453436,0.446874949,1.38E-12,1.92E-11
+Hint1,0.474562686,0.607642557,1.25E-17,3.18E-16
+Cox6a1,0.471517354,0.381822276,1.19E-10,1.11E-09
+Rab11a,0.466614196,0.531275305,1.83E-17,4.48E-16
+Hebp2,0.466349805,0.452959464,2.75E-19,8.15E-18
+Polr2e,0.463807451,0.417652782,5.43E-14,9.09E-13
+Ppp2ca,0.463600875,0.45859629,3.07E-18,8.26E-17
+Shisa5,0.46347224,0.544163696,8.56E-22,3.04E-20
+Serpinb1a,0.46296659,0.543331274,3.48E-17,8.22E-16
+Anxa5,0.460765897,0.822595888,1.81E-27,8.85E-26
+Hcfc1r1,0.45954638,0.325623329,2.19E-12,2.90E-11
+Sri,0.458473137,0.595635949,4.07E-21,1.34E-19
+Atp5j,0.458103924,0.384698087,2.72E-10,2.30E-09
+Sat1,0.455223124,0.730943444,3.71E-26,1.65E-24
+Gltp,0.4551206,0.611206666,1.46E-21,5.09E-20
+Uqcrb,0.45356604,0.109974433,2.47E-08,1.30E-07
+Rbm39,0.452947633,0.320200611,3.34E-11,3.54E-10
+Tagln2,0.450900805,0.704384441,4.58E-29,2.58E-27
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+Chrac1,0.208259497,0.102746873,8.36E-08,3.85E-07
+Dnlz,0.207833493,0.074725145,2.01E-07,8.56E-07
+Epb41l4b,0.207393139,0.137395353,2.10E-09,1.42E-08
+Sod1,0.207138244,-0.095934715,0.002225956,0.003440359
+Dsp,0.207011867,0.249023893,1.31E-08,7.41E-08
+Gdpd1,0.206363011,0.115724123,3.97E-08,1.99E-07
+Flii,0.205941642,0.184047117,7.04E-06,2.07E-05
+Fam63a,0.205586515,0.150545041,1.39E-10,1.26E-09
+Metrnl,0.205546236,0.180379301,1.68E-09,1.17E-08
+Coro2a,0.205423214,0.174281064,5.56E-07,2.13E-06
+Sult1b1,0.20486054,0.152024641,0.000401629,0.000747107
+Pkn2,0.204490094,0.116957895,4.35E-07,1.71E-06
+Pafah1b3,0.204488046,0.176599641,4.03E-06,1.25E-05
+Rhpn2,0.203731222,0.172679576,5.58E-09,3.43E-08
+Osbpl3,0.203344204,0.197741042,1.84E-07,7.94E-07
+Gtf3c6,0.203170812,0.144552063,4.80E-13,7.21E-12
+Arhgap10,0.202946595,0.238251702,7.77E-10,5.85E-09
+Ppp2cb,0.202703992,0.213354065,3.22E-07,1.30E-06
+Efhd2,0.202210175,0.231816007,1.13E-15,2.27E-14
+Serinc3,0.201870312,0.315723291,8.99E-11,8.65E-10
+1810043H04Rik,0.201843033,0.105973442,1.03E-08,5.99E-08
+Polr2j,0.201692702,0.20835499,1.01E-07,4.59E-07
+Rab14,0.20167063,0.346296076,3.08E-09,2.01E-08
+Nagk,0.201315331,0.144763383,1.19E-08,6.82E-08
+Trex2,0.201004435,0.210036804,1.16E-06,4.14E-06
+Insig2,0.199856225,0.16332268,1.10E-06,3.95E-06
+Vcpkmt,0.199608296,0.150133213,1.67E-07,7.23E-07
+Wwc1,0.199124529,0.137927735,3.08E-05,7.61E-05
+Slc35f5,0.198779649,0.187636422,3.39E-08,1.73E-07
+Srp14,0.198494742,0.125622661,9.21E-06,2.62E-05
+Slc35a1,0.198021767,0.185675827,6.21E-10,4.79E-09
+Pitpna,0.198017346,0.127548425,1.43E-06,5.01E-06
+Vps37b,0.197710845,0.241413701,6.90E-08,3.25E-07
+Rab2a,0.197631939,0.260542617,6.34E-12,7.77E-11
+Rras2,0.197565298,0.294562492,2.06E-07,8.72E-07
+Nhp2,0.19741701,0.215523341,1.66E-10,1.47E-09
+Gsk3b,0.197058516,0.187731973,0.0001892,0.000382003
+Csnk2b,0.196882078,0.216664487,6.18E-08,2.94E-07
+Sh3yl1,0.196748162,0.184189013,3.54E-09,2.28E-08
+Mkrn1,0.196587534,0.188539963,9.79E-09,5.73E-08
+Coro1b,0.196481958,0.328493645,4.64E-09,2.89E-08
+Msmo1,0.196450814,0.201733847,4.90E-08,2.39E-07
+Tmem14c,0.196296931,0.158140178,3.18E-08,1.64E-07
+Sbds,0.195958755,0.340164006,1.72E-08,9.49E-08
+Idnk,0.195821843,0.15926896,3.53E-11,3.70E-10
+Ece1,0.195730416,0.229992144,2.89E-13,4.51E-12
+Pdxdc1,0.195168977,0.072053816,6.12E-11,6.12E-10
+Necap2,0.195038029,0.293783647,3.20E-08,1.65E-07
+Tmem205,0.194870377,0.103439079,0.002273273,0.00349819
+Ndufb10,0.194628315,0.056040544,8.34E-13,1.20E-11
+1110059E24Rik,0.194377279,0.152897928,2.23E-05,5.71E-05
+Foxa1,0.194210357,0.061716422,4.30E-10,3.44E-09
+NCBP2-AS2,0.194090861,0.179776045,8.81E-09,5.22E-08
+Klc3,0.193875816,0.254988683,7.04E-07,2.64E-06
+Hsd17b11,0.193662873,0.103908276,1.86E-12,2.51E-11
+Rab1a,0.193426107,0.272508723,1.44E-10,1.29E-09
+Kbtbd11,0.193381123,0.149947602,4.88E-08,2.38E-07
+Mxd1,0.193269224,0.192469683,1.45E-09,1.03E-08
+Dctn3,0.193236067,0.292784641,6.85E-11,6.76E-10
+Parm1,0.193172774,0.109259752,6.65E-06,1.96E-05
+Alad,0.193111576,0.042238366,8.08E-07,2.98E-06
+Hiat1,0.19295003,0.24680087,3.65E-07,1.46E-06
+Fam83e,0.192867207,0.050558652,1.95E-09,1.34E-08
+Atp6v1d,0.192670869,0.265007762,1.20E-09,8.74E-09
+Sf3b2,0.192108381,0.084923194,2.62E-06,8.54E-06
+Ppp1cb,0.191862234,0.19594518,2.34E-09,1.57E-08
+Gfpt1,0.191562439,0.034327967,3.49E-10,2.87E-09
+Eps8l2,0.190964372,0.362553287,1.01E-10,9.63E-10
+Calcb,0.190948917,0.254949998,4.44E-09,2.78E-08
+Mrpl27,0.19094802,0.173564264,9.07E-09,5.36E-08
+Arl4c,0.190914424,0.195047481,1.46E-08,8.22E-08
+Hopx,0.190839093,0.154210388,2.05E-08,1.11E-07
+Itgb1,0.190741573,0.286045623,5.17E-09,3.20E-08
+Actn4,0.190050445,0.3883366,3.27E-12,4.21E-11
+Atxn7l3b,0.189850868,0.092217219,6.56E-06,1.94E-05
+Banf1,0.189787218,0.21272496,6.32E-09,3.83E-08
+Bag2,0.189347407,0.228337471,1.13E-09,8.29E-09
+Ndufs4,0.18933743,0.083046808,1.50E-08,8.40E-08
+Pam,0.189062342,0.034687296,1.06E-13,1.71E-12
+Ube2k,0.188641302,0.309348552,9.56E-09,5.62E-08
+Edn1,0.188485601,0.297011637,6.06E-08,2.90E-07
+Tmem106b,0.188459513,0.073737442,0.00212777,0.003305476
+Pvrl2,0.188208474,0.329767051,1.51E-10,1.35E-09
+Llgl2,0.187853993,0.144674049,0.000281164,0.000542867
+Lsr,0.18774866,0.214548773,1.11E-10,1.04E-09
+Ppp2r1a,0.187636291,0.249711727,1.06E-08,6.12E-08
+Apoa1bp,0.187555091,0.263199894,1.89E-10,1.65E-09
+Gna11,0.187494044,0.124331493,0.000229688,0.000454375
+Myo1c,0.187441898,0.249645135,7.28E-10,5.54E-09
+Gramd3,0.187426836,0.322961138,1.00E-08,5.85E-08
+Slc7a2,0.187363253,0.077832149,5.92E-05,0.000135569
+Pold4,0.187297168,0.230241351,1.23E-15,2.44E-14
+Tsn,0.187130843,0.089059174,1.99E-11,2.18E-10
+Sec62,0.187099369,0.229057217,9.05E-11,8.69E-10
+Aig1,0.187045954,0.186334185,6.07E-05,0.000138797
+Ivns1abp,0.186904584,0.186998341,0.00043629,0.000802662
+Cd55,0.186176203,0.071733754,1.26E-06,4.48E-06
+Syf2,0.186004797,0.284525153,4.78E-13,7.20E-12
+Wdr72,0.185982913,0.116899556,6.35E-12,7.77E-11
+Cgn,0.185956881,0.086510419,2.32E-07,9.71E-07
+BC005537,0.185881839,0.106478746,8.26E-09,4.91E-08
+Bri3,0.18586605,0.333461978,2.39E-14,4.12E-13
+Tprgl,0.18478907,0.386500916,1.19E-09,8.69E-09
+Rab3d,0.184630111,0.291198831,6.87E-09,4.15E-08
+Car5b,0.184585495,0.097489882,2.71E-09,1.81E-08
+Phc2,0.184341832,0.145354775,6.73E-05,0.000152085
+Dazap2,0.184276728,0.287014435,3.44E-11,3.62E-10
+Ccdc64b,0.183962545,0.080415353,4.84E-08,2.36E-07
+Ccdc129,0.183396952,-0.055160944,1.86E-07,7.97E-07
+Arl2,0.182946212,0.159985657,6.69E-10,5.12E-09
+Ubxn6,0.1829034,0.21616417,2.38E-08,1.27E-07
+Thoc7,0.18280467,0.14506906,1.01E-06,3.67E-06
+Bcl2l1,0.182529606,0.113111255,0.000261404,0.000509821
+Sptbn1,0.182235934,0.145555723,1.60E-06,5.50E-06
+Lamtor4,0.182232272,0.163038444,8.91E-10,6.68E-09
+Nek7,0.182004778,0.149942629,2.17E-05,5.58E-05
+Tmem40,0.181883432,0.135282253,6.92E-08,3.26E-07
+Sptlc3,0.181669634,0.148491398,2.15E-06,7.17E-06
+Bcl10,0.181654281,0.371401011,7.64E-12,9.20E-11
+Fam173a,0.181522256,0.127971651,3.00E-06,9.62E-06
+Hsbp1l1,0.181522091,0.165146289,0.000473784,0.000863153
+Cyb5b,0.181173198,0.173722353,4.94E-08,2.40E-07
+Map2k2,0.180973864,0.171280986,0.000119627,0.00025344
+Mrpl34,0.180558355,0.025005445,2.11E-06,7.07E-06
+Sypl,0.180387084,0.269080913,1.05E-08,6.09E-08
+Cyp2j6,0.180364556,0.17575606,1.39E-09,9.96E-09
+Mrpl54,0.18013768,0.027907033,9.26E-06,2.63E-05
+Mvb12a,0.180094371,0.08393585,5.53E-11,5.57E-10
+Hnrnpl,0.179891172,0.059906134,9.14E-06,2.60E-05
+Ptp4a1,0.179740353,0.150419596,1.69E-08,9.38E-08
+Naa38,0.179395686,0.087642231,3.28E-11,3.47E-10
+Mrpl52,0.179376313,0.019753118,3.93E-08,1.97E-07
+Ntan1,0.179369683,0.202318001,1.30E-10,1.19E-09
+Uba1,0.179324652,0.122559915,5.57E-10,4.34E-09
+Churc1,0.178932121,0.115154743,1.31E-06,4.60E-06
+Cd2ap,0.178864032,0.180185557,2.85E-08,1.49E-07
+Sec61b,0.178810962,0.017839269,0.003798912,0.005561943
+Adh1,0.178354992,0.265863077,9.10E-09,5.37E-08
+Eapp,0.178086673,0.153294187,1.71E-06,5.83E-06
+Tmem54,0.177584049,0.106005778,0.00019454,0.000391542
+Sdhb,0.177312364,0.200299055,1.12E-07,5.02E-07
+Lamc2,0.177127306,0.175998263,1.67E-05,4.44E-05
+Apobec3,0.177021123,0.312947432,1.78E-07,7.69E-07
+Yipf6,0.17654232,0.097880432,0.00022046,0.000438439
+Tmem9b,0.176114481,0.226553757,2.04E-11,2.24E-10
+Snrpd1,0.175673216,0.129392569,3.56E-09,2.29E-08
+Stx7,0.175511826,0.214807933,1.81E-05,4.76E-05
+Kcne3,0.175083942,-0.079942274,1.82E-07,7.85E-07
+Fam104a,0.174786945,0.122069716,1.91E-07,8.18E-07
+Pgrmc2,0.174580215,0.129431921,2.30E-09,1.55E-08
+Spcs1,0.174559139,0.093271265,3.39E-08,1.73E-07
+Me1,0.174389408,0.096032245,3.00E-11,3.20E-10
+Psmd3,0.174320411,0.11342183,1.02E-06,3.69E-06
+Cwc15,0.174276783,0.11637452,3.71E-09,2.36E-08
+Riok3,0.173674825,0.194239725,3.62E-06,1.14E-05
+Slc37a1,0.173660399,0.116609027,1.06E-07,4.81E-07
+Ywhaz,0.173505606,0.105265315,2.91E-07,1.19E-06
+Smox,0.17340682,0.198847544,3.38E-09,2.19E-08
+Csnk1g2,0.173347492,0.097330425,0.001410022,0.002290611
+Cadm4,0.173297599,0.196359424,7.10E-10,5.41E-09
+Gid8,0.173113635,0.093128878,3.85E-08,1.94E-07
+Slc25a35,0.172957546,0.157099436,3.09E-08,1.60E-07
+4930523C07Rik,0.172691584,0.315042061,4.79E-07,1.87E-06
+B3gat3,0.172501603,0.206526581,1.20E-06,4.28E-06
+Lgalsl,0.172345431,0.25042716,1.16E-05,3.21E-05
+2310033P09Rik,0.172343455,0.129856057,7.12E-06,2.09E-05
+Klf3,0.172292346,0.276435472,1.69E-05,4.49E-05
+Szrd1,0.17145432,0.15656526,4.30E-06,1.32E-05
+Sipa1l3,0.171283519,0.076158157,0.000618837,0.001097241
+Plscr3,0.171276691,0.207637541,1.89E-08,1.03E-07
+Arl6ip1,0.1711233,0.102046533,3.94E-06,1.22E-05
+Phf14,0.171026062,0.170921284,7.36E-08,3.43E-07
+Pop7,0.170686348,0.109621996,0.000319514,0.000608963
+Ptges3,0.170603218,0.157096161,0.000276407,0.000534981
+Arpc4,0.170260966,0.334507714,5.65E-09,3.46E-08
+Vopp1,0.170167946,0.250801504,1.03E-06,3.71E-06
+Fabp5,0.170122961,0.210100005,1.86E-05,4.89E-05
+Ppp1r1b,0.169851006,-0.132496246,2.21E-11,2.41E-10
+Ccdc34,0.169500669,0.102823317,0.000131252,0.000275226
+Nsmce1,0.169350045,0.083811717,3.00E-06,9.61E-06
+Pink1,0.169242896,0.115926731,9.50E-07,3.47E-06
+Tmprss2,0.16890958,0.196446387,6.98E-08,3.28E-07
+Acer3,0.168286992,0.281068589,2.89E-06,9.32E-06
+Mpv17l2,0.16804957,0.066312878,8.43E-08,3.88E-07
+Dnase2a,0.167935814,0.096230069,6.97E-08,3.28E-07
+Kcnk5,0.167807885,0.169053494,2.50E-10,2.14E-09
+Sorl1,0.167629942,0.069620373,1.05E-05,2.93E-05
+Smim20,0.167470429,0.053410504,1.08E-12,1.54E-11
+Emp1,0.167467605,0.796746511,7.69E-19,2.20E-17
+Mier1,0.167095615,0.124424635,4.70E-07,1.84E-06
+Runx1,0.166801945,0.040447619,6.52E-11,6.45E-10
+Nrbp1,0.166514083,0.19442951,2.55E-06,8.36E-06
+Sh3bgrl2,0.165906159,0.156915093,2.11E-05,5.44E-05
+Celf2,0.165863069,0.099618348,0.001109203,0.001839993
+Ndel1,0.165715486,0.148130626,2.24E-06,7.43E-06
+Mrpl17,0.165666209,0.032997374,4.10E-06,1.26E-05
+Nipsnap3b,0.165626199,0.22258639,4.28E-11,4.40E-10
+Bod1,0.165558003,0.111393631,7.48E-07,2.79E-06
+Serpinb11,0.165482798,0.102884275,0.019548734,0.024804195
+Plec,0.165376973,0.19747356,7.31E-07,2.74E-06
+Tsg101,0.165113295,0.252363067,6.60E-08,3.12E-07
+Pon3,0.164987896,0.096380595,4.64E-08,2.28E-07
+Tpd52l2,0.164959939,0.131572296,1.86E-08,1.02E-07
+Cpm,0.164478293,0.111709772,1.70E-05,4.50E-05
+Mfsd4,0.164074613,0.091408877,0.001636812,0.002614628
+Usp25,0.163577287,0.202319366,7.07E-07,2.65E-06
+Fam174a,0.163566786,0.056345342,3.82E-05,9.20E-05
+Ube2f,0.163221039,0.194560127,9.00E-13,1.29E-11
+Scd2,0.162992808,0.170033359,4.48E-06,1.37E-05
+Ppp3ca,0.162984471,0.224338034,0.000703012,0.001225982
+B4galnt1,0.162912994,0.149652161,3.81E-06,1.19E-05
+Bax,0.162501419,0.217985068,3.49E-10,2.87E-09
+Ier3ip1,0.162498808,0.141536134,5.40E-06,1.63E-05
+Vti1b,0.162473582,0.097261096,1.50E-06,5.23E-06
+Pef1,0.162267264,0.16352629,4.44E-06,1.36E-05
+Hexa,0.162013191,0.099676771,6.11E-05,0.000139511
+Snrnp27,0.161884933,0.095409464,3.91E-06,1.21E-05
+Ufm1,0.161849668,0.210958741,2.76E-07,1.13E-06
+Cab39l,0.161486216,0.189959334,1.68E-09,1.17E-08
+Bola3,0.16090667,0.147388427,4.91E-05,0.00011473
+Mrps24,0.160787312,0.030744966,3.36E-07,1.35E-06
+Tm2d3,0.160712019,0.10659403,1.49E-07,6.55E-07
+Ppp1ca,0.16050782,0.403589005,2.66E-10,2.26E-09
+Tomm5,0.160450629,0.163582967,3.63E-09,2.32E-08
+Lsm14a,0.160221004,0.245740343,1.11E-05,3.08E-05
+Hnrnpd,0.15994574,0.16147066,2.64E-08,1.39E-07
+Atp13a3,0.159155761,0.05760346,6.98E-08,3.28E-07
+Sertad2,0.159092704,0.112883374,9.65E-06,2.72E-05
+Actr3,0.15904104,0.342627887,2.03E-09,1.39E-08
+Gas2l1,0.158946582,0.131720033,1.98E-07,8.44E-07
+Ubxn4,0.158783627,0.159586893,1.72E-06,5.86E-06
+Cmc1,0.158454216,0.017927729,5.07E-10,3.98E-09
+Pcmtd1,0.158259534,0.131572379,0.004172582,0.006060202
+Dnaja2,0.157944674,0.234908587,4.93E-11,5.02E-10
+1700020I14Rik,0.157823567,0.115590295,0.000103361,0.000222237
+Arhgap32,0.157181047,0.045580118,3.05E-08,1.58E-07
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+Phf3,0.042801452,0.006568159,0.000258601,0.000505073
+Tmem184b,0.042786371,0.016525386,0.003678214,0.005405138
+Kmt2c,0.042716727,0.003725036,0.037442725,0.045178473
+Zbtb7a,0.042715008,0.184369701,4.66E-05,0.00010967
+Baz1b,0.042680279,0.020474999,0.005225925,0.007432219
+Sssca1,0.042650239,0.003968925,2.36E-07,9.88E-07
+Nrd1,0.042558223,-0.002674458,6.50E-06,1.92E-05
+Trappc3,0.042549443,0.100048538,0.001263353,0.002075135
+Pdia4,0.042544962,0.069134062,3.01E-05,7.46E-05
+Zswim7,0.042514149,-0.014580781,0.001617262,0.002586501
+Rmnd5a,0.042504419,0.016019135,1.70E-05,4.50E-05
+Nmd3,0.042456576,0.100478037,0.000534329,0.000960795
+Wipf2,0.042451414,0.037273074,0.041350498,0.049499185
+Emc2,0.042403761,0.051774479,4.17E-05,9.94E-05
+Pja2,0.042349213,0.047175103,0.041770876,0.049936612
+Fam132a,0.042290055,0.138895425,0.000372375,0.000698409
+Srpk2,0.042091598,0.059842471,0.002571835,0.003908452
+Hras,0.042083691,0.172633367,0.001869613,0.002942524
+Snx12,0.041963104,0.079976866,5.91E-05,0.000135471
+Ggct,0.041957471,0.015791707,0.030413839,0.037313274
+Prkrip1,0.041786937,0.017062366,0.00761705,0.010469945
+Kif23,0.041786553,0.037724294,0.029661206,0.036460238
+Lppos,0.041689793,-0.082237038,3.09E-12,4.02E-11
+Smn1,0.041655959,0.082433729,0.008089575,0.011057317
+Trappc13,0.041642162,0.073942519,0.031010494,0.037993978
+Derl2,0.041587484,-0.008584721,3.04E-07,1.24E-06
+Gcsh,0.041577939,0.004791392,0.000280806,0.00054234
+Ciapin1,0.041529914,0.161832433,0.001252692,0.002059752
+Copg1,0.041519361,-0.024567614,4.00E-11,4.14E-10
+Tmem125,0.041513767,0.023595756,0.010361018,0.013875779
+Nufip2,0.041508186,0.090814485,0.003023225,0.004530564
+Nudcd3,0.041499868,0.006245772,0.001823213,0.002876615
+Cdc37,0.041442274,0.139166051,1.65E-09,1.16E-08
+Akr7a5,0.041400958,0.09854592,9.72E-07,3.54E-06
+Ifi27l2a,0.04136577,-0.051649487,5.30E-05,0.00012302
+Tns2,0.04135487,0.005184971,3.87E-05,9.32E-05
+Commd4,0.041343535,0.171564071,3.76E-11,3.92E-10
+Gmppb,0.041330253,0.001666739,8.20E-06,2.36E-05
+Abt1,0.041298175,0.106101238,0.002690774,0.0040746
+Nit1,0.041258476,0.059751039,0.0013687,0.00223089
+Rnf115,0.041194764,0.061239475,0.001441912,0.002335757
+Slc25a38,0.041081285,0.063103824,0.021344848,0.026897808
+Smim10l1,0.040937847,0.034260255,2.27E-06,7.53E-06
+Htatsf1,0.040906826,0.011414972,0.005411573,0.007661978
+Tssc4,0.040888562,0.031771373,3.54E-05,8.60E-05
+Pdpk1,0.040850917,0.058781513,0.000667718,0.001173767
+Ltv1,0.040640217,0.051094711,0.000791723,0.001360908
+B4galt1,0.040532094,0.033234654,0.001802009,0.002845277
+Tor1a,0.040446695,0.026386454,0.002319352,0.003561343
+Aldh3a2,0.040425066,-0.000641831,0.000573226,0.001023216
+Spin1,0.040297918,0.061175404,5.08E-05,0.000118165
+Slc22a23,0.040292794,0.003219529,1.12E-05,3.10E-05
+Cenpv,0.040276055,-0.006768894,0.000236342,0.000465799
+Rapgef6,0.040269903,0.07818828,0.018099719,0.023106024
+Mbnl1,0.040205759,-0.007055192,0.004225019,0.006126567
+Liph,0.040198142,-0.024437273,3.52E-09,2.27E-08
+Ndufs7,0.040187097,0.191334399,1.63E-09,1.15E-08
+Tln1,0.040183802,0.034486293,5.70E-05,0.000131386
+Rest,0.040075174,0.050577878,0.013566355,0.017771786
+Bin3,0.040012253,0.062238924,0.0002586,0.000505073
+Brd8,0.039923854,-0.045271398,7.89E-05,0.000175034
+Dcaf11,0.039916819,0.087253574,2.15E-06,7.18E-06
+N4bp1,0.039904041,0.016210994,5.46E-05,0.000126259
+Sdccag3,0.039844029,0.104107155,0.000172079,0.000350888
+Immp1l,0.039805516,0.057566812,7.41E-07,2.77E-06
+Pmf1,0.039680928,0.025827484,0.016520105,0.021281723
+Trrap,0.039679434,0.010134078,0.014899209,0.019362273
+Dctn6,0.039637427,0.06916867,2.68E-05,6.75E-05
+Pfn2,0.039540018,-0.115743242,4.08E-07,1.61E-06
+Ppp6c,0.039479051,0.066399104,0.002559809,0.003892036
+Slc17a5,0.039248101,0.080391756,0.003618598,0.005329848
+Mau2,0.039221983,0.045471512,1.06E-05,2.95E-05
+Stx6,0.039029125,0.10956539,0.005303558,0.007529158
+Atp2c1,0.038970777,0.011682005,0.023760984,0.029677898
+Ppt1,0.038970159,0.059593821,0.000726868,0.001260326
+Tbc1d15,0.038912663,0.12526439,0.000201039,0.000402331
+Emc8,0.038842874,0.117042602,8.45E-06,2.43E-05
+Slco2a1,0.038777124,0.125722604,0.011983918,0.015855568
+Ank3,0.038774045,0.000423958,0.020728962,0.026157975
+Nkap,0.038686668,0.018323591,0.00079742,0.00136996
+Fbxl3,0.038648496,0.013323347,4.95E-05,0.000115693
+Grhl2,0.038623284,0.044043294,2.03E-05,5.28E-05
+Usp14,0.038602181,0.075490988,4.69E-09,2.92E-08
+Zcchc7,0.038539977,0.029058232,0.003033332,0.004543569
+Parl,0.038534696,0.048550001,4.53E-05,0.000107062
+Mob1a,0.038531015,0.008244316,0.001646818,0.002627637
+Ptdss1,0.038434843,0.051352239,6.63E-05,0.000150059
+Dad1,0.038322202,0.159113238,7.56E-06,2.20E-05
+Tbc1d17,0.038259238,0.051825952,0.000198209,0.000397548
+Foxn3,0.038165048,0.125743152,0.028507388,0.035137013
+Ubap1,0.038119536,0.105449452,0.000701254,0.001223924
+Spryd7,0.038108492,0.000486269,0.00012088,0.00025567
+Rnf121,0.037982724,0.021162781,0.011481683,0.015248174
+Cant1,0.037981188,0.013001444,0.014824305,0.01926887
+Rpp25l,0.037943691,0.01928918,8.90E-05,0.000194691
+Rnf138,0.037913897,0.049960416,1.12E-05,3.12E-05
+Rab7,0.037895462,0.13632213,1.38E-07,6.08E-07
+Tmem98,0.037837422,0.007212632,0.000204182,0.000408365
+Maf1,0.037803496,0.071910791,3.73E-05,8.99E-05
+Fam136a,0.037795887,0.071000655,0.000265299,0.000515836
+Rpa1,0.037742108,0.077256502,0.003761561,0.005512204
+Lcmt1,0.037737315,0.071832449,0.019392451,0.024637633
+Plaa,0.037736177,0.035599078,2.46E-06,8.10E-06
+Gba,0.037570438,0.065746157,0.00108288,0.001801967
+Zc3h13,0.037549447,0.037950618,0.000137748,0.000287238
+Drosha,0.037534024,0.0132353,0.008758863,0.011905614
+Met,0.037505794,0.014617336,3.82E-06,1.19E-05
+Ube2q1,0.037401145,-0.006751568,0.002270493,0.003494757
+Stat6,0.037386217,0.060773137,6.59E-06,1.95E-05
+Ndfip1,0.037358508,0.052081876,0.000249302,0.000489068
+Mitd1,0.037340108,0.061581057,9.11E-05,0.000198975
+Alg5,0.037322437,0.032322661,5.60E-08,2.70E-07
+Clip4,0.037262573,0.241399093,0.000430076,0.000793526
+3110040N11Rik,0.037206294,0.000606392,1.29E-05,3.52E-05
+Ngly1,0.037184162,0.052017252,9.06E-09,5.35E-08
+Yrdc,0.037048234,0.112149248,7.05E-05,0.000158583
+Krt18,0.03704709,0.523843204,6.31E-16,1.33E-14
+Tmem222,0.037006694,0.124792461,3.73E-05,8.99E-05
+Memo1,0.036974893,0.080160758,0.005692114,0.008023458
+Wdr33,0.036860188,0.0530165,0.002671115,0.004047722
+Ncor1,0.036814921,0.037589664,3.36E-05,8.22E-05
+Chmp7,0.03678877,0.059649984,0.003284007,0.004875417
+Ydjc,0.036696732,0.046103089,0.00033507,0.000635462
+Flad1,0.036639458,0.045460105,0.000986411,0.001658798
+Ick,0.036605813,-0.015772944,2.39E-08,1.27E-07
+Amn1,0.036557924,0.039425269,0.001069807,0.001783947
+Usf2,0.036519025,0.051879116,3.73E-06,1.17E-05
+Tceb3,0.036470899,0.112825997,9.19E-05,0.000200452
+Pde7a,0.036395879,0.055870765,1.65E-05,4.40E-05
+Trim29,0.036370066,0.222745388,0.000723566,0.001255971
+Tcf7l2,0.036368256,0.000758487,0.000113793,0.000242048
+Hexb,0.036157335,-0.050633667,1.33E-11,1.53E-10
+Cnot4,0.036109033,0.03489644,0.007608377,0.010460285
+Pddc1,0.036029908,0.032774316,1.52E-06,5.27E-06
+Dtx2,0.035994546,0.062073863,0.00189403,0.002973595
+Stambp,0.035990994,0.064426547,0.033127811,0.040416819
+Ap5s1,0.035987735,0.055714037,0.001389497,0.002258421
+Pex6,0.035969532,0.076858156,0.000540989,0.000970849
+Irak1,0.035899634,-0.009597806,0.001307195,0.002139414
+Wbp11,0.035747639,0.047199619,0.001752465,0.002773937
+Prr14,0.035615362,0.073543256,0.000820675,0.001407252
+Cand1,0.035506636,0.009605698,0.000912109,0.001544465
+Gm16192,0.035486319,0.049614319,0.001934672,0.003029923
+Sh2b1,0.035244176,0.047398028,0.033909337,0.041220066
+Rnf11,0.035172811,0.069627098,0.007174388,0.009915061
+Slc9a3r1,0.035169612,0.275782306,1.87E-07,8.05E-07
+Gkap1,0.035164247,-0.00570554,0.003657844,0.005380042
+Eci2,0.035102492,0.084136338,4.82E-05,0.000112959
+Fance,0.035080752,0.019054761,9.21E-05,0.000200854
+Dusp19,0.034913305,0.030072914,0.003359839,0.004981019
+Skap2,0.034828891,0.142257382,0.017823529,0.022803791
+Tmem50b,0.034809194,0.040768661,0.008010227,0.010960637
+Tor2a,0.034763471,0.012287336,0.000556401,0.000996539
+Adck5,0.034707121,0.022255343,0.010064108,0.013532289
+Lpar3,0.034705591,0.01013761,3.24E-06,1.03E-05
+Trim44,0.034674555,0.005999739,0.000917418,0.001552628
+Cxadr,0.034608529,0.078751418,2.24E-06,7.45E-06
+Slc25a36,0.034534241,0.01709072,0.016555043,0.02131378
+Celf1,0.034520521,0.066811059,0.022878147,0.028676589
+Cd164,0.034515399,0.020623761,0.001232808,0.002028631
+Fxr2,0.034485841,0.032604061,0.000389027,0.00072664
+Nkx2-1,0.034361436,0.171552113,2.57E-08,1.35E-07
+Zcchc9,0.034232926,0.075974716,0.001567894,0.002515086
+Ttbk2,0.034069046,0.016943073,0.001968993,0.003076854
+Adrbk2,0.034007858,-0.006114442,0.000522702,0.000942286
+Klhdc3,0.033968498,-0.000509301,0.00012925,0.000271386
+Asl,0.033935824,-0.020028664,1.60E-06,5.51E-06
+Orai1,0.03391734,0.033861031,3.27E-06,1.04E-05
+Tmem30a,0.033893049,-0.028677336,0.000624271,0.00110472
+Galnt12,0.03383739,0.014370761,0.000726199,0.001259854
+Tmco6,0.033820697,0.022877019,0.007286373,0.010053275
+Nr3c1,0.033786047,0.007882944,9.41E-06,2.66E-05
+Ddx21,0.033679651,0.01119799,9.16E-06,2.60E-05
+Sec23b,0.033557917,-0.020690701,1.83E-05,4.80E-05
+Slc30a7,0.03337323,0.003043868,0.000344196,0.000650934
+Hist3h2a,0.03335658,0.112726713,2.72E-06,8.84E-06
+Dctn5,0.033207527,0.039581352,0.000404934,0.000752596
+Arfgap1,0.033195597,0.028587284,0.001581253,0.002534468
+Smarcc2,0.033177814,-0.007262211,4.68E-08,2.30E-07
+Qk,0.03316421,0.059021288,0.030296213,0.037176137
+Prkar1a,0.033108862,0.195470153,4.14E-05,9.87E-05
+Atxn2l,0.033037191,0.057278177,0.00026933,0.000522317
+Vps37a,0.032951282,0.043072723,0.041670524,0.049835377
+Dapk2,0.032932538,0.074286404,0.005813332,0.008178012
+Kpnb1,0.032875797,0.011841807,0.00017567,0.000357753
+Sec13,0.032851,0.023135921,2.65E-11,2.84E-10
+Sec16a,0.032778384,0.007422224,0.000134475,0.000281117
+Urm1,0.032665352,0.020728319,0.00025515,0.000499464
+Ino80e,0.032655467,0.080557367,4.45E-05,0.00010554
+Lsm14b,0.032617139,-0.017424919,0.000683572,0.001196453
+Chpf,0.032561298,0.024816467,4.69E-05,0.000110107
+Gm2a,0.032520821,-0.039473088,0.000673241,0.001181515
+Prpf4b,0.032470014,0.006963215,9.36E-06,2.65E-05
+Slc44a1,0.032417507,0.039514601,0.000212451,0.000423702
+Fam195b,0.032355417,0.125898802,2.92E-09,1.93E-08
+Agap1,0.032319881,-0.015774996,0.000100552,0.00021671
+Setd3,0.032309484,0.055054987,5.45E-05,0.000126094
+Whamm,0.032278677,0.018406145,0.012999118,0.017102688
+Cutc,0.032268778,-0.040664575,4.31E-07,1.69E-06
+Ergic1,0.032236505,0.085310207,0.000704091,0.00122719
+Calu,0.032213936,0.031466833,0.000382786,0.000715614
+2810001G20Rik,0.032160157,0.036804022,0.027965223,0.034522287
+Cox11,0.032071773,0.053094133,0.000192396,0.000387718
+Trim47,0.032071083,0.126875527,0.000570716,0.001019021
+Rbm4b,0.03199376,0.024398705,0.004279432,0.006198403
+Usp16,0.03190937,0.033111161,0.000101321,0.000218293
+Xaf1,0.031899433,0.042783219,0.002497418,0.003808098
+Tmem37,0.031845859,-0.020847302,1.99E-05,5.18E-05
+Fbxw9,0.03168179,0.042328051,0.003794306,0.005556479
+Cib1,0.031593494,0.151586995,4.14E-07,1.63E-06
+Exosc10,0.031555222,0.031232279,9.95E-05,0.00021482
+Arfip2,0.031501358,-0.018158542,1.39E-10,1.26E-09
+Irak2,0.031498455,0.106218996,0.000138538,0.00028879
+Mcrs1,0.031494462,0.058795242,0.000400534,0.000745289
+Tradd,0.031483789,0.058337925,0.000157955,0.000325006
+Tnfaip2,0.03148303,-0.030460695,1.33E-05,3.61E-05
+Cbx6,0.031479702,0.020988731,7.17E-05,0.000160903
+Acyp2,0.03142639,-0.007408452,0.005618357,0.007929507
+B4galt3,0.031362617,0.107609598,0.001678946,0.002672197
+Mrps23,0.031337869,0.067252508,4.83E-05,0.00011315
+Ube2e2,0.031327639,0.05203088,9.50E-05,0.000206507
+Scly,0.031327024,0.015711249,0.00172596,0.002736067
+Pum3,0.031280619,0.071144477,0.000120674,0.000255488
+Zfp277,0.031256757,0.056731894,5.75E-05,0.000132242
+Map2k3,0.031184791,0.319349496,4.82E-11,4.92E-10
+Fgfr3,0.031176581,0.178329357,0.000801398,0.00137605
+2810474O19Rik,0.031076788,0.008952358,9.99E-05,0.000215508
+Ctage5,0.030979192,-0.000327417,0.000150426,0.000311125
+Cyp20a1,0.03090446,-0.001666718,0.000123544,0.000260611
+Tm9sf4,0.030887139,0.022907186,2.97E-05,7.37E-05
+Tcp11l2,0.030841255,0.040019572,3.88E-06,1.21E-05
+Sema3f,0.030781521,0.045666993,1.29E-05,3.53E-05
+Sytl2,0.030770986,-0.035452983,1.01E-06,3.65E-06
+Cnot7,0.030720167,0.071257107,0.002891425,0.004350476
+Dcun1d1,0.030705732,0.029261667,0.000106856,0.000228901
+Tceb1,0.030658171,0.079464084,1.29E-07,5.72E-07
+Klk13,0.030652075,0.032441413,0.005794114,0.008161809
+Med6,0.030614742,0.009308585,0.00031567,0.000602721
+2210016L21Rik,0.0305139,0.042516428,0.001506939,0.002428823
+Emc9,0.030443275,0.037025861,6.76E-06,2.00E-05
+Larp1,0.030399064,0.011946453,0.0003173,0.000605568
+Ndufs2,0.030387082,0.193619439,4.43E-10,3.53E-09
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+Nsmce2,0.018729138,0.088143186,2.11E-05,5.44E-05
+Tbcd,0.018721196,0.020257613,0.001306939,0.002139414
+Itln1,0.018608028,-0.051498539,2.06E-05,5.35E-05
+Rtp4,0.018399678,-0.048830228,0.000123731,0.000260918
+Fasn,0.018341828,0.010515474,0.016007766,0.020659374
+Snapin,0.018298037,0.103257571,0.000302188,0.000579239
+Arhgef19,0.0182654,0.015641092,0.015659477,0.020275707
+Med17,0.018218563,0.011872703,0.000377111,0.000706459
+Seh1l,0.018208235,0.078726144,0.01390681,0.018180331
+Ufsp1,0.018192526,0.002944866,0.00202929,0.003165633
+Prkag1,0.018138552,0.098297554,0.000160478,0.000329451
+Pik3r4,0.01813357,0.008410783,0.000812023,0.001393542
+Gorasp2,0.01812236,0.036976622,0.000718272,0.001247841
+Iscu,0.018068399,0.121523385,1.53E-05,4.11E-05
+Rbbp9,0.018061244,0.007985914,0.001818876,0.002870483
+Wbscr22,0.018027083,0.059079332,0.000209132,0.000418001
+Noc2l,0.017999275,0.042039855,0.003935046,0.005740802
+Serpinf1,0.017955909,-0.179270194,7.12E-09,4.29E-08
+Gpr107,0.017937296,-0.031703406,0.000157571,0.000324321
+Mgrn1,0.017826298,-0.043895711,0.011501181,0.015270879
+Bpgm,0.017771252,0.126288734,0.008041569,0.010998791
+Imp4,0.01770657,0.071613048,2.91E-06,9.36E-06
+Lims1,0.017685814,0.064463662,0.001490436,0.002404207
+Tmem19,0.017677928,0.052676535,8.55E-05,0.00018809
+Plscr1,0.0176335,0.251183201,0.000121116,0.000256083
+Stx16,0.017539719,0.028525812,0.023339302,0.029197081
+Ino80b,0.017537716,0.040845307,0.00016987,0.000346942
+Ikbip,0.017526142,-0.0106363,2.36E-05,6.01E-05
+Cbx1,0.017525168,0.031900967,0.004482595,0.006462492
+Cmtm6,0.017341221,-0.024714933,2.97E-07,1.21E-06
+Rpl22,0.017330983,-0.035219736,9.19E-05,0.000200452
+Vangl1,0.017185159,0.012013658,0.022047521,0.027728343
+Mef2a,0.017157783,0.060055179,0.010638604,0.01421162
+Herc1,0.017121001,0.003859709,0.034191101,0.041538758
+Pum1,0.017117058,0.023144239,0.00093506,0.001579544
+Kars,0.017047532,-0.008914141,0.00035466,0.000668338
+Cs,0.016939563,0.112077899,0.005506473,0.007784212
+Ube2w,0.016929012,0.025611933,0.000838479,0.001434685
+Znhit1,0.016915801,0.005038305,1.58E-08,8.85E-08
+Cog2,0.016912182,0.011971862,0.011401751,0.015148347
+Csrnp1,0.016902832,0.14737307,0.003207769,0.00477226
+Rbp4,0.016760505,-0.142933218,1.94E-11,2.14E-10
+Polr2a,0.016559548,0.054622912,0.00196006,0.003065154
+Tiam1,0.016485942,0.025818322,0.040261077,0.048304178
+Trpc4ap,0.016484601,-0.036179533,5.19E-13,7.75E-12
+Trmt6,0.016482736,0.008854228,0.012360177,0.016326215
+Brwd1,0.016479738,0.007511944,1.47E-05,3.97E-05
+Tcta,0.016398837,0.015726262,5.80E-06,1.74E-05
+Wdr83,0.016372273,0.036378016,0.000408305,0.000757754
+Ilf2,0.016260515,0.078657679,0.000104086,0.000223644
+Mrps22,0.016200704,0.022921412,0.035993141,0.043553344
+Rbck1,0.016151674,0.08734939,0.01363805,0.017862026
+Lemd1,0.016149057,0.049377212,0.036368624,0.04397423
+Paip2,0.016118668,0.306688241,6.33E-09,3.84E-08
+Tmem184a,0.016086799,0.018600043,6.85E-05,0.000154506
+Znhit2,0.016086658,0.040382558,0.005174783,0.007369373
+Bhlhe40,0.016060629,0.380939494,5.28E-09,3.25E-08
+Il17rc,0.01604583,0.036290924,6.78E-08,3.20E-07
+Whsc1l1,0.015933403,0.021753336,1.41E-08,7.97E-08
+Rcn2,0.015915642,0.053824081,0.000769277,0.001325549
+Oxld1,0.015909298,-0.053630469,7.47E-05,0.000166692
+Bckdha,0.015891634,0.05219855,1.52E-07,6.64E-07
+Syngr1,0.015754694,-0.071557325,4.83E-12,6.01E-11
+Atp2c2,0.015747014,-0.033639524,3.18E-07,1.29E-06
+Adipor2,0.015710501,-0.061945008,4.45E-06,1.36E-05
+Ccnl2,0.015709382,0.046296167,0.00107188,0.00178553
+Nfib,0.015656594,-0.025899574,1.10E-07,4.95E-07
+Commd10,0.01565079,0.095639965,0.006407256,0.008936987
+Tmem251,0.01563841,0.04525447,0.015872324,0.020513655
+Gtpbp8,0.015604973,-0.021323776,0.000757402,0.001308632
+Shkbp1,0.015580816,0.036207537,0.0001144,0.000243257
+Sarnp,0.015552129,0.197747424,6.86E-09,4.15E-08
+Serpinb12,0.01550104,0.007641917,0.014339031,0.018709921
+Prom1,0.015469625,-0.126310385,8.06E-09,4.81E-08
+Wdr6,0.015467217,0.006409266,0.024248132,0.030240225
+Tmem33,0.015439989,0.135140718,2.73E-05,6.86E-05
+Asb3,0.015413677,0.023509393,0.000190989,0.000385194
+Ptgr2,0.015349922,-0.040576206,1.72E-05,4.54E-05
+Itga6,0.015315098,0.165882157,0.006046242,0.008483146
+Xab2,0.015273982,-0.002974239,0.000180544,0.000365781
+Ensa,0.015257969,0.024363069,0.003437848,0.005086
+Uchl5,0.015164662,0.041492317,0.000493058,0.000893659
+1600012H06Rik,0.015152158,0.008874308,0.013346275,0.017515953
+Zfp652,0.014973899,-0.070212418,2.21E-05,5.68E-05
+Flywch2,0.014943653,-0.047766666,0.00010508,0.000225579
+Lyrm5,0.014939748,0.010297342,0.001286996,0.002111244
+Alkbh6,0.014937161,-0.052523161,0.00508603,0.007249474
+Man2c1,0.014920641,0.03791534,0.013561356,0.017768896
+Ndufb6,0.014905448,0.102374793,1.24E-05,3.42E-05
+Plrg1,0.014853243,0.044779702,0.017759016,0.022730397
+Cdkn2c,0.014846164,-0.021263368,0.002978825,0.004471401
+Igsf5,0.014825637,-0.000594872,0.002574138,0.003911018
+Tspyl1,0.014823803,0.014973477,0.017941746,0.022931975
+Mrpl13,0.014818039,-0.009852759,8.44E-08,3.88E-07
+Ptrh2,0.014809801,0.075469069,0.011611488,0.015401264
+Zcchc11,0.014795087,0.008495246,0.033136101,0.04041918
+Rbm18,0.014794925,0.068460508,0.00035389,0.000667281
+Fam96b,0.01477844,0.143148665,3.11E-05,7.67E-05
+Ikbkg,0.014776735,-0.023142753,0.000292635,0.000562284
+Usmg5,0.014746816,0.07194583,6.64E-05,0.000150412
+Cdc42ep4,0.014740424,0.091452155,0.000317447,0.000605568
+Rheb,0.014712737,0.214547733,3.95E-13,6.03E-12
+Nav2,0.014605645,-0.027593601,7.73E-05,0.000171739
+Ube2e3,0.014549846,0.058377703,1.93E-05,5.03E-05
+Dhps,0.014548489,-0.028843317,0.000362875,0.0006822
+Fam162a,0.014516214,0.020697568,4.28E-11,4.40E-10
+Arfgap2,0.014487957,0.007272193,4.80E-06,1.46E-05
+Scrib,0.014272584,0.02357608,2.75E-07,1.13E-06
+Pnisr,0.014041576,-0.012697763,0.016201159,0.020904721
+Chd4,0.014010706,0.027204219,0.00010858,0.000232279
+Insig1,0.013907432,-0.009528147,0.000228739,0.00045278
+Ubl7,0.013871664,0.068434688,9.57E-05,0.000207828
+Med10,0.013764051,0.050496256,2.90E-05,7.22E-05
+Exosc5,0.013758785,0.092018741,7.16E-05,0.00016084
+Zzef1,0.013665711,0.029880921,0.022978356,0.028790848
+Decr1,0.013664235,-0.000460548,4.15E-07,1.64E-06
+Zc2hc1a,0.013651686,0.116224014,0.004477137,0.006458288
+Acox1,0.013611497,0.031066082,3.02E-06,9.65E-06
+Baiap2l2,0.013600417,0.052544157,0.000954259,0.001607705
+2010107G23Rik,0.013540173,0.1013274,8.16E-05,0.00018031
+Ncln,0.013523899,0.026430184,0.003949484,0.005759852
+Mrpl2,0.013472871,0.000445093,1.65E-10,1.47E-09
+Sike1,0.013465567,0.037691753,4.67E-05,0.000109886
+Limk2,0.013400558,-0.018856263,6.14E-08,2.93E-07
+Slc44a2,0.013282797,0.091163481,0.005247281,0.007460923
+Ccng1,0.013262072,0.006187261,6.99E-08,3.28E-07
+Mul1,0.013257517,0.004034056,0.006855185,0.009500757
+Mat2b,0.013176257,0.075553924,1.73E-07,7.50E-07
+Gjb4,0.013118505,0.147711179,0.002651558,0.004020003
+Gpr87,0.012997793,0.171940493,0.00116606,0.001929277
+Uri1,0.012992149,0.026372066,0.005010052,0.007146114
+Tsnax,0.01291019,0.114490254,1.60E-07,6.94E-07
+Thap11,0.012886833,0.0312262,0.000405325,0.000753102
+Ndufaf4,0.012883473,0.014748854,0.000660107,0.001161671
+Gpr137,0.01285576,0.03902306,0.000234111,0.000461688
+Ctnnbl1,0.012842205,0.03226467,1.89E-05,4.96E-05
+Gmnn,0.012774556,-0.319710207,5.51E-15,1.02E-13
+Morf4l2,0.012710646,0.142720927,2.50E-05,6.33E-05
+Slc46a3,0.01258668,-0.026996638,6.97E-05,0.000156844
+Sf3a1,0.012583149,0.004863433,0.000504008,0.000910909
+Ndufb11,0.012555988,-0.012153434,0.000211222,0.000421648
+Nae1,0.012519309,-0.001415208,0.01009179,0.013560909
+Eif5,0.012473721,0.160500194,1.15E-05,3.18E-05
+Cxxc1,0.012426216,0.051009158,0.012271228,0.01621883
+Synpo,0.012415419,0.001257678,1.54E-05,4.14E-05
+Sdha,0.012413058,-0.012320446,6.31E-07,2.40E-06
+Dlat,0.012364428,0.084875587,0.018450093,0.023506129
+Polr1d,0.012330219,0.156339289,7.43E-08,3.46E-07
+Rpa3,0.01232436,-0.026483996,3.02E-07,1.23E-06
+Nkiras2,0.01226806,0.144719248,0.003523043,0.005198737
+Swi5,0.012261985,0.076246086,0.000388966,0.00072664
+Cpne8,0.012253356,0.051511103,0.005568584,0.007863276
+Ube2h,0.012172536,-0.008934639,7.23E-05,0.000162081
+Lypd6b,0.012132584,0.10913414,0.001728779,0.002739855
+Syncrip,0.012036489,-0.032808834,0.001380362,0.002245868
+Psmc2,0.01197174,0.098105864,3.84E-08,1.94E-07
+Rmnd5b,0.011925027,0.034369735,0.004988558,0.007123312
+Cmc2,0.011922828,0.021935706,0.006668863,0.009264737
+Pyurf,0.011823891,0.033357558,3.84E-06,1.20E-05
+Bag5,0.011797929,0.048077474,2.35E-05,5.99E-05
+Ngrn,0.011753231,0.051371859,0.000545208,0.000977869
+Smu1,0.011686312,0.085081149,8.01E-07,2.96E-06
+Tmem106c,0.011668275,0.105142482,1.11E-05,3.09E-05
+Cebpg,0.011667756,0.063840302,0.008060703,0.011022591
+Rps6ka1,0.011637759,0.059338928,0.004135724,0.006013536
+Fbxw4,0.011601147,0.044989024,0.006964835,0.00964012
+Msra,0.011512377,0.051873942,0.002275775,0.003501192
+Proser2,0.011493134,0.070964783,0.005006144,0.007143612
+5-Mar,0.011481965,0.121085412,0.000501886,0.000907849
+Smndc1,0.011444612,0.020127902,0.001205384,0.001987103
+Tcf4,0.011429534,-0.035319922,0.00036676,0.000688893
+Tmem109,0.011338493,0.24724554,4.58E-10,3.63E-09
+Pym1,0.011337287,0.033333883,0.001580759,0.002534315
+Brcc3,0.011322045,0.045217164,8.13E-05,0.000179796
+Rras,0.011304651,0.025146064,3.85E-05,9.26E-05
+Safb,0.011230629,0.053467085,0.004893385,0.006997
+Fundc2,0.011208294,-0.004662674,8.07E-06,2.33E-05
+Zfand5,0.011045773,0.575982864,1.07E-10,1.01E-09
+Nrarp,0.011033708,0.104647964,0.001049962,0.001753855
+Asgr1,0.010970247,-0.167443626,2.74E-10,2.31E-09
+Tmem55a,0.010967477,0.022285127,0.003180941,0.004738999
+Tmem246,0.010965293,-0.01691493,0.000270626,0.00052459
+Eftud2,0.010944718,0.012780997,0.010800413,0.014406592
+Rpp14,0.010904012,0.027072645,1.30E-05,3.53E-05
+Cog8,0.010874657,0.035392865,6.21E-06,1.85E-05
+Tssc1,0.010799201,0.047156095,0.003346378,0.004964423
+Sergef,0.010700992,-0.038585079,0.010380391,0.013892974
+Gtpbp4,0.01069764,0.038420465,5.08E-05,0.000118247
+Lrrc8d,0.010673525,0.034503801,0.031275375,0.038274271
+Pqlc3,0.010534201,0.044121433,0.000488392,0.000886212
+Cd151,0.01051053,0.384694148,5.10E-09,3.15E-08
+Exoc3l4,0.01049898,-0.040358042,5.01E-06,1.52E-05
+Stard7,0.010457244,0.011640077,0.000128536,0.000270066
+Mad2l1bp,0.010426034,0.037407457,0.007121753,0.009844457
+Rnft1,0.010392299,0.037480488,1.47E-07,6.46E-07
+Nphp1,0.01038718,0.020438321,0.002334999,0.003581909
+Cbfb,0.010355075,0.082223828,0.013537483,0.017748586
+Mllt10,0.010302591,-0.001772676,4.85E-05,0.000113476
+Acly,0.010300042,0.022216909,0.022168474,0.027869439
+Ide,0.010226824,-0.007993022,7.94E-10,5.97E-09
+Slc13a2,0.010224871,-0.021330875,0.000162622,0.00033353
+Gemin2,0.010200368,0.035441659,0.000855334,0.001459598
+Limd1,0.010152958,0.044271296,0.031995495,0.039125427
+Slc30a5,0.010152441,0.025166974,0.002235055,0.003452745
+Fbxl5,0.010144071,0.024532771,0.000335116,0.000635462
+Mrpl21,0.010066277,0.087572198,2.44E-05,6.22E-05
+Igbp1,0.009996069,0.022784459,0.001698926,0.00269792
+Rce1,0.009948589,0.070195712,1.50E-06,5.22E-06
+Nsun2,0.009878063,0.068348737,0.014614968,0.019023986
+Ppap2a,0.009798263,0.036309772,0.001203791,0.001984991
+Gpn3,0.009711904,0.010037595,4.49E-06,1.37E-05
+Opn4,0.009690411,-0.01485698,0.02449276,0.030502046
+Foxa3,0.009684639,-0.024980495,0.000758599,0.001310344
+Ptges2,0.009677074,0.033956161,0.008511415,0.011599014
+Wash1,0.009622279,0.030932005,0.003110869,0.00465204
+Zfp771,0.009553313,0.006733929,9.88E-07,3.59E-06
+Nt5m,0.009527573,-0.0042256,0.035906367,0.043464883
+Brd3,0.009497193,0.00868096,0.008718093,0.01185273
+Fam175b,0.009272057,0.028401552,0.031427047,0.038452486
+Jagn1,0.009176906,0.057629587,0.00032049,0.000610456
+Edem1,0.009170458,-0.014873107,0.00295857,0.004443094
+Zpr1,0.009129266,0.049441082,0.002224612,0.003439118
+Leng9,0.009121008,0.058190686,0.000311356,0.000595378
+Rnf6,0.009119859,0.052427548,0.004067506,0.005918403
+Heatr6,0.009110506,0.009329108,0.002758367,0.004167034
+Ndufaf3,0.009016506,-0.047033765,0.000406653,0.000755129
+Wdsub1,0.008972165,0.03886535,0.000223755,0.000444574
+Sephs2,0.00890566,0.011455695,7.58E-06,2.20E-05
+Pex16,0.008893418,0.06151226,0.000103668,0.000222821
+Spns1,0.008810221,0.04368279,0.004784415,0.006849489
+Mtch1,0.008808309,0.052667477,8.16E-05,0.000180427
+Tars2,0.008783538,0.027850554,0.013885831,0.018156638
+Slc31a1,0.008781802,0.050478296,6.45E-08,3.06E-07
+Mrps30,0.008728823,0.016819128,0.004775517,0.006840605
+Upf3a,0.008708618,0.033576704,0.014718048,0.019146407
+Ucp2,0.008608032,0.200420778,3.33E-05,8.15E-05
+Zdhhc7,0.008544738,0.027626676,0.009494059,0.012817282
+Ugp2,0.0085254,0.125853855,0.000120762,0.000255589
+Slc39a7,0.008505169,-0.046652002,1.14E-06,4.06E-06
+Agfg2,0.008443101,0.092750121,2.81E-05,7.03E-05
+Slc39a9,0.008426694,0.006180695,8.57E-05,0.000188328
+Kdm6b,0.008277665,-0.011493358,1.04E-05,2.92E-05
+Phf5a,0.0082528,0.145441015,3.06E-07,1.25E-06
+Mocs3,0.008242408,0.00431986,0.020403969,0.0257888
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diff --git a/genesets/genes.deg.BE.csv b/genesets/genes.deg.BE.csv
index 5afc74235cd55d0a0a18ac8b016ae72937ba44c1..54efe2b8c14ea9d5c959f0a5823cdd1d3423c300 100644
--- a/genesets/genes.deg.BE.csv
+++ b/genesets/genes.deg.BE.csv
@@ -1,32 +1,33 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
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diff --git a/genesets/genes.deg.Endo.csv b/genesets/genes.deg.Endo.csv
index a20eb92f1b16474b412a813d44997eb9323bd6c9..b8def7233a303b2a3996cbcbcff3b90ba480ccd1 100644
--- a/genesets/genes.deg.Endo.csv
+++ b/genesets/genes.deg.Endo.csv
@@ -1,105 +1,113 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
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+"TMEM255B",2.80454244961454e-232,0.860681487938916,0.432,0.03,6.5205611953538e-228
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+"MSN",1.40256434381965e-210,0.890540145017829,0.751,0.322,3.26096209938068e-206
+"HLA-E",3.6344306599811e-210,0.751516257557139,0.959,0.75,8.45005128445605e-206
+"CFLAR",6.74283607349663e-204,0.961571403003376,0.79,0.373,1.56770938708797e-199
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+"ARPC1B",1.86595491968936e-192,0.815704046676398,0.744,0.304,4.33834518827776e-188
+"ESAM",3.40100297395025e-190,0.834185014388266,0.471,0.077,7.90733191443433e-186
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+"ITM2A",1.39707160270379e-183,0.890381793095951,0.497,0.098,3.24819147628631e-179
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+"ATP1A1",2.56093851346436e-175,0.798780790394714,0.816,0.468,5.95418204380464e-171
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+"LUZP1",6.85989301521989e-174,0.809127784647689,0.634,0.218,1.59492512603862e-169
+"FXYD5",1.51062450951668e-172,0.758209712887919,0.657,0.225,3.51220198462627e-168
+"MCTP1",1.33482501640548e-170,0.713936056658763,0.31,0.014,3.10346816314274e-166
+"MMP1",3.14565523819617e-169,2.20760149825212,0.326,0.023,7.3136484288061e-165
+"RAMP2",5.70921996909349e-167,0.88738725909783,0.358,0.037,1.32739364281424e-162
+"NOP10",1.79581165767344e-166,0.817713832614927,0.724,0.341,4.17526210409075e-162
+"ZEB1",5.17231473653779e-162,0.738096753559833,0.504,0.123,1.20256317624504e-157
+"HSPG2",4.59843086105139e-160,0.737773840518233,0.435,0.083,1.06913517519445e-155
+"FKBP1A",1.8084329087042e-159,0.823445691978731,0.727,0.363,4.20460651273727e-155
+"RND1",2.92170292956629e-159,1.31422556044679,0.308,0.021,6.79295931124162e-155
+"THBD",6.75453723345942e-157,1.12704145856541,0.468,0.106,1.57042990677932e-152
+"CDC42EP3",1.19244038090686e-154,0.766440554093496,0.602,0.206,2.77242388560844e-150
+"CRIP2",4.54548280879056e-153,0.833214077756429,0.534,0.151,1.05682475304381e-148
+"PPFIBP1",3.60364927839601e-152,0.730114163119552,0.458,0.104,8.37848457227072e-148
+"TSC22D1",1.89122041219108e-150,0.887044020994936,0.854,0.507,4.39708745834426e-146
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+"RAB13",2.1936541420331e-146,0.718152358908408,0.75,0.396,5.10024588022695e-142
+"APP",1.28805515132911e-142,0.797848562987232,0.722,0.375,2.99472822684018e-138
+"C2CD4B",3.44280290764093e-138,0.813775757171602,0.251,0.01,8.00451676026516e-134
+"CARHSP1",1.51161597819225e-137,0.766042313664704,0.484,0.142,3.51450714929698e-133
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+"AP1S2",5.08605141477263e-135,0.695192445117044,0.527,0.165,1.18250695393464e-130
+"DUSP23",9.91725475359695e-135,0.831560782614988,0.408,0.097,2.30576173021129e-130
+"GJA1",1.00014557058011e-134,0.902484840127658,0.523,0.177,2.32533845159875e-130
+"UPP1",2.29665403478599e-132,0.796244863121148,0.521,0.166,5.33972063087742e-128
+"PRSS23",1.72784851724629e-131,0.873221040643264,0.452,0.126,4.01724780259764e-127
+"SEC14L1",1.19210724179709e-130,0.704189373033159,0.423,0.104,2.77164933717825e-126
+"ASPH",8.53020809339658e-129,0.789792999516886,0.501,0.17,1.98327338171471e-124
+"MRPL33",8.48717362728843e-127,0.728387240562748,0.593,0.244,1.97326786834456e-122
+"TXNRD1",6.45456425970849e-124,0.86902690625259,0.702,0.404,1.50068619038222e-119
+"ANGPT2",2.55188578011304e-123,1.39243862701965,0.364,0.077,5.93313443876281e-119
+"C4orf32",5.919789203813e-118,0.700550225181616,0.496,0.17,1.37635098988652e-113
+"ICAM1",1.79981290032169e-117,0.787249841642591,0.632,0.292,4.18456499324793e-113
+"INSR",5.77417317407639e-103,0.917754940727712,0.395,0.121,1.34249526297276e-98
+"SLC9A3R2",3.853265811619e-101,0.777444115459207,0.37,0.1,8.95884301201418e-97
+"CSF3",1.66871138253636e-95,0.873413796874229,0.506,0.19,3.87975396439704e-91
+"SQSTM1",1.35207931188533e-91,0.715918949808855,0.895,0.781,3.14358440013339e-87
+"EMP1",6.09356663357739e-89,0.696552481614684,0.811,0.541,1.41675424230674e-84
+"RCAN1",1.03294348645462e-86,0.786099691522489,0.447,0.172,2.40159360600699e-82
+"ENG",5.42971604621474e-76,0.705817689757429,0.33,0.106,1.26240898074493e-71
+"PGF",6.9758050696494e-58,0.771897749798884,0.266,0.085,1.62187467869349e-53
+"CXCL2",2.57986516997583e-47,0.902126647976652,0.508,0.286,5.9981865201938e-43
+"SOCS3",5.79236086472243e-27,0.763805550249794,0.506,0.358,1.34672390104797e-22
diff --git a/genesets/genes.deg.Epi.csv b/genesets/genes.deg.Epi.csv
index 85c36169984852a290fee9991a231b82f759c62c..56b5c01aa34c17f4dcb75276f990a88da8e96708 100644
--- a/genesets/genes.deg.Epi.csv
+++ b/genesets/genes.deg.Epi.csv
@@ -1,97 +1,101 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"KRT17",0,2.58938400797297,0.9,0.322,0
-"TACSTD2",0,2.48592161102793,0.976,0.254,0
-"KRT19",0,2.37656912425916,0.862,0.17,0
-"CLDN4",0,2.23223983107903,0.805,0.192,0
-"S100A2",0,2.11027968973883,0.783,0.271,0
-"KRT15",0,2.05098032713226,0.687,0.124,0
-"SFN",0,2.01048836143528,0.803,0.112,0
-"KRT8",0,1.93588592417168,0.846,0.148,0
-"KRT23",0,1.91416919936357,0.621,0.102,0
-"KRT7",0,1.84027917077937,0.737,0.124,0
-"SLPI",0,1.79658376815771,0.581,0.114,0
-"AQP3",0,1.71892889410552,0.678,0.119,0
-"WFDC2",0,1.71312196278939,0.674,0.126,0
-"KLF5",0,1.699250308667,0.783,0.113,0
-"KRT18",0,1.6331407730637,0.866,0.195,0
-"DST",0,1.6081395719577,0.598,0.184,0
-"KRT5",0,1.59879931816845,0.636,0.073,0
-"FXYD3",0,1.53485393343251,0.749,0.115,0
-"ERRFI1",0,1.50764260205658,0.655,0.182,0
-"AZGP1",0,1.47397056868542,0.388,0.059,0
-"PERP",0,1.44289236540893,0.891,0.267,0
-"ACTG1",0,1.40927890930988,0.99,0.794,0
-"ELF3",0,1.35219796098009,0.581,0.095,0
-"F3",0,1.30673626095317,0.532,0.128,0
-"SPINT2",0,1.3057498845568,0.756,0.127,0
-"FHL2",0,1.30306739941313,0.692,0.191,0
-"GADD45A",0,1.258480274153,0.821,0.421,0
-"S100A14",0,1.25173738037139,0.547,0.067,0
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-"S100A16",0,1.09657537591032,0.832,0.359,0
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-"CEACAM1",0,0.987709477461549,0.462,0.077,0
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-"CD9",0,0.928446508700755,0.942,0.572,0
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-"HMGA1",0,0.892455170275484,0.799,0.44,0
-"ZG16B",0,0.891717600115833,0.376,0.035,0
-"GSTP1",0,0.868516036638084,0.926,0.753,0
-"EPCAM",0,0.865412796025363,0.438,0.048,0
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-"IRF6",0,0.830037247493429,0.421,0.041,0
-"PRSS22",0,0.813712947600702,0.326,0.027,0
-"PRDX5",0,0.812013255548144,0.752,0.388,0
-"S100A6",0,0.807761754209761,0.979,0.952,0
-"VAMP8",0,0.79787944435212,0.553,0.111,0
-"TSPAN1",0,0.785094012814534,0.349,0.041,0
-"ITGA2",0,0.779535472589544,0.551,0.173,0
-"PHLDA3",0,0.777638476351216,0.45,0.101,0
-"JUP",0,0.774860888048379,0.433,0.064,0
-"IRF2BP2",0,0.763604279476099,0.523,0.178,0
-"HEBP2",0,0.731794004522045,0.631,0.295,0
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-"TPM4",0,0.706690024360295,0.856,0.574,0
-"CD47",0,0.7013154526421,0.552,0.2,0
-"TNFRSF21",0,0.69675566468842,0.37,0.062,0
-"PPDPF",0,0.695568636301807,0.791,0.46,0
-"CXCL17",2.68694981108922e-307,1.16390353660727,0.345,0.048,6.15660810214873e-303
-"SDC4",7.790133412747e-295,0.728197915307017,0.45,0.13,1.78495326886272e-290
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-"MAL2",1.76939628476127e-272,0.71258710956365,0.313,0.04,4.05421770727349e-268
-"HSPB1",1.23478427749855e-271,0.735815300790782,0.885,0.761,2.82926121503244e-267
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-"ID1",4.66741976631916e-255,0.879974872976305,0.455,0.167,1.06944589105671e-250
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-"AGR2",7.70558607511663e-213,0.997659361946383,0.266,0.039,1.76558093739147e-208
-"KRT14",1.72500610907661e-210,1.60825564385883,0.281,0.053,3.95250649772723e-206
-"AREG",2.63908314824736e-206,0.738635477739827,0.425,0.157,6.04693121757919e-202
-"ZFP36L2",1.57190422246903e-195,0.700460124407409,0.629,0.377,3.60170414494328e-191
-"MMP7",1.73076330752804e-194,1.23575314971371,0.254,0.041,3.965697966539e-190
-"KRT13",8.07721119029167e-188,1.49558900672051,0.265,0.056,1.85073140003153e-183
-"S100P",4.30108472802187e-183,1.42914016410278,0.313,0.098,9.85507543731652e-179
-"MTRNR2L1",3.01627513063481e-171,0.785837689292135,0.487,0.274,6.91119120682355e-167
-"CD24",1.35356980943557e-137,0.883526069723824,0.299,0.114,3.10143450435972e-133
-"DKK1",5.02572663568815e-121,0.820881908241992,0.278,0.102,1.15154474403522e-116
-"MSMB",2.94042573991532e-14,1.95128640415309,0.253,0.203,6.73739749786798e-10
+"KRT17",0,2.64673644764602,0.91,0.38,0
+"TACSTD2",0,2.58231159715341,0.981,0.282,0
+"KRT19",0,2.45083620114524,0.872,0.185,0
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+"KRT15",0,2.13730992361203,0.705,0.122,0
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+"SLPI",0,1.97212133924044,0.609,0.126,0
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+"KRT7",0,1.85832624877284,0.762,0.135,0
+"WFDC2",0,1.82603184536208,0.706,0.142,0
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+"KRT18",0,1.65532949882324,0.889,0.214,0
+"FXYD3",0,1.61927290958347,0.793,0.123,0
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+"KRT5",0,1.61473814532591,0.661,0.08,0
+"AZGP1",0,1.59595095398688,0.423,0.063,0
+"ERRFI1",0,1.5002166398309,0.671,0.207,0
+"PERP",0,1.43991512228113,0.913,0.305,0
+"ELF3",0,1.39422648108229,0.616,0.113,0
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+"S100A14",0,1.29343286078518,0.589,0.071,0
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+"EHF",0,1.08296266097339,0.531,0.042,0
+"SERPINB5",0,1.08108443063903,0.462,0.034,0
+"S100A16",0,1.0769615457348,0.858,0.416,0
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+"HBEGF",0,1.06681378224294,0.522,0.201,0
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+"ACTB",0,1.05079544839747,0.992,0.9,0
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+"MPZL2",0,0.994372861783234,0.644,0.149,0
+"CEACAM1",0,0.98928633223492,0.501,0.086,0
+"ZG16B",0,0.979605923698475,0.429,0.036,0
+"CD9",0,0.939348912075797,0.955,0.613,0
+"STK17A",0,0.937434104556968,0.612,0.222,0
+"SLC14A1",0,0.921059272534142,0.443,0.052,0
+"HMGA1",0,0.882636420446482,0.838,0.494,0
+"ALDH1A3",0,0.876037021829772,0.475,0.13,0
+"EPCAM",0,0.870929113732984,0.478,0.045,0
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+"IRF6",0,0.857811859218995,0.471,0.038,0
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+"PRDX5",0,0.822551687733958,0.789,0.438,0
+"TNFRSF12A",0,0.808337370482687,0.892,0.483,0
+"PHLDA3",0,0.795531021308692,0.494,0.111,0
+"S100A6",0,0.784779708737913,0.981,0.977,0
+"JUP",0,0.784069000314477,0.488,0.074,0
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+"SDC4",0,0.753410062764128,0.503,0.146,0
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+"CD47",0,0.71273810568372,0.599,0.22,0
+"CXCL16",0,0.704014318224997,0.426,0.071,0
+"KLK11",0,0.702290293393313,0.352,0.037,0
+"PPDPF",0,0.70023197306758,0.851,0.544,0
+"FAM110C",4.68811670147243e-302,0.81952198692582,0.321,0.023,1.08998713309234e-297
+"LMO7",3.54562564288941e-287,0.776064729336601,0.34,0.045,8.24357961971787e-283
+"LCN2",1.29929397078246e-279,1.98321221152763,0.43,0.13,3.02085848206921e-275
+"GPX2",1.75911908897727e-269,0.849509542409469,0.325,0.043,4.08995188187215e-265
+"RAB11FIP1",3.69529627971261e-269,0.720818871919051,0.341,0.055,8.59156385033181e-265
+"HSPB1",7.16440246438237e-267,0.785961433480702,0.893,0.779,1.6657235729689e-262
+"HIST1H1C",1.61000939082964e-254,0.719287302119213,0.48,0.184,3.74327183367892e-250
+"AGR2",2.68285137014948e-231,1.0612067064208,0.295,0.044,6.23762943559755e-227
+"KRT14",1.00746316626082e-212,1.65359002160063,0.295,0.056,2.3423518615564e-208
+"MMP7",9.3259028722788e-212,1.30588565024517,0.278,0.042,2.16827241780482e-207
+"KRT13",2.33641834478255e-210,1.63851273006006,0.292,0.056,5.43217265161943e-206
+"KRT16",1.07784000202821e-200,1.19125071652985,0.258,0.034,2.50597800471559e-196
+"S100P",8.37182577735041e-198,1.57588848571193,0.35,0.117,1.94644949323397e-193
+"ZFP36L2",2.94915164836327e-188,0.715517638044633,0.652,0.404,6.85677758244461e-184
+"MTRNR2L1",4.92681915776347e-166,0.796880879549293,0.498,0.282,1.14548545418001e-161
+"CD24",5.22646762822138e-146,0.921382790745211,0.331,0.131,1.21515372356147e-141
+"DKK1",8.30819005061725e-110,0.756949927526965,0.291,0.115,1.93165418676851e-105
+"GDF15",5.94555679467146e-81,1.18807270039704,0.276,0.139,1.38234195476112e-76
+"MSMB",6.76126653486279e-16,2.27369721884818,0.289,0.234,1.5719944693556e-11
diff --git a/genesets/genes.deg.Fib.csv b/genesets/genes.deg.Fib.csv
index 2e769eb6be439dd11ae5901ce59596f5fa691efc..0aa7439e950fb91357bc3bf197857d5a1df4ee9e 100644
--- a/genesets/genes.deg.Fib.csv
+++ b/genesets/genes.deg.Fib.csv
@@ -1,125 +1,124 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"APOD",0,3.79291322944109,0.777,0.06,0
-"FBLN1",0,3.3110242926498,0.946,0.066,0
-"PTGDS",0,3.11269248420061,0.689,0.099,0
-"CFD",0,3.05773009205437,0.815,0.099,0
-"DCN",0,2.79665117830106,0.942,0.09,0
-"PTGS2",0,2.64717143841423,0.729,0.093,0
-"SERPINE2",0,2.56717518293175,0.634,0.042,0
-"LUM",0,2.46952248951602,0.737,0.034,0
-"MGST1",0,2.22814451325941,0.807,0.071,0
-"SERPINF1",0,2.19776166557231,0.808,0.101,0
-"PTN",0,2.10754944208958,0.786,0.056,0
-"MEG3",0,2.01536248070107,0.897,0.192,0
-"MMP2",0,1.86015698489987,0.745,0.031,0
-"FGF7",0,1.84181197828367,0.601,0.039,0
-"HSD11B1",0,1.74941215466598,0.502,0.005,0
-"CLMP",0,1.64924063894724,0.6,0.006,0
-"MFAP4",0,1.64696295266947,0.618,0.069,0
-"PDPN",0,1.55916058841103,0.583,0.016,0
-"C1S",0,1.48311223089352,0.807,0.154,0
-"LTBP4",0,1.27122457366478,0.611,0.063,0
-"RHOBTB3",2.55677173099832e-307,1.63895158656124,0.683,0.119,5.85833106723644e-303
-"AKR1C1",1.48675705604655e-305,1.80881952509314,0.603,0.065,3.40660644251946e-301
-"C1R",9.95282082398624e-293,1.48034143175726,0.77,0.183,2.28048983539997e-288
-"FGF2",1.63900042037956e-287,1.80763442657704,0.562,0.063,3.75544166321569e-283
-"TNFAIP6",2.28031126818e-275,2.00801711372423,0.487,0.031,5.22487720878084e-271
-"IGFBP5",2.41548953887207e-268,1.42367261825101,0.854,0.26,5.53461118041758e-264
-"TIMP1",3.83740333739115e-252,1.6697669464491,0.972,0.747,8.79264226696434e-248
-"MGP",4.32329211053931e-244,1.96048328030165,0.884,0.476,9.90595921287872e-240
-"SFRP2",5.96733164202278e-226,1.3302204271487,0.348,0.005,1.36729469913668e-221
-"IGFBP2",1.19369130891238e-217,1.48790247759478,0.77,0.3,2.73510489611093e-213
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-"LAPTM4A",1.23652438181679e-199,0.906292425948359,0.938,0.658,2.83324831605681e-195
-"RARRES2",1.25125999594663e-198,1.03953426961611,0.606,0.137,2.86701202871252e-194
-"PRRX1",2.19665008007407e-194,1.07646697666392,0.531,0.099,5.03318432847372e-190
-"SPON2",1.44028625738932e-188,0.998338428659164,0.359,0.024,3.30012790155615e-184
-"SERPING1",4.09369229192475e-185,1.04313043482511,0.783,0.334,9.37987714848718e-181
-"COL6A2",1.44418434355694e-183,0.971530422720157,0.737,0.249,3.30905958639203e-179
-"ANXA5",2.81902205573643e-183,0.894118203692843,0.899,0.634,6.45922523630889e-179
-"DKK3",1.3968124019238e-179,0.921903552629984,0.415,0.052,3.20051625652801e-175
-"GPM6B",9.07525560292286e-176,0.989416627024534,0.442,0.069,2.07941331629771e-171
-"SPOCK3",4.36726555299016e-169,0.804917551648696,0.292,0.011,1.00067155615664e-164
-"PCOLCE2",1.56873092285193e-167,1.09060206965549,0.287,0.01,3.59443316353064e-163
-"FBLN2",4.69976881508865e-167,0.743570026003104,0.279,0.008,1.07685802860126e-162
-"CTSK",5.93556412567764e-166,0.885094915999654,0.308,0.018,1.36001580811652e-161
-"SNCA",1.09079522676813e-165,1.17162452750872,0.352,0.036,2.49933910309382e-161
-"PDGFRA",9.02550188673434e-164,0.790622058187118,0.27,0.007,2.06801324730744e-159
-"LGALS3BP",4.27315702045721e-163,0.864996289341099,0.454,0.083,9.79108468097361e-159
-"CEBPB",1.55592326371343e-160,1.05889934807228,0.851,0.474,3.56508697414658e-156
-"TWIST2",3.97779626522621e-157,0.866720842832254,0.317,0.025,9.11432458251281e-153
-"C7",5.17367488401873e-156,1.34212134276454,0.36,0.046,1.18544412617521e-151
-"PCOLCE",1.72787231359232e-155,0.850007526629659,0.403,0.06,3.95907383213408e-151
-"SFRP1",1.92908947834341e-154,1.25204288891544,0.349,0.041,4.42012272172826e-150
-"AEBP1",5.21045622384098e-154,0.859398326398701,0.515,0.123,1.19387183456868e-149
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-"IGF1",3.3409644907872e-147,1.09373747313418,0.271,0.015,7.6551519377407e-143
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-"KCNK1",2.60167661213819e-144,0.944700145946652,0.387,0.068,5.96122162139222e-140
-"MPZL1",3.38512984470124e-143,0.93221790132296,0.614,0.226,7.75634801316395e-139
-"SDC2",7.49270568242611e-142,0.915616687099867,0.515,0.138,1.71680365301429e-137
-"PID1",4.88774217447953e-139,0.812602683117633,0.296,0.027,1.11992836443849e-134
-"TNFRSF12A",7.68974360878832e-137,0.973294926750149,0.699,0.326,1.76195095308167e-132
-"EFEMP1",5.37458351902809e-136,0.841723009137495,0.302,0.032,1.23147832171491e-131
-"THBS2",5.39387494024329e-136,0.860787142469933,0.276,0.021,1.23589856505795e-131
-"BTG3",1.38486192819091e-134,0.881877109697442,0.756,0.404,3.17313413606383e-130
-"FGFR1",1.59546573472453e-134,0.819525693533352,0.652,0.264,3.65569063797431e-130
-"FXYD6",6.56119295839467e-133,0.852710209073764,0.441,0.103,1.50336614255697e-128
-"NBL1",1.71688570431808e-132,0.927974462220251,0.662,0.292,3.93390021430401e-128
-"BNIP3L",2.32203414355335e-129,0.98073769939853,0.652,0.289,5.3204768331238e-125
-"CST3",7.9044301135554e-128,0.721206183180666,0.962,0.797,1.81114207191895e-123
-"IL6",4.10058905857732e-125,1.83926192910522,0.601,0.242,9.39567970991822e-121
-"TFPI2",5.97324788333105e-123,2.01650584697686,0.387,0.09,1.36865028750764e-118
-"RARRES1",1.09655412850828e-122,1.16984998733001,0.331,0.054,2.51253447465103e-118
-"UFM1",7.046656095606e-120,0.819729595189626,0.648,0.299,1.6146003111862e-115
-"CCK",1.20477994946141e-119,1.66345639052783,0.261,0.026,2.76051229820092e-115
-"CREB5",9.49828698534922e-119,1.0732522310626,0.479,0.154,2.17634249695307e-114
-"IGFBP6",1.81567267336723e-118,0.872112569106283,0.721,0.313,4.16025079648634e-114
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-"SLC39A14",8.48193334368416e-117,0.792950852529106,0.484,0.15,1.94346538703835e-112
-"LARP6",1.70208474717915e-115,0.711617192361809,0.418,0.107,3.89998678121159e-111
-"CCDC80",3.32448372250784e-112,0.866093762213918,0.312,0.052,7.61738955338221e-108
-"REEP5",4.00063537286379e-112,0.849325535611733,0.633,0.312,9.1666558298428e-108
-"TFPI",4.097835174632e-112,0.838614588932489,0.694,0.337,9.38936973563429e-108
-"ARSG",5.0336535082344e-112,0.953515700981924,0.267,0.033,1.15336102834175e-107
-"GSTM3",2.79633421613976e-111,0.760382639890069,0.475,0.152,6.40724058944103e-107
-"IL32",3.1155632722741e-110,0.859660971518005,0.504,0.175,7.13869012576164e-106
-"COL6A1",3.70636465392149e-110,0.728556575109675,0.481,0.146,8.49239333153031e-106
-"FSTL1",3.12214306712902e-109,0.780802906724348,0.56,0.223,7.15376640971273e-105
-"MATN2",3.36182802802237e-109,0.702353546811879,0.26,0.031,7.70295656060765e-105
-"G0S2",3.86063721449966e-106,2.28005970172357,0.529,0.209,8.84587804958306e-102
-"CFH",7.96789125721341e-98,0.734833628862579,0.367,0.092,1.82568292376531e-93
-"PGRMC1",1.25509081146662e-96,0.730840965769153,0.538,0.224,2.87578957631346e-92
-"GSTO1",1.30801907407352e-94,0.781013301283037,0.75,0.475,2.99706410442466e-90
-"RHOQ",2.85052219332319e-94,0.950633217860001,0.479,0.181,6.53140150156143e-90
-"ERN1",4.30789398232046e-86,0.730728254225978,0.437,0.155,9.87067748169087e-82
-"LMO4",4.73987976243994e-83,0.803549060902857,0.492,0.204,1.08604864996786e-78
-"IER3",7.81272728941523e-83,1.34277974660946,0.752,0.519,1.79013020382371e-78
-"GYPC",1.85105003144379e-82,0.737893369275458,0.591,0.296,4.24131093704716e-78
-"UAP1",1.83404093298896e-81,0.839610191041379,0.492,0.207,4.2023379897576e-77
-"OSBPL8",1.16263169895172e-74,0.715754287709372,0.46,0.195,2.66393801180807e-70
-"CRYAB",6.77650031146148e-70,1.07190754215473,0.649,0.355,1.55269951636517e-65
-"OAF",2.37847140674618e-68,0.734390217928351,0.425,0.181,5.44979153427753e-64
-"GPRC5A",1.20840413843122e-67,0.750794896874201,0.43,0.181,2.76881640238746e-63
-"THBS1",1.89830858042468e-67,0.734047053846689,0.509,0.239,4.34959445032708e-63
-"PLPP3",3.58197836972971e-67,0.737574619051028,0.706,0.444,8.20738703856167e-63
-"THAP2",3.07954325518128e-63,0.945978492812044,0.36,0.134,7.05615746059688e-59
-"AKAP12",5.07160114989225e-62,0.703538701047952,0.7,0.431,1.16205597147481e-57
-"HSPA5",5.86318245652516e-52,0.91810967953059,0.665,0.44,1.34343099626361e-47
-"ADM",1.56560780767144e-50,0.852825338580146,0.439,0.226,3.58727716971757e-46
-"GSN",3.76637263789759e-46,0.840584164193668,0.727,0.572,8.62988962521475e-42
-"CYR61",2.73922168439818e-45,1.24668199019618,0.374,0.181,6.27637864546156e-41
-"APOE",3.7670968310229e-42,0.812185729243535,0.299,0.122,8.63154896892278e-38
-"CXCL1",1.21189255275331e-36,1.58128378589305,0.368,0.2,2.77680940612366e-32
-"PLIN2",2.13673504218494e-36,0.787069392283872,0.537,0.353,4.89590100215835e-32
-"PLAT",1.99767202748509e-30,0.761826737576409,0.377,0.21,4.5772659165766e-26
-"CCND1",3.85691207535271e-28,0.721149347007639,0.297,0.148,8.83734263825567e-24
-"IL33",6.60172339072715e-28,1.02374042117753,0.253,0.122,1.51265288051731e-23
-"CCL2",4.42839667616448e-15,0.710162054289814,0.413,0.291,1.01467853040957e-10
-"CXCL8",1.65590145091556e-11,0.975118073926779,0.667,0.615,3.79416699448281e-07
-"HERPUD1",4.2899720579533e-07,0.748295820888725,0.442,0.388,0.00982961297638839
+"APOD",0,3.8923501915822,0.825,0.076,0
+"FBLN1",0,3.2721555053362,0.953,0.076,0
+"PTGDS",0,3.09068526002133,0.709,0.114,0
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+"PTGS2",0,2.66808159367801,0.755,0.103,0
+"SERPINE2",0,2.48169709195106,0.642,0.054,0
+"LUM",0,2.43450601264945,0.761,0.039,0
+"MGST1",0,2.23842968640903,0.83,0.07,0
+"SERPINF1",0,2.21301816161794,0.848,0.112,0
+"PTN",0,2.14236031472684,0.8,0.058,0
+"MEG3",0,2.00541948571759,0.92,0.209,0
+"TNFAIP6",0,1.98385649030731,0.515,0.031,0
+"MMP2",0,1.86513229296865,0.801,0.037,0
+"AKR1C1",0,1.83526512687148,0.618,0.067,0
+"FGF7",0,1.77273086344674,0.627,0.046,0
+"FGF2",0,1.75435953320123,0.58,0.07,0
+"HSD11B1",0,1.68429879022444,0.525,0.006,0
+"MFAP4",0,1.63073520088028,0.662,0.082,0
+"RHOBTB3",0,1.62066625157783,0.719,0.128,0
+"CLMP",0,1.60507396447907,0.626,0.01,0
+"PDPN",0,1.53076705497695,0.591,0.019,0
+"C1R",0,1.45996687322777,0.822,0.214,0
+"C1S",0,1.44679811145353,0.838,0.172,0
+"LTBP4",0,1.2322514204452,0.675,0.088,0
+"IGFBP5",2.30172738481131e-287,1.41308236511827,0.871,0.275,5.35151616968629e-283
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+"AEBP1",1.03893221347569e-164,0.825514863151504,0.558,0.15,2.41551739633099e-160
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+"FSTL1",1.80328977472523e-130,0.770659713629198,0.613,0.247,4.19264872623615e-126
+"COL6A1",3.43071461921023e-130,0.699868176942725,0.538,0.167,7.97641148966379e-126
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+"GSTM3",1.52625301753633e-126,0.722568369222526,0.515,0.169,3.54853826577197e-122
+"TFPI2",1.69870953481948e-125,1.94001929705757,0.397,0.1,3.9494996684553e-121
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+"SLC39A14",2.08305677994999e-123,0.768642818463747,0.508,0.169,4.84310701338372e-119
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+"RHOQ",5.3558501817157e-111,0.949667069415368,0.516,0.196,1.2452351672489e-106
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+"G0S2",2.21270991123476e-106,2.1404486522104,0.537,0.221,5.14455054362081e-102
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+"MT2A",6.34494393088657e-105,0.701816915093939,0.915,0.72,1.47519946393113e-100
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+"IER3",8.67127590826899e-86,1.43549981219215,0.776,0.569,2.01607164867254e-81
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+"GPRC5A",3.3406377925895e-84,0.780127275618112,0.482,0.203,7.7669828677706e-80
+"DKK1",5.63674954653546e-82,1.2557703348848,0.253,0.052,1.31054426956949e-77
+"THBS1",5.08764856641079e-78,0.77092415579397,0.541,0.256,1.18287829169051e-73
+"CRYAB",5.06484913358495e-76,1.09325977191152,0.668,0.376,1.1775774235585e-71
+"PLPP3",5.36019667695455e-73,0.728173982522608,0.729,0.477,1.24624572739193e-68
+"AKAP12",1.40968340828309e-71,0.709650872902638,0.738,0.456,3.27751392425819e-67
+"INHBA",5.46522870992119e-61,0.775104376850911,0.268,0.078,1.27066567505668e-56
+"ADM",1.37941557171573e-58,0.890873158561427,0.475,0.246,3.20714120423908e-54
+"HSPA5",1.71678502597039e-57,0.946834116191769,0.713,0.485,3.99152518538116e-53
+"CYR61",1.78055485004698e-52,1.26823634090115,0.406,0.2,4.13979002635924e-48
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+"APOE",1.36482192127557e-46,0.835893703286247,0.309,0.126,3.1732109669657e-42
+"CXCL1",1.68724858146573e-39,1.56045219508845,0.393,0.221,3.92285295190781e-35
+"PLAT",2.5770417830082e-37,0.767115234054684,0.404,0.219,5.99162214549407e-33
+"PLIN2",1.12273915711162e-35,0.786092372899825,0.552,0.384,2.61036854028452e-31
+"CCND1",1.64342535149945e-33,0.696333849889495,0.321,0.159,3.82096394223621e-29
+"IL33",3.47941552126021e-22,0.93358925366071,0.254,0.141,8.08964108692999e-18
+"CXCL8",1.71297080184632e-12,0.982592829835716,0.713,0.652,3.98265711429269e-08
+"HERPUD1",1.55942871473637e-07,0.757026402746263,0.483,0.427,0.00362567176176205
diff --git a/genesets/genes.deg.LE.csv b/genesets/genes.deg.LE.csv
index 500ac08728e2083dd798fb9787bfd575a83b62e4..da2020b38bba0b4d14c255766b80f6f9d9dc3dc0 100644
--- a/genesets/genes.deg.LE.csv
+++ b/genesets/genes.deg.LE.csv
@@ -1,74 +1,80 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"MSMB",0,4.08708058619315,0.625,0.218,0
-"KLK3",0,3.57415058895005,0.622,0.066,0
-"ACPP",0,3.05853700045096,0.553,0.026,0
-"PLA2G2A",0,2.65306909791252,0.395,0.016,0
-"KLK2",0,2.35096653843629,0.54,0.022,0
-"TFF1",0,2.1077547925766,0.289,0.034,0
-"AZGP1",0,1.9646469946998,0.872,0.316,0
-"CLDN3",0,1.78638625072587,0.628,0.068,0
-"TSPAN8",0,1.77728666076375,0.705,0.069,0
-"NEAT1",0,1.64828762451604,0.987,0.917,0
-"SEC11C",0,1.48599410014509,0.576,0.138,0
-"AGR2",0,1.39327617509035,0.522,0.169,0
-"CPE",0,1.37342695246021,0.551,0.176,0
-"RDH11",0,1.36753102861056,0.476,0.086,0
-"CD24",0,1.18578314540027,0.624,0.231,0
-"ADIRF",0,1.18291698738611,0.594,0.226,0
-"TMPRSS2",0,1.15529088153922,0.538,0.086,0
-"NPDC1",0,1.07189940605503,0.624,0.173,0
-"SORD",0,1.04120043921947,0.346,0.086,0
-"ALDH1A3",0,1.0370065828055,0.668,0.364,0
-"SMIM14",0,1.02147096540552,0.634,0.176,0
-"LMO7",0,1.01424087631419,0.566,0.225,0
-"DHRS7",0,1.0070779934005,0.482,0.155,0
-"SLC12A2",0,1.00132518402253,0.417,0.048,0
-"KLK4",0,0.945036887392528,0.333,0.006,0
-"TPD52",0,0.941733748407522,0.605,0.221,0
-"CIB1",0,0.932402656942045,0.774,0.488,0
-"TMC5",0,0.932339641135605,0.395,0.053,0
-"RASEF",0,0.901378852784184,0.382,0.035,0
-"DSC2",0,0.894592865354611,0.426,0.106,0
-"PSCA",0,0.886196498491514,0.368,0.063,0
-"PPP3CA",0,0.884458690481338,0.424,0.082,0
-"SLC44A4",0,0.882654139286795,0.503,0.078,0
-"PART1",0,0.86713924670892,0.359,0.033,0
-"SLC39A6",0,0.852497140898053,0.509,0.161,0
-"SERF2",0,0.84338330957257,0.994,0.921,0
-"B2M",0,0.812630550100555,0.996,0.988,0
-"ABHD2",0,0.780044222545769,0.477,0.137,0
-"RAB27B",0,0.775644184806369,0.32,0.03,0
-"CDC42EP5",0,0.769070047197154,0.554,0.184,0
-"STEAP2",0,0.760905765567124,0.331,0.054,0
-"BACE2",0,0.753817594413803,0.601,0.258,0
-"FLJ20021",0,0.727292945177611,0.264,0.039,0
-"GOLM1",0,0.724853164275204,0.32,0.032,0
-"LIPH",0,0.719805976124413,0.308,0.05,0
-"LURAP1L",0,0.719635677339998,0.352,0.086,0
-"ERBB3",0,0.699654034742545,0.377,0.06,0
-"ELOVL5",2.47598993989341e-306,0.72041306337574,0.514,0.203,5.67323574927777e-302
-"ELF3",4.0173559246634e-302,0.848829908931687,0.801,0.512,9.20496763018125e-298
-"SPINK1",1.70714333921701e-299,0.891522281423165,0.268,0.057,3.91157753314793e-295
-"UQCRQ",3.23748755769427e-295,0.834242566721423,0.754,0.498,7.41805524094487e-291
-"ANKRD36C",4.03990485505453e-292,0.88126106322938,0.367,0.111,9.25663399438645e-288
-"MT1F",9.49618395176625e-292,0.799316183018215,0.251,0.053,2.1758606288682e-287
-"ZG16B",1.49149823961995e-285,1.08285207200042,0.64,0.336,3.41746991644119e-281
-"FXYD3",2.00195828630758e-279,0.785161463783,0.877,0.706,4.58708702141655e-275
-"INSIG1",1.03090691016796e-276,0.816462981522158,0.377,0.121,2.36211700326785e-272
-"MARCKSL1",9.26325268239139e-274,0.755627569388129,0.563,0.242,2.12248908711634e-269
-"GDF15",1.92032015502048e-261,1.06224695421362,0.435,0.159,4.40002957119842e-257
-"RNF144B",6.31172373989389e-259,0.768658030495642,0.333,0.102,1.44620526052189e-254
-"IL6ST",3.66196783696009e-257,0.743658899049098,0.487,0.21,8.39066690482664e-253
-"TSC22D1",6.53339219041608e-246,0.907744426031988,0.679,0.408,1.49699615259004e-241
-"HMGCS1",2.65482459947549e-231,0.87674124316359,0.307,0.097,6.0829996047782e-227
-"DBI",9.72319148108536e-229,0.824004713468524,0.642,0.403,2.22787486406109e-224
-"PLPP1",1.89916574467349e-220,0.838970783606746,0.324,0.11,4.35155847077037e-216
-"H2AFJ",7.35167009584579e-215,0.695326939969595,0.749,0.514,1.68448816906115e-210
-"NDRG1",8.14137126410103e-208,0.817723327044579,0.51,0.261,1.86543239774347e-203
-"SAT1",4.57784119881594e-193,0.811687388829258,0.981,0.96,1.0489207538847e-188
-"RPS27L",1.35376097431934e-189,0.848621277675737,0.639,0.408,3.10187252045791e-185
-"TXNIP",3.04120061608283e-187,0.824075919340205,0.526,0.281,6.9683029716306e-183
-"GLRX",2.43047346789762e-135,0.742920736668475,0.267,0.104,5.56894385699382e-131
-"MT1E",1.33007537111688e-133,1.98110804195228,0.413,0.232,3.0476016978401e-129
-"MGST1",7.20030674012427e-108,0.777288924842078,0.444,0.263,1.64980628336467e-103
-"MT2A",2.57231051097369e-45,1.30955170600812,0.639,0.567,5.89393507379401e-41
+"MSMB",0,4.37447239718553,0.686,0.25,0
+"KLK3",0,3.78840323642459,0.672,0.08,0
+"ACPP",0,3.13382648140614,0.596,0.031,0
+"PLA2G2A",0,2.81892272901388,0.444,0.02,0
+"KLK2",0,2.49353927858673,0.594,0.025,0
+"TFF1",0,2.15334059243419,0.329,0.041,0
+"AZGP1",0,2.0049490413152,0.897,0.345,0
+"MT1G",0,1.98581083516144,0.254,0.053,0
+"TSPAN8",0,1.82868329126073,0.741,0.077,0
+"CLDN3",0,1.81872600017444,0.678,0.078,0
+"NEAT1",0,1.66342555320245,0.992,0.932,0
+"SEC11C",0,1.50139213870143,0.616,0.159,0
+"RDH11",0,1.43938695807039,0.54,0.1,0
+"CPE",0,1.42726881338742,0.609,0.195,0
+"AGR2",0,1.38739010258592,0.569,0.185,0
+"ADIRF",0,1.20378597343587,0.662,0.266,0
+"TMPRSS2",0,1.17657374095478,0.598,0.1,0
+"CD24",0,1.169691225058,0.679,0.256,0
+"NPDC1",0,1.09945973647627,0.691,0.197,0
+"ZG16B",0,1.09632759033173,0.705,0.381,0
+"DHRS7",0,1.0780600230455,0.538,0.175,0
+"SLC12A2",0,1.05453438337529,0.48,0.056,0
+"ALDH1A3",0,1.00938272421439,0.708,0.409,0
+"SORD",0,1.00762400392571,0.38,0.101,0
+"KLK4",0,1.00075010108915,0.383,0.007,0
+"SMIM14",0,0.990064601095013,0.664,0.201,0
+"LMO7",0,0.981449368568302,0.611,0.256,0
+"TMC5",0,0.944131304887237,0.446,0.062,0
+"HMGCS1",0,0.928927221396835,0.375,0.112,0
+"TPD52",0,0.921812891053796,0.65,0.253,0
+"PPP3CA",0,0.918524421978158,0.497,0.095,0
+"RASEF",0,0.918474385055297,0.443,0.041,0
+"SLC44A4",0,0.915536056294867,0.565,0.098,0
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+"ELF3",0,0.90825329652683,0.83,0.543,0
+"PART1",0,0.897849167503269,0.422,0.041,0
+"PSCA",0,0.883834790597298,0.406,0.073,0
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+"UQCRQ",0,0.851514992774378,0.826,0.57,0
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+"FXYD3",0,0.795341516329355,0.919,0.751,0
+"STEAP2",0,0.786976946361527,0.386,0.061,0
+"ABHD2",0,0.779715640605612,0.533,0.159,0
+"CDC42EP5",0,0.774674582069486,0.613,0.217,0
+"RAB27B",0,0.766534607182507,0.37,0.038,0
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+"MT1F",0,0.735175225812285,0.275,0.06,0
+"BACE2",0,0.734623852847882,0.652,0.299,0
+"FLJ20021",0,0.722227423027725,0.301,0.047,0
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+"LURAP1L",0,0.701460739959854,0.38,0.098,0
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+"RNF144B",1.55475455202509e-306,0.760182455666201,0.38,0.119,3.61480433345833e-302
+"GDF15",2.01211114811691e-304,1.02000284299098,0.482,0.18,4.67815841937181e-300
+"MARCKSL1",3.87076430258232e-298,0.770455303625736,0.608,0.273,8.99952700350389e-294
+"DBI",1.31508887521865e-297,0.859804208266948,0.708,0.443,3.05758163488335e-293
+"ANKRD36C",1.31868558656178e-293,0.835820434758738,0.393,0.13,3.06594398875615e-289
+"IL6ST",3.47797112066833e-286,0.72159960498644,0.532,0.237,8.08628285555386e-282
+"TSC22D1",8.48846185126225e-286,0.981143608106769,0.72,0.435,1.97356738041847e-281
+"H2AFJ",1.02086674628759e-266,0.715945859194024,0.799,0.556,2.37351518511864e-262
+"NDRG1",1.60403620345049e-258,0.831848305281009,0.566,0.291,3.72938417302238e-254
+"PLPP1",3.7845405697958e-257,0.852158040389265,0.364,0.126,8.79905682477522e-253
+"SAT1",1.77156969700026e-217,0.792072293664311,0.988,0.968,4.1188995455256e-213
+"TXNIP",1.17916945396995e-214,0.824032953148113,0.559,0.3,2.74156898048013e-210
+"RPS27L",3.3815667813779e-198,0.802242921285638,0.675,0.444,7.86214276670362e-194
+"NKX3-1",4.7758881227118e-173,0.714910742253142,0.291,0.107,1.11039398853049e-168
+"GLRX",1.82073919060387e-148,0.705291464806051,0.296,0.119,4.233218618154e-144
+"MT1E",1.64237321428792e-145,1.85089781749558,0.454,0.266,3.81851772321941e-141
+"MGST1",1.23115980748549e-121,0.741661437165127,0.481,0.29,2.86244655240376e-117
+"FDPS",4.05857338821562e-111,0.779405255968596,0.412,0.229,9.43618312760133e-107
+"GADD45B",2.47436197380962e-62,0.957716958200775,0.512,0.375,5.75289158910737e-58
+"MT2A",4.48785503840556e-60,1.21424445779221,0.712,0.623,1.04342629642929e-55
+"JUN",6.73977419884717e-60,0.807603248779742,0.684,0.58,1.56699750123197e-55
diff --git a/genesets/genes.deg.Leu.csv b/genesets/genes.deg.Leu.csv
index c08f33894ffc6b655e4f1d17046104095422d873..d016acc0c01449b12eee25a25c2345a344981d67 100644
--- a/genesets/genes.deg.Leu.csv
+++ b/genesets/genes.deg.Leu.csv
@@ -1,125 +1,134 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"RGS1",0,3.1616182660362,0.767,0.005,0
-"C1QA",0,3.00130933166645,0.573,0,0
-"C1QB",0,2.92662688690031,0.545,0.003,0
-"TYROBP",0,2.79640624689908,0.692,0.002,0
-"C1QC",0,2.33174235120382,0.487,0,0
-"LYZ",0,2.287857825507,0.509,0.001,0
-"FCER1G",0,2.22717096535074,0.627,0.027,0
-"GPR183",0,2.103066091906,0.532,0.002,0
-"LAPTM5",0,1.83909757549662,0.659,0.01,0
-"ALOX5AP",0,1.82781596170231,0.556,0.004,0
-"BCL2A1",0,1.77728913248683,0.425,0.004,0
-"AIF1",0,1.74021430095879,0.478,0.001,0
-"SAMSN1",0,1.68355727344237,0.543,0.006,0
-"MS4A6A",0,1.67943781825005,0.463,0,0
-"MS4A7",0,1.49422453525511,0.44,0.001,0
-"LST1",0,1.39586422099601,0.448,0.001,0
-"PTPRC",0,1.1815035982877,0.403,0.001,0
-"EVI2B",6.24212201611821e-293,1.15173880680242,0.386,0.002,1.43025741755317e-288
-"CORO1A",9.38118668305525e-284,1.00068646023129,0.373,0.002,2.14951130468845e-279
-"VSIG4",5.02845560728893e-283,1.19516761748223,0.36,0,1.15217003329811e-278
-"FCGR2A",1.71783701751203e-281,1.53337365682598,0.401,0.006,3.93607995822532e-277
-"CD53",1.10922560393092e-279,1.0645045191219,0.384,0.004,2.54156862628691e-275
-"ITGB2",1.1461594048921e-277,0.988537056618028,0.353,0,2.62619504442926e-273
-"OLR1",1.49855436414013e-277,1.26641826166549,0.353,0,3.43363761455429e-273
-"SPI1",1.31945910930945e-268,0.909827633318586,0.345,0.001,3.02327665716074e-264
-"DOK2",1.39934413947024e-266,1.1732477045826,0.345,0.001,3.20631722676817e-262
-"RNASE6",4.29536090355707e-260,1.04612428566844,0.332,0,9.84196043832031e-256
-"CCL4",2.99381052728909e-259,2.75330971124266,0.347,0.002,6.8597180611775e-255
-"C1orf162",3.49977017476956e-257,1.00915032680022,0.341,0.002,8.0190234014495e-253
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-"CCL3",6.94881307253417e-244,2.85703769038597,0.343,0.004,1.59218153930975e-239
-"AREG",1.05111709860452e-231,2.22535266085484,0.651,0.09,2.40842460803255e-227
-"PLEK",5.58105855962501e-224,1.1660155185141,0.306,0.003,1.27878794776688e-219
-"CXCR4",3.64486408615435e-216,1.76529510379718,0.53,0.053,8.35147708060546e-212
-"C5AR1",2.27186874405179e-213,0.931705361112353,0.291,0.002,5.20553285324587e-209
-"MS4A4A",2.4708861810563e-211,0.851371811325581,0.272,0,5.6615415066543e-207
-"IL1B",5.11045508718239e-204,2.01136813835359,0.267,0.001,1.1709585741261e-199
-"LCP1",3.32417490173197e-203,0.793076056192161,0.289,0.004,7.61668195233845e-199
-"CD48",2.73876832234284e-202,0.81599313376797,0.263,0.001,6.27533985698416e-198
-"HCST",7.27908845384959e-202,0.872919345980171,0.274,0.002,1.66785753743056e-197
-"CD163",3.37067949631155e-199,0.894345556575781,0.256,0,7.72323792989864e-195
-"CCR7",3.25173133306844e-196,1.39390714696109,0.269,0.002,7.45069200345972e-192
-"UCP2",2.74409866023385e-193,0.841170659270686,0.284,0.005,6.28755326019382e-189
-"CD37",5.7966571041786e-190,0.773857170527433,0.287,0.006,1.32818804228044e-185
-"VAMP8",6.19240963941357e-190,1.12187059150004,0.504,0.059,1.41886682067883e-185
-"SRGN",2.44238271844211e-188,2.08510732857579,0.95,0.452,5.59623152276641e-184
-"EVI2A",1.61876206563652e-187,0.838331282086886,0.265,0.003,3.70906952099296e-183
-"FAM26F",1.04428581417604e-182,0.98431769422513,0.312,0.012,2.39277208602157e-178
-"CYBA",1.59841720440562e-182,1.75638571706879,0.784,0.251,3.66245334045459e-178
-"EREG",2.98004188606301e-182,1.6903266533144,0.3,0.01,6.82816997353618e-178
-"GPSM3",6.90774153938218e-170,0.886860054296885,0.377,0.029,1.58277081891864e-165
-"LSP1",1.51833941573244e-168,0.768556389852859,0.282,0.01,3.47897110326773e-164
-"CAPG",9.92371922741866e-159,0.991031888600718,0.414,0.045,2.27382178657844e-154
-"C15orf48",4.08250409297453e-158,1.78439173414569,0.384,0.036,9.35424162823255e-154
-"RNASET2",1.64341327379079e-155,1.154217098011,0.478,0.07,3.76555283423683e-151
-"CD68",1.75887191274386e-154,1.39322435538592,0.483,0.074,4.03010321367e-150
-"SMAP2",1.17336543879909e-147,0.82553749185222,0.356,0.031,2.68853222992035e-143
-"CTSS",7.25689012794448e-146,1.17311519799358,0.463,0.071,1.66277123501592e-141
-"ARHGDIB",1.92682431741314e-145,1.09684987836342,0.513,0.089,4.41493255848872e-141
-"DUSP2",3.18731670513375e-144,1.46123386758676,0.364,0.036,7.30309876647296e-140
-"RGS2",2.23148757308181e-142,1.80294810307203,0.569,0.115,5.11300747620234e-138
-"CTSZ",2.07020030579475e-141,1.74071836407592,0.504,0.097,4.74344996066751e-137
-"CXCL16",5.03787107807647e-132,0.946756886529456,0.416,0.059,1.15432740011966e-127
-"GNA15",3.75501022189974e-131,0.702306283862705,0.274,0.018,8.60385492143888e-127
-"CD83",4.79100668765071e-131,1.37389022428095,0.425,0.064,1.09776336234141e-126
-"IL1R2",7.93711773939928e-128,1.0967188986897,0.28,0.02,1.81863178762856e-123
-"FAM49B",9.60404783841779e-128,0.871359397945319,0.412,0.06,2.20057548121667e-123
-"FGL2",5.71838598584395e-124,0.871828340345889,0.3,0.026,1.31025378093642e-119
-"S100A9",3.13571790826049e-120,1.61833294225216,0.265,0.019,7.18487044319725e-116
-"ACSL1",4.93406839318815e-117,0.796053705210022,0.256,0.018,1.1305430909312e-112
-"MAFB",1.12586620867578e-115,1.05412403536967,0.381,0.055,2.57969724393883e-111
-"HLA-DMB",1.12072818023427e-108,0.722370584103276,0.291,0.031,2.56792447937079e-104
-"ARL4C",2.81893725914953e-108,1.0143326149034,0.373,0.059,6.45903094188931e-104
-"HSPA6",1.14054283073244e-106,1.15275566344352,0.504,0.109,2.61332578805723e-102
-"KYNU",1.26660002950391e-106,0.713948224091152,0.254,0.021,2.90216064760231e-102
-"FAM49A",5.65522310331012e-106,0.716339549260789,0.278,0.028,1.29578126966145e-101
-"CTSD",2.11279658977043e-105,1.54200044240034,0.586,0.18,4.84105082614099e-101
-"BASP1",8.21435169320772e-101,1.31492935066204,0.502,0.125,1.88215440346469e-96
-"HCLS1",6.86036094885182e-100,0.693423717124109,0.284,0.033,1.57191450421042e-95
-"TAOK3",1.49125023227456e-99,0.835956806845044,0.369,0.062,3.41690165721069e-95
-"SERPINB9",2.10021129822808e-99,1.0336410930612,0.416,0.085,4.81221414762999e-95
-"GPX1",1.36908692728007e-87,1.57066136016659,0.778,0.509,3.13698887647682e-83
-"NPC2",4.87287673010902e-85,1.38604130537907,0.81,0.553,1.11652224516988e-80
-"OGFRL1",2.50645197998204e-84,0.908840547367093,0.347,0.067,5.74303342173284e-80
-"CHCHD10",3.55705420081761e-78,0.789974863891858,0.547,0.178,8.15027829033339e-74
-"LIPA",1.65660672753563e-75,0.802204376201174,0.306,0.057,3.79578299480238e-71
-"HLA-DRA",2.97946906774637e-75,1.96948711714976,0.629,0.333,6.82685747492726e-71
-"CD74",2.0853115307839e-72,1.57906593417606,0.739,0.426,4.77807431048514e-68
-"HLA-DPA1",2.20107974157758e-72,1.59188521706448,0.573,0.256,5.0433340118767e-68
-"HLA-DPB1",5.95441046268805e-71,1.77198163931118,0.578,0.276,1.36433406931571e-66
-"ASAH1",1.16672512614601e-70,0.95416761020459,0.506,0.175,2.67331728153835e-66
-"RNF130",1.45661389159247e-70,0.705981218201062,0.373,0.091,3.33753940980582e-66
-"CTSH",4.00211523564678e-70,0.757150125261596,0.373,0.094,9.17004663943747e-66
-"RGS10",4.80293309429447e-70,0.845723415626544,0.448,0.136,1.10049605989569e-65
-"GRN",7.46642270532399e-70,1.02543771332222,0.483,0.17,1.71078143447088e-65
-"HSPH1",1.92860140985531e-69,1.06229681579665,0.791,0.495,4.41900441040147e-65
-"HSPE1",6.7176228949885e-69,1.13790225564564,0.851,0.713,1.53920893392872e-64
-"HSP90AA1",1.00179768682725e-67,1.13458636214331,0.946,0.932,2.29541903982728e-63
-"HLA-DMA",8.11669589475996e-67,0.903025993696264,0.431,0.13,1.85977853036635e-62
-"COTL1",1.63049337260666e-64,1.15032196284262,0.562,0.259,3.73594946465364e-60
-"CTSB",1.27348716683292e-63,1.11281706021161,0.666,0.369,2.91794114536427e-59
-"TSC22D3",3.68168689585104e-63,1.29958666363122,0.552,0.205,8.43584918446348e-59
-"ZFAND2A",5.37082003414146e-62,1.59370876815024,0.466,0.165,1.23061599442283e-57
-"DNAJB1",8.41410861083501e-61,1.19630952523129,0.733,0.408,1.92792470600063e-56
-"HLA-DQA1",3.01146824160245e-59,0.922216339250932,0.364,0.102,6.90017718198369e-55
-"ANXA1",2.6183876354665e-57,1.37103977764667,0.772,0.465,5.99951158914439e-53
-"HLA-DQB1",7.03448705530196e-57,1.05831053467003,0.472,0.181,1.61181201898134e-52
-"IER5",4.04884814680631e-56,1.30845235733594,0.45,0.167,9.27712575877729e-52
-"SAT1",2.95240402386202e-55,0.740812298637329,0.966,0.942,6.76484333987504e-51
-"TYMP",3.38482130372201e-53,0.752104476481369,0.433,0.155,7.75564105321824e-49
-"FABP5",1.61710589293475e-49,1.06974369850706,0.347,0.107,3.70527473248139e-45
-"ID2",8.66109205272158e-46,1.1438350975173,0.567,0.288,1.98451602204009e-41
-"ARPC3",3.99541004608801e-45,0.702794431350082,0.696,0.471,9.15468303860145e-41
-"REL",1.22867605845192e-43,0.850600412673426,0.562,0.297,2.81526545273088e-39
-"KLF6",1.39935094839126e-41,0.853273199202862,0.754,0.499,3.20633282804891e-37
-"HSPD1",3.53587527571534e-41,0.794665052751431,0.828,0.689,8.10175101924655e-37
-"CACYBP",2.32635174059762e-40,0.850924794635431,0.547,0.277,5.33036974323133e-36
-"DNAJB6",1.23025074928442e-38,0.809244282110905,0.752,0.593,2.8188735418354e-34
-"DNAJA4",1.54781456106669e-38,0.801493018573203,0.371,0.143,3.54650750377211e-34
-"EZR",4.97723438590937e-35,0.713203807498668,0.463,0.219,1.14043371484341e-30
-"TXNIP",2.15414919744848e-33,0.827001232553294,0.453,0.219,4.93580205611371e-29
-"NINJ1",8.63441869809079e-33,0.777750304459285,0.515,0.284,1.97840435629354e-28
-"HLA-DRB1",2.56680132306094e-29,0.9875645566641,0.575,0.372,5.88131187152953e-25
-"KRT17",5.3148211380731e-08,0.748950362524677,0.427,0.309,0.00121778496736669
+"RGS1",0,3.15271226740144,0.745,0.007,0
+"C1QA",0,3.0407364430771,0.602,0.001,0
+"C1QB",0,2.95093000958509,0.567,0.005,0
+"TYROBP",0,2.8390570332063,0.723,0.003,0
+"C1QC",0,2.39565804200875,0.53,0,0
+"LYZ",0,2.28930977214812,0.539,0.002,0
+"FCER1G",0,2.26307402939843,0.665,0.028,0
+"GPR183",0,2.15304914606611,0.561,0.004,0
+"LAPTM5",0,1.89439202586894,0.688,0.012,0
+"BCL2A1",0,1.84851436209113,0.444,0.005,0
+"ALOX5AP",0,1.83923048673943,0.565,0.005,0
+"AIF1",0,1.76577445261958,0.528,0.001,0
+"SAMSN1",0,1.69340372539675,0.556,0.006,0
+"MS4A6A",0,1.68550693207464,0.498,0.001,0
+"FCGR2A",0,1.60003239494476,0.457,0.006,0
+"MS4A7",0,1.49248198420201,0.485,0,0
+"LST1",0,1.42060845282261,0.483,0.002,0
+"OLR1",0,1.33630293226257,0.392,0,0
+"DOK2",0,1.26462364627682,0.374,0.001,0
+"VSIG4",0,1.22587077458666,0.403,0,0
+"EVI2B",0,1.18194074508324,0.439,0.002,0
+"CD53",0,1.11387083397745,0.42,0.006,0
+"RNASE6",0,1.07956763289294,0.381,0.001,0
+"ITGB2",0,1.00547860306432,0.392,0,0
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+"PTPRC",1.15332055272361e-306,1.12769969028028,0.381,0.002,2.6814702850824e-302
+"C1orf162",3.24102758980405e-299,1.05099639455811,0.377,0.002,7.53538914629441e-295
+"PLEK",8.46430610415529e-277,1.23468308940113,0.348,0.002,1.96795116921611e-272
+"CCL3",9.12590782683666e-275,3.00845101422871,0.383,0.007,2.12177356973952e-270
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+"CCL4",4.75622542460079e-268,2.84523375607199,0.351,0.004,1.10582241121968e-263
+"CYTIP",8.94810040934232e-258,1.13025980905268,0.338,0.004,2.08043334517209e-253
+"C5AR1",1.31328928945589e-252,1.00188366080481,0.333,0.004,3.05339759798494e-248
+"CD37",2.33160982767203e-247,0.854886596021359,0.338,0.005,5.42099284933746e-243
+"MS4A4A",3.96996827380675e-246,0.899543935025453,0.297,0,9.23017623660069e-242
+"IL1B",2.78468120708551e-245,2.16979121650695,0.307,0.002,6.47438380647382e-241
+"LCP1",1.58587741925227e-243,0.794699563018129,0.327,0.004,3.68716499976153e-239
+"AREG",8.19388027776377e-236,2.2018835489592,0.66,0.097,1.90507716458008e-231
+"CD163",1.04553489345486e-232,0.934806833622465,0.286,0.001,2.43086862728254e-228
+"UCP2",2.8361715817244e-221,0.839683861298311,0.318,0.007,6.59409892750922e-217
+"CD48",6.99464318269275e-218,0.809113864119857,0.268,0.001,1.62625453997606e-213
+"CXCR4",5.75897641554028e-209,1.74327251261904,0.524,0.058,1.33896201661312e-204
+"EVI2A",4.25040936906197e-208,0.83261966284701,0.281,0.004,9.88220178306908e-204
+"ITGAX",6.36318923387646e-208,0.811978950108375,0.264,0.002,1.47944149687628e-203
+"CCR7",1.09417965591445e-202,1.39024211282688,0.273,0.004,2.54396770000109e-198
+"FAM26F",2.67686339347655e-201,0.985085658987306,0.338,0.014,6.22370738983299e-197
+"EREG",2.0428010026761e-200,1.71767151306068,0.318,0.011,4.74951233122193e-196
+"VAMP8",7.8860318135981e-192,1.13322338047461,0.537,0.073,1.83350239666156e-187
+"GPSM3",1.53519008771071e-191,0.938251849900614,0.418,0.035,3.5693169539274e-187
+"CCL3L3",9.84010695363195e-191,1.91276136524528,0.275,0.006,2.28782486671943e-186
+"CYBA",5.15417410881055e-190,1.75716148587906,0.807,0.28,1.19834548029845e-185
+"LSP1",4.85802553266083e-187,0.788659970455497,0.327,0.015,1.12949093634364e-182
+"ARRB2",6.83679306062504e-185,0.711949922177363,0.307,0.012,1.58955438659532e-180
+"SRGN",6.12324216920336e-184,2.10697508909011,0.942,0.483,1.42365380433978e-179
+"CAPG",5.40536264641506e-168,1.03909255383824,0.461,0.06,1.2567468152915e-163
+"CD68",1.35948750350382e-165,1.41072015380046,0.532,0.091,3.16080844564637e-161
+"RNASET2",3.36227710819995e-162,1.18790386936211,0.515,0.085,7.81729427656489e-158
+"CTSS",1.55996176680343e-157,1.22692621762623,0.506,0.085,3.62691110781797e-153
+"SMAP2",1.59474422438205e-155,0.801693116420637,0.377,0.037,3.70778032168828e-151
+"C15orf48",3.97863988703568e-153,1.77263328928997,0.379,0.04,9.25033773735796e-149
+"CTSZ",1.1754359763173e-147,1.78664249125959,0.543,0.117,2.73288864493773e-143
+"ACSL1",8.90599664981642e-144,0.883063849837258,0.312,0.024,2.07064422108232e-139
+"ARHGDIB",7.84066706336103e-139,1.1114879185057,0.526,0.105,1.82295509223144e-134
+"RGS2",1.57568920167575e-134,1.69813945273371,0.595,0.14,3.66347739389612e-130
+"CD83",2.57354669603479e-134,1.45877460120715,0.47,0.083,5.98349606828089e-130
+"CXCL16",2.63816007075847e-131,0.976370327367783,0.437,0.071,6.13372216451344e-127
+"IL1R2",1.93931130065328e-129,1.09448353442885,0.29,0.024,4.50889877401888e-125
+"FAM49B",1.58539778596067e-127,0.878732817954401,0.429,0.07,3.68604985235855e-123
+"RNF144B",6.89169600520563e-126,0.744642627166922,0.31,0.03,1.60231932121031e-121
+"DUSP2",2.12704213089929e-125,1.48962722165251,0.372,0.05,4.94537295434084e-121
+"FGL2",6.8984329761343e-125,0.892678213804374,0.316,0.032,1.60388566695123e-120
+"HSPA6",4.43362008607224e-121,1.16453011186814,0.541,0.115,1.03081667001179e-116
+"KYNU",6.93466998573415e-121,0.712283946674304,0.284,0.025,1.61231077168319e-116
+"ARL4C",1.21941227601424e-118,1.03032986384391,0.407,0.068,2.83513354173311e-114
+"SERPINB9",9.75403797668269e-116,1.10822018207998,0.461,0.095,2.26781382957872e-111
+"S100A9",3.04796679826859e-115,1.6378349948128,0.26,0.021,7.08652280597448e-111
+"HCLS1",2.17197354673284e-114,0.708699069417833,0.316,0.037,5.04983849615386e-110
+"BASP1",1.88894077341986e-110,1.39738649987668,0.53,0.136,4.39178729820117e-106
+"HLA-DMB",9.49582048674253e-109,0.706021352837301,0.303,0.036,2.20777826316764e-104
+"MAFB",3.06934643387122e-105,0.998481547873155,0.409,0.076,7.13623045875058e-101
+"OGFRL1",1.05112764290857e-101,0.948517524881195,0.39,0.074,2.44387176976242e-97
+"CTSD",4.05491006773026e-101,1.53472367613653,0.606,0.208,9.42766590747285e-97
+"TAOK3",6.24455300879636e-97,0.803801330217374,0.4,0.081,1.45185857454515e-92
+"PDE4DIP",3.98113213568388e-85,0.731484785914728,0.333,0.06,9.25613221546503e-81
+"GPX1",4.11549624356742e-85,1.55112028578286,0.775,0.576,9.56852876629425e-81
+"NPC2",2.00791407656614e-83,1.36559851319455,0.803,0.6,4.66840022801626e-79
+"RGS10",1.17083663139429e-80,0.891536821376032,0.485,0.148,2.72219516799173e-76
+"LIPA",4.33410249520298e-80,0.836639761636526,0.342,0.07,1.00767883013469e-75
+"RNF130",1.33124268268682e-79,0.734901414108624,0.403,0.099,3.09513923724686e-75
+"HLA-DRA",2.06037012799471e-79,1.99531283063559,0.645,0.349,4.79036054758771e-75
+"HLA-DPA1",1.2060825301606e-78,1.62011735319805,0.606,0.277,2.8041418826234e-74
+"ASAH1",3.55123041854186e-77,0.939175277882291,0.55,0.197,8.25661072310983e-73
+"GRN",2.07420947156122e-76,1.06170230978128,0.522,0.195,4.82253702137984e-72
+"HSPE1",4.58480545645448e-75,1.21081648284507,0.859,0.744,1.06596726862567e-70
+"HSP90AA1",7.70330087042844e-75,1.21616081343376,0.95,0.943,1.79101745237461e-70
+"HLA-DPB1",1.89085603562323e-73,1.81401937713685,0.61,0.316,4.396240282824e-69
+"HSPH1",2.98277372193912e-73,1.1385114846465,0.792,0.526,6.93494890350846e-69
+"CD74",1.7828256111026e-71,1.56166371515851,0.738,0.453,4.14506954581354e-67
+"CHCHD10",7.17871976703353e-68,0.743828123558737,0.543,0.203,1.6690523458353e-63
+"CTSH",3.04786358083118e-67,0.724122677280842,0.409,0.119,7.08628282543249e-63
+"HLA-DQA1",1.05265493731785e-66,0.935606570478245,0.405,0.115,2.44742272926399e-62
+"CTSB",2.65771307350493e-65,1.16878607512925,0.682,0.408,6.17918289589897e-61
+"MXD1",1.5946786619377e-64,0.710289048282117,0.316,0.074,3.70762788900514e-60
+"ZFAND2A",1.67964470590727e-64,1.6494921563596,0.489,0.185,3.9051739412344e-60
+"COTL1",2.00780851445753e-64,1.16261664347945,0.587,0.293,4.66815479611377e-60
+"RIPK2",3.52639793061669e-64,0.704765904049254,0.361,0.096,8.19887518868381e-60
+"IER5",1.18710459948977e-59,1.30009996006691,0.509,0.208,2.76001819381371e-55
+"HLA-DQB1",5.88893702987379e-59,1.09579724939656,0.502,0.205,1.36917785944566e-54
+"ANXA1",1.75733274368925e-58,1.4428194408429,0.79,0.505,4.08579862907749e-54
+"HLA-DMA",5.76664198085773e-58,0.886059073076106,0.437,0.156,1.34074426054942e-53
+"SAT1",1.01590339070225e-57,0.770828982999314,0.959,0.952,2.36197538338274e-53
+"DNAJB1",2.3412521625804e-56,1.12819071447852,0.74,0.461,5.44341127799943e-52
+"TYMP",7.90878251502591e-56,0.806481899217291,0.463,0.178,1.83879193474352e-51
+"TSC22D3",5.64825550751786e-53,1.21822127895999,0.569,0.241,1.3132194054979e-48
+"ARPC3",4.12619726432702e-51,0.735411425483727,0.721,0.5,9.59340863956031e-47
+"FABP5",2.22812914237501e-50,1.10483057695144,0.364,0.118,5.18040025602191e-46
+"CACYBP",3.92890486658072e-49,0.878485406075925,0.591,0.288,9.13470381480016e-45
+"HSPD1",7.73887936896764e-46,0.869587065215232,0.818,0.714,1.79928945328498e-41
+"REL",4.88402190372331e-45,0.821657977945736,0.604,0.35,1.13553509261567e-40
+"DNAJB6",1.46378914897207e-44,0.849190451352474,0.79,0.638,3.40330977136006e-40
+"ID2",1.79605426742959e-43,1.122182169735,0.597,0.335,4.17582617177381e-39
+"CMTM6",4.0481238133995e-43,0.693341680755024,0.535,0.276,9.41188786615385e-39
+"DNAJA4",1.8364103464819e-42,0.829672394207371,0.407,0.163,4.26965405557042e-38
+"KLF6",1.31962932385925e-40,0.797065722851252,0.781,0.554,3.06813817797275e-36
+"NINJ1",2.49933700743028e-37,0.816016119069385,0.556,0.317,5.81095854227539e-33
+"HLA-DRB1",1.56799878838072e-34,1.00903821611476,0.621,0.394,3.64559718298518e-30
+"EZR",1.97494609778902e-34,0.719720207128509,0.491,0.253,4.59174967735948e-30
+"TXNIP",2.83918783850078e-31,0.753379508272443,0.498,0.266,6.60111172451431e-27
+"HLA-DRB5",1.9786037858996e-26,0.701243804867745,0.498,0.293,4.60025380221657e-22
+"PSAP",9.4874939991351e-24,0.718832722458439,0.686,0.59,2.20584235479891e-19
+"BAG3",7.96586803841414e-13,0.702499696980814,0.556,0.451,1.85206431893129e-08
+"PLAUR",1.15273408207863e-12,0.707640038564076,0.584,0.504,2.68010674083281e-08
diff --git a/genesets/genes.deg.NE.csv b/genesets/genes.deg.NE.csv
index d24b5fff27da53b5e039ca006dc60ba4fc462e0c..9daf91bc6dd81ed70bd3a8259c87c45ce0e06fe0 100644
--- a/genesets/genes.deg.NE.csv
+++ b/genesets/genes.deg.NE.csv
@@ -1,545 +1,562 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"CHGA",0,3.13179353656507,0.48,0,0
-"GRP",0,2.86671760121558,0.44,0,0
-"CALCA",0,2.82079061746645,0.84,0.001,0
-"SCG2",0,2.10787088966068,0.44,0,0
-"TPH1",0,1.97658779180308,0.4,0,0
-"ASCL1",0,1.93208749617821,0.28,0,0
-"SCG5",0,1.42686444398741,0.28,0,0
-"MS4A8",0,1.05817903461271,0.32,0.001,0
-"MIAT",0,1.02386259221154,0.36,0.001,0
-"MAOB",0,1.01083628578688,0.32,0.001,0
-"PHGR1",0,0.958065540287562,0.28,0.001,0
-"ST18",0,0.921476647360348,0.4,0,0
-"FGF14",0,0.780893137250009,0.28,0.001,0
-"ZACN",0,0.76203736683408,0.2,0,0
-"DDC",0,0.728954870589537,0.24,0,0
-"SCG3",0,0.637779762741102,0.2,0,0
-"KCNJ6",0,0.614981806822988,0.2,0,0
-"ELAVL4",0,0.564860543990522,0.16,0,0
-"TAAR1",0,0.398223758803844,0.12,0,0
-"INSM1",0,0.369681102611242,0.12,0,0
-"PPFIA2",0,0.339672136729334,0.12,0,0
-"CRMP1",0,0.280169863972218,0.12,0,0
-"PCSK2",0,0.277021578530649,0.08,0,0
-"LINGO2",0,0.272935518782618,0.08,0,0
-"SLC18A1",0,0.254852422817072,0.08,0,0
-"CDK5R2",0,0.241449253154293,0.08,0,0
-"C11orf16",0,0.177192494007059,0.08,0,0
-"SLC35D3",1.29593134918278e-288,0.403110039771405,0.08,0,2.96936750038251e-284
-"LINC01497",1.29593134918278e-288,0.254728512634844,0.08,0,2.96936750038251e-284
-"TMEM176A",4.66670054074994e-265,1.40840922804289,0.32,0.002,1.06928109490203e-260
-"NELL2",2.28100549214907e-243,0.490911090609139,0.12,0,5.22646788416117e-239
-"TMEM176B",5.22893757795095e-242,1.16890529354075,0.36,0.003,1.1981064672359e-237
-"KLK12",1.34559277553295e-229,1.31573008978095,0.28,0.002,3.08315672657865e-225
-"NPPA",3.47493283390663e-217,0.148034802400583,0.04,0,7.96211360233027e-213
-"VIP",3.47493283390663e-217,0.134385037515179,0.04,0,7.96211360233027e-213
-"KCNB2",3.47493283390663e-217,0.108773243557467,0.04,0,7.96211360233027e-213
-"KCNMB2",3.47493283390663e-217,0.107543767868315,0.04,0,7.96211360233027e-213
-"RP11-1C8.7",3.47493283390663e-217,0.107543767868315,0.04,0,7.96211360233027e-213
-"PKD2L1",3.47493283390663e-217,0.107543767868315,0.04,0,7.96211360233027e-213
-"PIANP",3.47493283390663e-217,0.107543767868315,0.04,0,7.96211360233027e-213
-"GPR55",3.47493283390663e-217,0.0952647469427283,0.04,0,7.96211360233027e-213
-"NOL4",3.47493283390663e-217,0.0772584831371316,0.04,0,7.96211360233027e-213
-"NR0B2",3.47493283390663e-217,0.0484649657216059,0.04,0,7.96211360233027e-213
-"NAT8L",3.47493283390663e-217,0.0484649657216059,0.04,0,7.96211360233027e-213
-"CCDC187",3.47493283390663e-217,0.0484649657216059,0.04,0,7.96211360233027e-213
-"STMN2",8.05381518720924e-217,0.406094561701655,0.08,0,1.84537067384525e-212
-"CELF3",8.05381518720924e-217,0.231429695277094,0.08,0,1.84537067384525e-212
-"PTPRN",1.67702464019563e-216,0.447854676525282,0.12,0,3.84256655808025e-212
-"MIR7-3HG",1.76884817021447e-216,0.55054220191113,0.12,0,4.05296181241241e-212
-"SRRM4",1.76884817021447e-216,0.476564959993523,0.12,0,4.05296181241241e-212
-"HEPACAM2",1.77888819517444e-192,0.578500236507383,0.2,0.001,4.07596652160319e-188
-"NRXN1",4.77772437728651e-192,0.393958218538516,0.16,0.001,1.09471998656766e-187
-"AOC1",4.49086934486951e-182,0.581851059751671,0.16,0.001,1.02899289298995e-177
-"NELL1",5.05176670579498e-182,0.36353952338759,0.16,0.001,1.1575113052988e-177
-"SYT4",1.01601603573648e-173,0.289367779631863,0.08,0,2.327997542683e-169
-"ST8SIA5",6.22888430507627e-145,0.202428897340601,0.08,0,1.42722426082213e-140
-"SCGN",7.04538685211783e-144,0.902943093753577,0.24,0.002,1.61430948942576e-139
-"SYT1",2.95781942147209e-142,1.47650545879426,0.4,0.006,6.77725164041901e-138
-"LY6H",1.60533804442495e-138,0.694618021090979,0.16,0.001,3.67831106119089e-134
-"DOK6",2.2498360665704e-124,0.201604706016762,0.08,0,5.15504937933277e-120
-"EPHB1",2.30181948446259e-124,0.0935146359201502,0.08,0,5.27415898474912e-120
-"ANK2",2.3550018287432e-124,0.176342471722702,0.08,0,5.3960156901993e-120
-"NKAIN2",2.3550018287432e-124,0.121562924542309,0.08,0,5.3960156901993e-120
-"SLC38A11",1.04389798553508e-122,0.891058879469837,0.28,0.003,2.39188345425652e-118
-"LINC00261",4.46885162871072e-122,0.421615757243385,0.12,0.001,1.02394797368649e-117
-"SYT13",2.18470962375624e-117,0.467295387738912,0.2,0.002,5.00582516091268e-113
-"INA",5.35632822293128e-115,0.337762385669982,0.12,0.001,1.22729548572024e-110
-"RGS7",2.12268186915255e-109,0.161531409118034,0.04,0,4.86370096678923e-105
-"FLJ46066",2.12268186915255e-109,0.161495204341149,0.04,0,4.86370096678923e-105
-"AC010746.3",2.12268186915255e-109,0.161472830202249,0.04,0,4.86370096678923e-105
-"KIAA1644",2.12268186915255e-109,0.161426049518999,0.04,0,4.86370096678923e-105
-"RP11-1250I15.3",2.12268186915255e-109,0.147996166169587,0.04,0,4.86370096678923e-105
-"RBFOX1",2.12268186915255e-109,0.147917269308623,0.04,0,4.86370096678923e-105
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diff --git a/genesets/genes.deg.OE1.csv b/genesets/genes.deg.OE1.csv
index 734d213e3754b96bb3f4fafef9bac0834ffc662b..078a7115998a3484d02e14fdcf403bd9a9404873 100644
--- a/genesets/genes.deg.OE1.csv
+++ b/genesets/genes.deg.OE1.csv
@@ -1,106 +1,95 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"SCGB3A1",0,4.1124947280724,0.888,0.061,0
-"LCN2",0,3.81706111873414,0.999,0.37,0
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-"PSCA",0,2.71909390800949,0.954,0.112,0
-"OLFM4",0,2.48484392642809,0.686,0.103,0
-"SPINK1",0,2.36247840124069,0.808,0.071,0
-"RARRES1",0,2.14620613418282,0.943,0.246,0
-"CD74",0,2.13354701163472,0.941,0.233,0
-"S100P",0,2.09005852979383,0.973,0.293,0
-"FCGBP",0,1.98786772530701,0.619,0.01,0
-"HLA-DRA",0,1.90285407007538,0.804,0.05,0
-"AGR2",0,1.76840227566895,0.927,0.247,0
-"C15orf48",0,1.69694918558957,0.713,0.102,0
-"WFDC2",0,1.65661544118042,0.994,0.665,0
-"FAM3D",0,1.60652820795041,0.736,0.07,0
-"DUOXA2",0,1.59060551781152,0.639,0.066,0
-"PI3",0,1.46792878534917,0.486,0.013,0
-"BPIFB1",0,1.46619409289496,0.378,0.002,0
-"TFF1",0,1.28339242059369,0.562,0.052,0
-"VSIG2",0,1.27490131626248,0.758,0.112,0
-"HLA-DRB1",0,1.26873763152403,0.633,0.04,0
-"ADGRF1",0,1.26665399539301,0.726,0.114,0
-"CXCL17",0,1.26404650776078,0.93,0.328,0
-"AGR3",0,1.20607827135485,0.513,0.037,0
-"B2M",0,1.18843900076809,1,0.99,0
-"CEACAM6",0,1.14334804822342,0.461,0.044,0
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-"CP",0,1.11541285367159,0.56,0.031,0
-"TMEM45B",0,1.04966833663736,0.619,0.076,0
-"HLA-DRB5",0,0.989580365657235,0.458,0.013,0
-"SCCPDH",0,0.986741729983921,0.609,0.131,0
-"PDZK1IP1",0,0.963757824407082,0.474,0.05,0
-"CEACAM5",0,0.920433223212185,0.371,0.025,0
-"LINC01207",0,0.90962658383503,0.536,0.088,0
-"LYZ",0,0.856639026439207,0.33,0.003,0
-"MUC1",0,0.798075162238608,0.481,0.074,0
-"FA2H",0,0.786367576803822,0.51,0.079,0
-"ENTPD5",0,0.750256474967235,0.361,0.026,0
-"HLA-DMA",0,0.737291127517338,0.417,0.049,0
-"TMSB4X",2.85004514691397e-303,1.21301246766425,0.999,0.914,6.53030844512398e-299
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-"ASS1",8.70357960002451e-283,0.950165181784436,0.725,0.192,1.99425119375362e-278
-"SLPI",3.62749252902871e-275,1.1080723290973,0.99,0.569,8.31167363176349e-271
-"HPGD",4.83636011570897e-271,2.01303685077178,0.62,0.161,1.1081551933124e-266
-"TSPAN3",6.58427029321693e-264,1.14745488929218,0.784,0.281,1.50865385228479e-259
-"S100A6",2.61339169703315e-263,1.19205969173905,0.999,0.978,5.98806439541206e-259
-"MUC4",7.99360535504149e-262,0.735245284707279,0.493,0.093,1.83157479500066e-257
-"NEAT1",8.57840232074648e-262,1.38385691225363,1,0.93,1.96556932375264e-257
-"GDF15",3.39494316551975e-259,1.58433424211008,0.755,0.229,7.77883327515539e-255
-"FTH1",5.42454121558998e-255,1.37240176194085,1,0.999,1.24292512872813e-250
-"ADIRF",2.40256618096882e-253,1.22458974796668,0.831,0.295,5.50499989045385e-249
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-"FAM102A",2.73591388860211e-248,0.774089585835047,0.53,0.113,6.26879949295402e-244
-"HLA-DPB1",1.9565627698906e-241,0.705804476115092,0.384,0.061,4.48307227465033e-237
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-"FOXO3",4.9777139293057e-238,0.917850454720227,0.642,0.179,1.14054359262181e-233
-"C19orf33",1.04955664854898e-235,0.71620231452715,0.491,0.102,2.40484914882028e-231
-"SERPINB3",6.07146579480166e-225,0.908931099748512,0.308,0.042,1.3911549575629e-220
-"RHOV",6.638788919175e-225,0.947370642300071,0.486,0.105,1.52114570505057e-220
-"SERF2",5.64257000088186e-222,0.700482471319848,0.999,0.934,1.29288206430206e-217
-"ERBB3",3.14314230532611e-220,0.706737417369951,0.479,0.102,7.20188196419371e-216
-"TRIM31",4.30732811834001e-216,0.764452668892545,0.317,0.046,9.86938091755247e-212
-"PPDPF",2.59797036843151e-214,0.844984033096486,0.979,0.786,5.95272950518712e-210
-"DUSP5",4.1452020737438e-213,1.08167600702689,0.872,0.396,9.49790151156918e-209
-"GLUL",6.53434058143594e-197,1.14462713321015,0.923,0.562,1.49721345742442e-192
-"TSPAN13",3.04094539840879e-196,0.787508742430631,0.691,0.228,6.96771819137406e-192
-"CLDN3",2.35646433073632e-191,0.931287503311564,0.577,0.153,5.39936672101614e-187
-"MAL2",4.22614206427891e-186,0.85099707703385,0.765,0.3,9.68335931188226e-182
-"RNF39",3.95500357411641e-185,0.795759871497253,0.52,0.135,9.06209968937294e-181
-"ELF3",5.76733632600108e-185,0.879824913605809,0.96,0.57,1.32146977237663e-180
-"CYP3A5",1.31680450488315e-183,0.819105968218579,0.749,0.285,3.01719416203877e-179
-"CST3",7.41577051226538e-183,0.784534090401724,0.971,0.721,1.69917549747537e-178
-"TMPRSS2",2.32183049776624e-182,0.695132926136489,0.55,0.148,5.32001021953179e-178
-"REEP3",1.05955547639246e-181,0.8963654713009,0.759,0.31,2.42775946305804e-177
-"SERPINB1",8.62012797588338e-178,0.739651167655734,0.756,0.279,1.97512992311416e-173
-"CDC42EP5",1.09066270833155e-174,0.760272939796342,0.699,0.256,2.49903546360008e-170
-"SERINC2",3.52358843762388e-173,0.843859517336698,0.742,0.309,8.07359818712759e-169
-"CD24",1.45790986975575e-169,1.13759656198858,0.711,0.287,3.34050888457134e-165
-"WASL",1.2448117716908e-168,0.721272146846374,0.602,0.193,2.85223721247514e-164
-"CYP1B1",2.55032101540371e-165,1.01799685051191,0.658,0.237,5.84355054259451e-161
-"CXCL6",9.71589756229758e-164,1.0474513819191,0.54,0.156,2.22620360844924e-159
-"KIAA1551",1.65411978512097e-160,0.832374442044217,0.529,0.159,3.79008466364768e-156
-"CYB5A",6.11476749715031e-159,0.746315598891439,0.663,0.244,1.40107667662205e-154
-"TMEM165",8.03828989169426e-159,0.940741448573535,0.848,0.52,1.84181336288391e-154
-"GPX2",6.8284494397683e-157,1.14204682326155,0.681,0.281,1.56460262013411e-152
-"ZG16B",3.30759149917924e-156,1.00206253957429,0.769,0.365,7.57868440206939e-152
-"CRABP2",4.18611077221111e-156,0.799758061051285,0.659,0.234,9.59163561236732e-152
-"SDCBP2",5.82125536901053e-153,0.782997708843492,0.716,0.282,1.33382424270138e-148
-"CD164",1.18736149075203e-149,0.730733469681182,0.834,0.42,2.72060138376012e-145
-"SAA1",2.58139394866653e-148,1.09044802004244,0.384,0.091,5.91474795457962e-144
-"CSTB",3.20767313868183e-145,0.759241892007445,0.937,0.674,7.34974146266168e-141
-"SMAD3",2.91928248290007e-138,0.730550445748154,0.656,0.258,6.68895195306893e-134
-"GPRC5A",1.94604058082355e-135,0.839911215972417,0.845,0.447,4.458962782841e-131
-"MALL",4.59666406159424e-135,0.756805872413288,0.645,0.243,1.05323363643309e-130
-"AGPAT2",1.30675286842938e-133,0.817481153262901,0.533,0.187,2.99416284743225e-129
-"HIST1H2AC",3.00271191554515e-127,0.735755377973835,0.623,0.24,6.8801138120886e-123
-"CD55",2.99842206937818e-123,0.775844878806573,0.809,0.448,6.87028448756622e-119
-"PPP1CB",5.65519952013661e-119,0.74283545790441,0.798,0.43,1.2957758660489e-114
-"ATP1B1",1.47349288145319e-113,0.739571383387986,0.625,0.27,3.3762142392737e-109
-"AZGP1",1.82845047323069e-113,0.733656030181467,0.779,0.377,4.18952856931347e-109
-"MMP7",1.04552095947187e-101,0.993533861407442,0.6,0.244,2.3956021744379e-97
-"HIST1H1C",3.61564777243258e-100,0.700568920341025,0.795,0.437,8.28453374097477e-96
-"SNCG",2.29813618267087e-49,0.839259372413833,0.292,0.116,5.26571943535375e-45
+"SCGB3A1",0,4.14227762863768,0.887,0.076,0
+"LCN2",0,3.74110598395262,0.995,0.411,0
+"PIGR",0,3.08739687062705,0.865,0.03,0
+"PSCA",0,2.59293280086489,0.939,0.13,0
+"OLFM4",0,2.33551859432896,0.654,0.116,0
+"SPINK1",0,2.32246432548486,0.798,0.08,0
+"CD74",0,2.09781092653468,0.941,0.265,0
+"RARRES1",0,2.07011087196216,0.931,0.267,0
+"S100P",0,2.01842671064021,0.979,0.328,0
+"FCGBP",0,1.92381703428596,0.613,0.012,0
+"HLA-DRA",0,1.84518233507332,0.812,0.059,0
+"PI3",0,1.72511945920153,0.535,0.016,0
+"AGR2",0,1.66859602006345,0.93,0.273,0
+"WFDC2",0,1.60422731123709,0.994,0.696,0
+"FAM3D",0,1.59647073508933,0.765,0.081,0
+"C15orf48",0,1.58663622537748,0.72,0.116,0
+"DUOXA2",0,1.54536394211001,0.63,0.072,0
+"TXNIP",0,1.45397636098515,0.834,0.327,0
+"BPIFB1",0,1.44718208337208,0.398,0.002,0
+"HLA-DRB1",0,1.26427359925309,0.663,0.048,0
+"VSIG2",0,1.26152732752903,0.8,0.134,0
+"TFF1",0,1.25705589423506,0.575,0.064,0
+"CXCL17",0,1.22777743186616,0.927,0.356,0
+"ADGRF1",0,1.21853380141488,0.739,0.134,0
+"TMSB4X",0,1.18252612975164,1,0.931,0
+"SLPI",0,1.12226619951529,0.99,0.596,0
+"B2M",0,1.11043930658512,1,0.993,0
+"TSPAN3",0,1.09041027373105,0.83,0.32,0
+"CEACAM6",0,1.08133457981252,0.492,0.052,0
+"AGR3",0,1.07564444223733,0.523,0.041,0
+"SRD5A3",0,1.06939725808826,0.551,0.056,0
+"CP",0,1.03291641211904,0.607,0.035,0
+"TMEM45B",0,1.01147425706208,0.652,0.086,0
+"CEACAM5",0,0.990514785666894,0.43,0.03,0
+"ASS1",0,0.958291000853374,0.77,0.227,0
+"HLA-DRB5",0,0.935648841715902,0.472,0.016,0
+"PDZK1IP1",0,0.915740306023287,0.509,0.058,0
+"SCCPDH",0,0.910971855622186,0.619,0.151,0
+"LINC01207",0,0.847730691406637,0.565,0.104,0
+"LYZ",0,0.795100138097547,0.332,0.003,0
+"MUC1",0,0.782107569971761,0.536,0.088,0
+"C19orf33",0,0.749964315039821,0.606,0.133,0
+"HLA-DMA",0,0.741419230648311,0.48,0.057,0
+"FA2H",0,0.737834637939463,0.541,0.094,0
+"ERBB3",3.36428630563964e-294,0.706092438838021,0.563,0.123,7.82196566061215e-290
+"NEAT1",9.24656669587456e-288,1.32680453019732,1,0.944,2.14982675679083e-283
+"S100A6",4.8283775481163e-287,1.14649315728448,0.996,0.981,1.12259777993704e-282
+"MUC4",1.49283380501009e-285,0.698435574012441,0.534,0.111,3.47083859664845e-281
+"GDF15",1.98910529130254e-283,1.58912550982082,0.785,0.259,4.6246698022784e-279
+"FTH1",4.20209872606161e-283,1.32270957829822,1,1,9.76987953809324e-279
+"ADIRF",1.4402562414185e-272,1.23497051787901,0.852,0.344,3.34859576129802e-268
+"FOXO3",2.27093159003144e-268,0.880541081953685,0.687,0.21,5.27991594682311e-264
+"BIK",1.19377936899398e-267,0.793219621300765,0.585,0.144,2.77553703291101e-263
+"HPGD",7.79197747494012e-264,1.92669451250119,0.611,0.179,1.81163476292358e-259
+"ANKRD36C",1.51011498305301e-262,0.979632706445473,0.667,0.189,3.51101733559826e-258
+"PPDPF",1.56743067470171e-259,0.837017970675501,0.988,0.846,3.64427631868147e-255
+"SERPINB3",3.44219459380704e-257,0.978973837302065,0.334,0.049,8.00310243060136e-253
+"MGST1",4.22886728399971e-252,1.05409862400626,0.836,0.348,9.83211643529933e-248
+"B4GALT4",1.02472300727642e-251,0.73586263550554,0.48,0.104,2.38248099191769e-247
+"RHOV",2.19806777992175e-250,0.96461762628169,0.526,0.126,5.11050758831807e-246
+"RNF39",3.13166984093962e-239,0.794220890570539,0.576,0.15,7.28113238018461e-235
+"DUSP5",7.27073732614613e-225,1.01985456316633,0.884,0.428,1.69044642832898e-220
+"GLUL",2.60082883930321e-224,1.13294109589209,0.941,0.604,6.04692705137996e-220
+"ELF3",1.75962592954452e-213,0.897142217837726,0.966,0.604,4.09113028619101e-209
+"MAL2",7.67795385043164e-211,0.803719903901724,0.809,0.339,1.78512427022536e-206
+"TSPAN13",2.83267615774706e-209,0.748908984676635,0.709,0.26,6.58597206676191e-205
+"CST3",1.66872841510166e-207,0.737732997134328,0.979,0.758,3.87979356511137e-203
+"CLDN3",2.22530795173207e-207,0.861051941238368,0.611,0.177,5.17384098777706e-203
+"ZG16B",1.62877171974192e-204,0.989926023598204,0.838,0.415,3.78689424839996e-200
+"REEP3",4.28316982034694e-202,0.851172314657521,0.782,0.35,9.95836983230664e-198
+"SERINC2",5.22036136496032e-201,0.844085212584235,0.776,0.352,1.21373401735327e-196
+"CYP3A5",3.50639725451782e-199,0.781979693754768,0.765,0.319,8.15237361675392e-195
+"WASL",8.11045231650809e-197,0.710935209327625,0.641,0.222,1.88568016358813e-192
+"CDC42EP5",4.55717812568056e-195,0.729587045199203,0.748,0.298,1.05954391422073e-190
+"KIAA1551",1.46012421484612e-193,0.807053070917877,0.578,0.182,3.39478879951723e-189
+"SDCBP2",2.30323431960629e-183,0.768648256221205,0.763,0.314,5.35501979308463e-179
+"CD24",6.19920049206571e-179,1.10035233783084,0.72,0.318,1.44131411440528e-174
+"CRABP2",1.51640879109876e-177,0.754109723096428,0.699,0.259,3.52565043930462e-173
+"TMEM165",3.67155284160173e-170,0.908736990506982,0.858,0.565,8.53636035672403e-166
+"CYP1B1",9.16860974850453e-169,0.941938373141569,0.668,0.261,2.1317017665273e-164
+"GPX2",2.80362533218768e-163,1.08724105170565,0.693,0.313,6.51842889733635e-159
+"SAA1",2.70518670431658e-162,1.02006112943803,0.409,0.105,6.28955908753605e-158
+"CXCL6",1.41173635203807e-160,0.93947299296586,0.532,0.169,3.28228701848851e-156
+"CSTB",4.90184494649728e-159,0.770635548844781,0.951,0.718,1.13967895006062e-154
+"AGPAT2",9.78936840506016e-153,0.775609328264555,0.573,0.217,2.27602815417649e-148
+"MALL",7.59711655507711e-143,0.693567842841213,0.676,0.277,1.76632959905543e-138
+"GPRC5A",2.58434202086223e-139,0.762407980646115,0.851,0.48,6.00859519850468e-135
+"CD55",2.8150334741031e-139,0.715156268979011,0.854,0.494,6.54495282728971e-135
+"PPP1CB",2.21936467175293e-138,0.706162579442297,0.849,0.481,5.16002286182557e-134
+"TSPAN1",2.67059899500518e-135,0.709538522415159,0.753,0.38,6.20914266338705e-131
+"TFF3",4.44321868683593e-123,1.2137409767212,0.274,0.063,1.03304834468935e-118
+"MMP7",9.04524720421491e-117,0.946556374315693,0.624,0.266,2.10301997497997e-112
+"SNCG",1.92405958863697e-61,0.901111659477719,0.323,0.132,4.47343854358095e-57
+"NUPR1",4.63771165624957e-34,0.696176082262582,0.652,0.493,1.07826796007803e-29
diff --git a/genesets/genes.deg.OE2.csv b/genesets/genes.deg.OE2.csv
index 64e8405c022500e8de785ba48b0e9b40ad550608..3443fcd0cfd1198e4cbb6c58aa0fd54b375e4537 100644
--- a/genesets/genes.deg.OE2.csv
+++ b/genesets/genes.deg.OE2.csv
@@ -1,62 +1,53 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"KRT13",0,2.07270139814174,0.88,0.198,0
-"S100P",0,1.95174910781215,0.941,0.244,0
-"GDF15",0,1.65668152236332,0.729,0.191,0
-"CSTB",0,1.62806563976663,0.963,0.651,0
-"APOBEC3A",0,1.60211151200491,0.361,0.017,0
-"DUOXA2",0,1.39253882118528,0.457,0.041,0
-"CXCL17",0,1.37452377394215,0.863,0.288,0
-"LYPD3",0,1.35947955086603,0.678,0.122,0
-"OLFM4",0,1.34437219160446,0.483,0.079,0
-"GPX2",0,1.34432929350863,0.832,0.233,0
-"SERPINB1",0,1.23250049085033,0.777,0.24,0
-"AKR1C1",0,1.22950880937823,0.371,0.037,0
-"IL1RN",0,1.11811214080471,0.619,0.12,0
-"AKR1C2",0,1.11282043631758,0.365,0.024,0
-"IGFBP3",0,1.08932479600833,0.601,0.19,0
-"SDCBP2",0,1.06460433542149,0.836,0.234,0
-"HPGD",0,1.05771140779012,0.473,0.141,0
-"MUC4",0,1.00835912059137,0.608,0.049,0
-"ADIRF",0,0.992780966531525,0.691,0.268,0
-"CLDN4",0,0.992589520853902,0.966,0.787,0
-"EMP1",0,0.967085275949553,0.84,0.421,0
-"DHRS9",0,0.958922769935908,0.347,0.031,0
-"GPRC5A",0,0.945112298318574,0.89,0.411,0
-"C15orf48",0,0.93138558432206,0.355,0.093,0
-"PLAUR",0,0.923848362072027,0.83,0.495,0
-"TRIM31",0,0.921872040747593,0.382,0.018,0
-"RAB11FIP1",0,0.90964684401651,0.782,0.252,0
-"TMSB4X",0,0.890853220353238,0.999,0.907,0
-"SNCG",0,0.885857041696339,0.397,0.091,0
-"MGST1",0,0.877233785111273,0.77,0.284,0
-"CLDN3",0,0.867568812174985,0.464,0.132,0
-"DUSP5",0,0.867489899024141,0.821,0.364,0
-"ADGRF1",0,0.863067680165359,0.56,0.085,0
-"SDC1",0,0.855079197991529,0.771,0.266,0
-"MAL2",0,0.829214510888916,0.763,0.264,0
-"C9orf16",0,0.814183727203243,0.892,0.518,0
-"PPARG",0,0.800380811661097,0.518,0.111,0
-"TMPRSS4",0,0.795414111107558,0.583,0.079,0
-"ASS1",0,0.789484681436934,0.63,0.161,0
-"HEBP2",0,0.775333313964007,0.946,0.596,0
-"ANKRD36C",0,0.774694332463871,0.555,0.141,0
-"PSCA",0,0.76950257349792,0.483,0.098,0
-"PIM1",0,0.762437223080405,0.709,0.276,0
-"DAPP1",0,0.752452728119962,0.507,0.077,0
-"CLDN7",0,0.749132294099714,0.884,0.432,0
-"CLCA4",0,0.746229648530777,0.417,0.052,0
-"AQP3",0,0.744435084806878,0.96,0.647,0
-"OAS1",0,0.737674558805654,0.345,0.037,0
-"AGR2",0,0.736693258779718,0.781,0.209,0
-"ELF3",0,0.732571682114414,0.904,0.545,0
-"UGCG",0,0.720193826768467,0.778,0.336,0
-"OAF",0,0.709838754431922,0.456,0.075,0
-"FA2H",0,0.709303774847737,0.447,0.052,0
-"KIAA1551",0,0.708818780514771,0.462,0.137,0
-"RHOV",0,0.703524304562652,0.413,0.083,0
-"S100A9",1.1150607009699e-277,1.18219980623418,0.347,0.1,2.55493858413232e-273
-"CCL20",6.77607397394455e-180,1.02041376650979,0.373,0.147,1.55260182964991e-175
-"DDIT4",7.11148817886943e-173,0.7220233013543,0.415,0.177,1.62945528642435e-168
-"CD24",3.12769070457912e-135,0.738582866062415,0.504,0.277,7.16647771140215e-131
-"AREG",2.0738560684765e-128,0.773001703198323,0.648,0.4,4.75182640970021e-124
-"MARCKSL1",7.59116015117376e-77,0.700488217765786,0.454,0.279,1.73936252543844e-72
+"KRT13",0,2.01597974586173,0.894,0.219,0
+"S100P",0,1.90822949993826,0.955,0.276,0
+"APOBEC3A",0,1.64479513614821,0.373,0.02,0
+"GDF15",0,1.63652784022573,0.753,0.218,0
+"CSTB",0,1.55719488136333,0.968,0.696,0
+"DUOXA2",0,1.35668543845155,0.476,0.044,0
+"LYPD3",0,1.33911533216507,0.71,0.14,0
+"OLFM4",0,1.32626886913112,0.498,0.09,0
+"GPX2",0,1.322374009836,0.861,0.261,0
+"CXCL17",0,1.26746318407033,0.862,0.316,0
+"AKR1C1",0,1.23618585262563,0.395,0.043,0
+"SERPINB1",0,1.1392745613162,0.786,0.271,0
+"AKR1C2",0,1.1037845543013,0.387,0.029,0
+"IL1RN",0,1.08260189545751,0.642,0.139,0
+"IGFBP3",0,1.07991485363553,0.626,0.21,0
+"MUC4",0,1.02714308408923,0.658,0.061,0
+"SDCBP2",0,1.00728839913211,0.852,0.266,0
+"CLDN4",0,0.991751768397351,0.97,0.813,0
+"HPGD",0,0.971227671436239,0.491,0.157,0
+"ADIRF",0,0.968987738055083,0.733,0.316,0
+"GPRC5A",0,0.945982290379014,0.908,0.442,0
+"TRIM31",0,0.94197001483728,0.427,0.021,0
+"EMP1",0,0.932030682935755,0.852,0.464,0
+"DHRS9",0,0.924902007896113,0.361,0.036,0
+"C15orf48",0,0.894472391879342,0.378,0.107,0
+"PLAUR",0,0.881994715624181,0.841,0.533,0
+"DUSP5",0,0.876866666835571,0.844,0.395,0
+"SNCG",0,0.861773450438171,0.422,0.104,0
+"ADGRF1",0,0.859900050256145,0.609,0.099,0
+"RAB11FIP1",0,0.858445494078961,0.788,0.287,0
+"SDC1",0,0.838644943633723,0.801,0.297,0
+"TMSB4X",0,0.835345625287976,0.999,0.925,0
+"MGST1",0,0.831798136576865,0.782,0.314,0
+"CLDN3",0,0.822274870101125,0.499,0.154,0
+"TMPRSS4",0,0.798897316332515,0.632,0.094,0
+"MAL2",0,0.791449468589868,0.79,0.302,0
+"C9orf16",0,0.778392764226278,0.901,0.565,0
+"ASS1",0,0.773901199975319,0.679,0.193,0
+"PIM1",0,0.765415316262707,0.756,0.307,0
+"PPARG",0,0.762636291288148,0.558,0.131,0
+"DAPP1",0,0.746683058174609,0.551,0.092,0
+"CLDN7",0,0.739260170039693,0.907,0.477,0
+"HEBP2",0,0.723276756724657,0.953,0.64,0
+"AQP3",0,0.716987363265918,0.968,0.684,0
+"OAS1",0,0.714196432000364,0.377,0.043,0
+"CLCA4",0,0.707315046155253,0.435,0.063,0
+"ELF3",0,0.706139364505989,0.918,0.58,0
+"OAF",0,0.699851508133468,0.503,0.091,0
+"S100A9",1.15985558458396e-247,1.04617618672697,0.352,0.114,2.6966642341577e-243
+"DDIT4",3.24254500877931e-193,0.717825181616735,0.443,0.192,7.5389171454119e-189
+"CCL20",3.07768429677462e-176,0.949878582556194,0.387,0.162,7.15561599000099e-172
+"AREG",1.7114723937272e-139,0.772695140628557,0.669,0.416,3.97917331541575e-135
diff --git a/genesets/genes.deg.SM.csv b/genesets/genes.deg.SM.csv
index 2bec57e2a6bb1191b03d9247c9dfe58d552070d1..ccaae9c3608bdce0eedae2c855099d371f377c44 100644
--- a/genesets/genes.deg.SM.csv
+++ b/genesets/genes.deg.SM.csv
@@ -1,101 +1,99 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"TAGLN",0,3.22761469018998,0.888,0.153,0
-"MYL9",0,3.17643068893703,0.925,0.173,0
-"RGS5",0,2.90029461427289,0.705,0.049,0
-"TPM2",0,2.86857125264117,0.885,0.251,0
-"ACTA2",0,2.7495850285709,0.67,0.049,0
-"MT1A",0,2.65683119186406,0.767,0.139,0
-"MYH11",0,2.31653878971377,0.672,0.026,0
-"GJA4",0,2.29173507197837,0.72,0.054,0
-"CALD1",0,2.0299817139831,0.978,0.413,0
-"PPP1R14A",1.66798802683812e-285,1.4812698115742,0.489,0.029,3.82186096589418e-281
-"CRISPLD2",5.29877331647043e-268,1.47286246782131,0.794,0.215,1.21410793000287e-263
-"TPM1",2.08425095846774e-260,2.15770419397078,0.765,0.243,4.77564422113713e-256
-"NDUFA4L2",3.62347886421405e-245,1.64966711602042,0.427,0.023,8.30247712157365e-241
-"ADIRF",2.97752396064964e-240,1.70717663368776,0.862,0.401,6.82240065103652e-236
-"MT1M",1.67979995442768e-230,1.77044465969477,0.501,0.061,3.84892563558015e-226
-"TPPP3",7.17724908777075e-227,1.37296592610368,0.404,0.025,1.64452308348091e-222
-"C11orf96",8.75031365168414e-215,1.34109408351927,0.933,0.521,2.00495936701039e-210
-"PLN",9.42515089980193e-213,1.10931106756257,0.308,0.002,2.15958482567162e-208
-"PDK4",9.39365014782062e-211,2.06588025994171,0.739,0.257,2.15236705837014e-206
-"HES4",4.12923993295621e-204,1.31574182925402,0.814,0.357,9.46132745838255e-200
-"SYNPO2",4.91333353360298e-199,1.10572152192694,0.394,0.033,1.12579211255445e-194
-"MFGE8",5.9593966780143e-195,1.2567868097746,0.684,0.21,1.36547656083342e-190
-"CRYAB",8.67697153274983e-193,0.951055660451087,0.848,0.317,1.98815448729897e-188
-"C2orf40",2.06765249241979e-186,1.24208180928384,0.449,0.062,4.73761215588146e-182
-"MT2A",6.0148976387391e-182,1.15570364689463,0.955,0.677,1.37819349596429e-177
-"MYLK",6.38621398049611e-182,1.56962468402609,0.568,0.141,1.46327320935107e-177
-"FRZB",2.90636257488918e-178,1.25995739466656,0.365,0.034,6.65934856784357e-174
-"ID4",5.25021361605349e-178,1.88514756844141,0.54,0.119,1.20298144584634e-173
-"FOXC2",5.49039524130676e-171,0.934633322889935,0.303,0.015,1.25801426164062e-166
-"SORBS2",7.40601617765911e-168,1.14783598478455,0.329,0.026,1.69694048678703e-163
-"NOTCH3",3.06064504170724e-167,0.801391963587603,0.3,0.016,7.0128559840638e-163
-"EFHD1",4.34996690290387e-162,0.85290403447158,0.32,0.025,9.96707916462365e-158
-"CNN1",2.31380607964942e-160,1.1989333254286,0.319,0.025,5.3016238703007e-156
-"SLC25A4",2.21099144971809e-159,1.12507223888982,0.422,0.071,5.06604470873906e-155
-"PCP4",9.110561190065e-159,1.67023141905025,0.262,0.009,2.08750288547959e-154
-"MT1X",3.21462387170939e-156,1.81654085289549,0.701,0.301,7.36566767724772e-152
-"LPP",5.24361516120995e-156,1.2676557913508,0.652,0.261,1.20146954188804e-151
-"ADAMTS4",3.51695284370658e-155,1.22440945130736,0.77,0.391,8.05839405078489e-151
-"ADRA2A",4.45825494112897e-153,1.12297380740452,0.262,0.011,1.02151995466088e-148
-"TIMP3",4.86119742520819e-151,1.14799481558043,0.819,0.424,1.11384616603795e-146
-"CPE",2.12436700128431e-148,1.0341977021274,0.628,0.212,4.86756211004273e-144
-"MT1E",1.12418745870634e-146,1.44037267554926,0.495,0.123,2.57585072413384e-142
-"ACTG2",7.22987127247064e-144,2.32131736478209,0.279,0.02,1.6565804046612e-139
-"PTP4A3",1.34459688519711e-141,1.0981118419095,0.311,0.033,3.08087484305214e-137
-"GADD45B",6.70145030875033e-141,1.27674550488024,0.777,0.408,1.53550330924396e-136
-"STEAP4",7.69844460303095e-138,1.10666272341122,0.279,0.022,1.76394461189248e-133
-"KCNE4",3.05495042133843e-137,1.14326878929739,0.367,0.057,6.99980790041274e-133
-"MAP1B",3.25490101621326e-137,1.03541956079708,0.667,0.275,7.45795469844944e-133
-"DSTN",7.86066374204483e-133,1.34715700444701,0.837,0.668,1.80111388321473e-128
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-"SYNM",6.95310078321202e-132,0.97388633719862,0.347,0.052,1.59316398245737e-127
-"RCAN2",1.07018252181472e-130,0.739154808643224,0.277,0.025,2.45210921223407e-126
-"PDGFRB",9.9275238863182e-130,0.863676100169998,0.359,0.058,2.27469354807209e-125
-"FLNA",3.44747002245754e-128,1.11133924806039,0.489,0.146,7.89918806245697e-124
-"DES",3.89190486557352e-125,2.2045629363668,0.258,0.022,8.9175216184886e-121
-"ISYNA1",3.61677706414607e-114,0.727844029899243,0.272,0.032,8.28712128707789e-110
-"BGN",8.58452791273594e-114,0.949642986731032,0.515,0.167,1.96697288064519e-109
-"IGFBP6",1.57510779575251e-111,0.960342370967063,0.735,0.337,3.60904449240773e-107
-"PALLD",2.16371523630599e-109,0.925024099728227,0.474,0.145,4.95772072094791e-105
-"RHOB",1.50140340051427e-107,1.44361401460441,0.561,0.234,3.44016561159836e-103
-"MYL6",1.88093512951034e-107,0.859170175740856,0.962,0.903,4.30978666224704e-103
-"FHL1",1.20974331743751e-106,1.02627972232095,0.353,0.076,2.77188486324457e-102
-"SOD3",7.59531808100461e-106,0.775083723730539,0.653,0.264,1.74031523190059e-101
-"CPM",5.77537854337427e-100,0.800395655986518,0.29,0.049,1.32331248564335e-95
-"ADAMTS1",6.71981406906474e-100,1.08263989060193,0.582,0.242,1.5397109976448e-95
-"CKB",2.98472887875052e-97,1.03187831895226,0.485,0.175,6.83890927988108e-93
-"TINAGL1",9.5581683770862e-93,0.827843731249677,0.49,0.185,2.19006312024176e-88
-"ZNF331",1.96332240471964e-89,0.999545335489653,0.399,0.117,4.49856062593411e-85
-"LBH",3.09493233047746e-89,1.05597535827296,0.37,0.103,7.091418448823e-85
-"MTHFD2",3.70006261442677e-89,0.85968749137476,0.56,0.26,8.47795346843605e-85
-"GPX3",1.54951153332095e-87,0.773955846632048,0.656,0.337,3.55039577629829e-83
-"KLF9",1.6603990616852e-87,0.799550140471024,0.577,0.27,3.8044723700393e-83
-"ZFHX3",3.69359873098965e-84,0.875878825688,0.424,0.146,8.46314277231658e-80
-"NDUFS2",8.61346503604616e-82,0.801736762336735,0.399,0.133,1.97360324370926e-77
-"CCDC107",1.13698030852118e-81,0.837538984180377,0.441,0.169,2.60516298091457e-77
-"NR4A1",3.10558158028137e-81,0.776726786889858,0.546,0.242,7.1158190748987e-77
-"EPS8",4.32374218622101e-80,0.743241781600473,0.441,0.162,9.9069904712882e-76
-"SH3BGRL",1.8709993184276e-79,0.765310126167337,0.585,0.3,4.28702073831317e-75
-"ATF3",1.07394329857376e-73,0.881263438150261,0.538,0.262,2.46072628002205e-69
-"PRKCDBP",1.45315263163846e-72,0.838677736325367,0.337,0.102,3.3296086248732e-68
-"PDLIM3",1.65637939201082e-69,0.821183132915366,0.408,0.157,3.79526210091438e-65
-"KIAA0040",2.14618412691004e-69,0.782596685260843,0.343,0.11,4.91755168998897e-65
-"EPAS1",3.24107588513384e-69,0.783266143992348,0.58,0.31,7.42627717560716e-65
-"ARID5B",6.78101548536086e-68,0.70776416744692,0.698,0.447,1.55373407816073e-63
-"HSPB1",1.00188284463443e-67,0.970075218085223,0.87,0.729,2.29561416191088e-63
-"CSRP1",4.26768721230421e-66,0.862528989922883,0.371,0.134,9.77855170955264e-62
-"JUNB",1.67038894709763e-65,0.828900757257739,0.805,0.653,3.82736219448479e-61
-"NR2F2",1.02662314284662e-63,0.701792138530261,0.411,0.162,2.35230160720446e-59
-"BCAM",2.24717550618385e-62,0.913745799160338,0.327,0.113,5.14895323731906e-58
-"AXL",2.99259006601586e-61,0.705066634923237,0.506,0.238,6.85692161826214e-57
-"CDKN1A",1.27330784451419e-60,0.722183445080421,0.801,0.631,2.91753026413536e-56
-"CCNH",4.82708595617335e-49,0.705662834568355,0.432,0.219,1.106030205138e-44
-"APOLD1",6.0740441589554e-48,0.803310228450407,0.361,0.153,1.39174573814145e-43
-"NUDT4",5.95239673946483e-47,0.753297356939209,0.452,0.246,1.36387266491358e-42
-"S100A4",3.38147345389777e-46,0.747492629679075,0.512,0.285,7.74797012491596e-42
-"CREM",1.50306903923449e-42,0.758063261049986,0.701,0.524,3.44398208959799e-38
-"MAT2A",8.84192862792204e-42,0.768042451881537,0.466,0.265,2.02595110651578e-37
-"MYC",2.67432935524288e-37,0.693923699888954,0.51,0.316,6.12769085166802e-33
-"LMCD1",5.63185595860579e-27,0.765688989240422,0.331,0.183,1.29042715579534e-22
-"C8orf4",2.06314282776079e-11,0.69487782812544,0.258,0.173,4.7272791612483e-07
+"TAGLN",0,3.23162659529245,0.903,0.176,0
+"MYL9",0,3.14917398934124,0.936,0.2,0
+"TPM2",0,2.86267975440181,0.904,0.288,0
+"ACTA2",0,2.79872216700026,0.698,0.058,0
+"RGS5",0,2.74246435802674,0.679,0.058,0
+"MT1A",0,2.5636863665765,0.77,0.164,0
+"MYH11",0,2.27935388569363,0.687,0.03,0
+"GJA4",0,2.24331181583654,0.734,0.062,0
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+"KIAA0040",4.44948921190248e-63,0.694856114969486,0.334,0.119,1.03450624176733e-58
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+"NDUFA4",7.09316222575543e-60,0.734847408988811,0.741,0.641,1.64916021748814e-55
+"ATF3",1.91207076300283e-58,0.801249226945017,0.57,0.329,4.44556452398158e-54
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+"RGS16",1.98685799637613e-45,0.835026734875246,0.289,0.11,4.61944484157451e-41
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+"MAT2A",7.8754108891864e-40,0.720063927901717,0.478,0.289,1.83103303173584e-35
+"MYC",1.20348876285353e-39,0.75775141294433,0.543,0.354,2.79811137363445e-35
diff --git a/genesets/genes.deg.St.csv b/genesets/genes.deg.St.csv
index 5e5bff11774f2660e36c2e176d8accd51abcf90d..015986317ed1c70b827af9f5132112cc0b36f0b9 100644
--- a/genesets/genes.deg.St.csv
+++ b/genesets/genes.deg.St.csv
@@ -1,123 +1,159 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"C11orf96",0,3.27106187814317,0.615,0.026,0
-"IGFBP7",0,3.06433927438808,0.844,0.174,0
-"IL6",0,2.99677467380374,0.342,0.01,0
-"APOD",0,2.90321606186878,0.261,0.026,0
-"VIM",0,2.89517714526119,0.915,0.045,0
-"PTGDS",0,2.83305722702714,0.264,0.01,0
-"SPARCL1",0,2.41214911118489,0.802,0.2,0
-"HMOX1",0,2.33397863680387,0.4,0.063,0
-"IGFBP5",0,2.33017645197054,0.427,0.016,0
-"SRGN",0,2.24971760681818,0.511,0.011,0
-"DCN",0,2.20430319642958,0.329,0.005,0
-"MGP",0,2.19933849805852,0.59,0.162,0
-"IGFBP6",0,2.15600801118863,0.427,0.089,0
-"TIMP1",0,2.12770135667465,0.81,0.653,0
-"MT1A",0,2.10768994082431,0.281,0.025,0
-"IFI27",0,2.08722618478112,0.368,0.026,0
-"LGALS1",0,2.05056499914394,0.789,0.172,0
-"CSF3",0,1.99691194202204,0.292,0.013,0
-"TPM2",0,1.91768202275908,0.395,0.166,0
-"HLA-DRA",0,1.77518949542287,0.368,0.071,0
-"AKAP12",0,1.73709815427037,0.506,0.045,0
-"ADAMTS4",0,1.70390711855119,0.477,0.005,0
-"PLPP3",0,1.6265408955977,0.517,0.042,0
-"GEM",0,1.62401969264343,0.409,0.085,0
-"HLA-DRB1",0,1.62083602620716,0.396,0.057,0
-"CREM",0,1.59915821731665,0.565,0.135,0
-"SERPINE1",0,1.43649666604458,0.338,0.04,0
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-"CRISPLD2",0,1.36512025162769,0.347,0.018,0
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-"FTL",0,1.20080431920271,0.997,0.994,0
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-"IGFBP4",0,1.16578880070247,0.536,0.185,0
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-"TCF4",0,1.12013976715615,0.381,0.069,0
-"SLC2A3",0,1.11975779462095,0.371,0.006,0
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-"CD93",0,1.07138141657855,0.271,0.002,0
-"COL4A1",0,1.0567976310139,0.386,0.016,0
-"BNIP3L",0,1.04270940521051,0.39,0.162,0
-"GPX3",0,1.03218155022731,0.41,0.148,0
-"INSIG1",0,1.01504482442216,0.467,0.16,0
-"IFITM2",0,1.01175622649404,0.682,0.338,0
-"TMSB4X",0,1.00324904289417,0.992,0.916,0
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-"MFGE8",0,0.988804247545929,0.318,0.055,0
-"SOD3",0,0.958159368225089,0.352,0.118,0
-"CD200",0,0.95554124070796,0.263,0.032,0
-"HLA-DRB5",0,0.942538456898411,0.29,0.026,0
-"SELM",0,0.931705587568027,0.66,0.417,0
-"MAP1B",0,0.916840322930248,0.364,0.087,0
-"CTSL",0,0.867085213202827,0.387,0.156,0
-"ARID5A",0,0.863621671800372,0.38,0.093,0
-"IFITM3",0,0.855173586192412,0.833,0.631,0
-"PCAT19",0,0.846562009148716,0.253,0.004,0
-"BST2",0,0.843264230442278,0.328,0.039,0
-"HLA-E",0,0.838973760031802,0.803,0.624,0
-"B2M",0,0.822367635930407,0.999,0.99,0
-"HLA-B",0,0.815789709180547,0.878,0.815,0
-"SOD2",0,0.798036870889999,0.839,0.693,0
-"MSN",0,0.789358773464697,0.45,0.16,0
-"PNP",0,0.78571908464889,0.371,0.138,0
-"HLA-A",0,0.785396299546927,0.922,0.85,0
-"LDHA",0,0.779675777238688,0.797,0.615,0
-"PTMA",0,0.775910164622214,0.997,0.991,0
-"CLIC4",0,0.773311948224073,0.464,0.16,0
-"UPP1",0,0.749173850166689,0.285,0.054,0
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-"TUBB6",0,0.73093596216287,0.382,0.116,0
-"LIMS1",0,0.716773620543538,0.389,0.162,0
-"TIMP2",0,0.712548010418072,0.27,0.022,0
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-"TAGLN2",2.89895597959621e-303,0.699536263974395,0.711,0.542,6.64237783604879e-299
-"SDCBP",6.10675981122709e-296,0.734996038237472,0.731,0.574,1.39924187554646e-291
-"BTG1",2.13267841692268e-288,0.714070409432708,0.875,0.766,4.88660605669493e-284
-"CDKN1A",2.89706724512976e-278,0.812393317927415,0.67,0.469,6.63805017876582e-274
-"RHOQ",1.07336598020178e-277,0.72817013838081,0.264,0.085,2.45940347043634e-273
-"EPAS1",8.83266978075275e-276,0.757041800837743,0.372,0.161,2.02382962686388e-271
-"CD74",8.51333374896344e-274,1.57377671686508,0.463,0.253,1.95066016189999e-269
-"SOCS3",1.09004981556389e-272,1.02478484112462,0.363,0.156,2.49763114240153e-268
-"ISG15",1.25812904359817e-271,0.753530207285179,0.276,0.092,2.8827510775965e-267
-"CSRP2",7.3191357847714e-267,0.774928570598611,0.383,0.166,1.67703358236467e-262
-"CFD",1.24349850006057e-254,2.2955488363463,0.3,0.122,2.84922811318878e-250
-"PTGS2",3.74462007013607e-240,1.63135368848195,0.271,0.1,8.58004796670277e-236
-"DNAJB9",1.07380167229278e-234,0.869693567288508,0.441,0.236,2.46040177172445e-230
-"FTH1",2.32334827442042e-222,0.735874506490252,0.997,0.999,5.32348790117952e-218
-"TSC22D1",6.30352684116661e-206,0.960353542048819,0.61,0.449,1.44432710511651e-201
-"RHOB",3.85619071119156e-199,0.950984306713293,0.308,0.136,8.83568977655322e-195
-"ID2",1.60077710606478e-197,0.916032027708706,0.321,0.145,3.66786058312624e-193
-"ADIRF",1.00902805950261e-192,0.902131281830799,0.506,0.31,2.31198599273833e-188
-"CEBPB",1.39841293275697e-167,0.899292857278355,0.58,0.455,3.20418355282605e-163
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-"THBS1",5.36833296557979e-156,0.820025799330769,0.315,0.159,1.2300461324033e-151
-"EMP1",8.45598413175745e-149,0.693856878992838,0.613,0.462,1.93751964410959e-144
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-"RHOBTB3",7.51917557465814e-127,0.823450230603365,0.277,0.148,1.72286869942142e-122
-"CALD1",2.16017465311969e-120,1.02938797630946,0.541,0.421,4.94960818269313e-116
-"PDK4",4.41122402620442e-89,1.39706207479039,0.367,0.259,1.01074376112422e-84
-"IER3",5.05441947116057e-47,1.14403548504987,0.585,0.586,1.15811913342702e-42
-"G0S2",7.24342164483186e-34,1.59441319319703,0.299,0.236,1.65968520148032e-29
-"MEG3",1.24129340079753e-31,0.81671683595657,0.39,0.357,2.84417556924739e-27
-"TAGLN",1.23335741691569e-24,1.58789306236008,0.32,0.28,2.82599184937891e-20
-"SERPINF1",3.12440849484094e-15,0.746249993644589,0.299,0.279,7.15895718422904e-11
-"DNAJB1",5.76796650893014e-14,0.811756190456719,0.446,0.444,1.32161416619116e-09
-"TPM1",5.3159985879149e-13,0.845101158077249,0.361,0.347,1.21805475644894e-08
+"C11orf96",0,3.35657963778659,0.708,0.036,0
+"IGFBP7",0,3.15209871939752,0.951,0.191,0
+"APOD",0,3.14186916624101,0.321,0.038,0
+"IL6",0,3.06378549509199,0.398,0.015,0
+"PTGDS",0,2.984059301983,0.313,0.016,0
+"VIM",0,2.90884774131888,0.944,0.054,0
+"SPARCL1",0,2.51839371967671,0.914,0.215,0
+"IGFBP5",0,2.46788937022088,0.496,0.019,0
+"HMOX1",0,2.42981899011226,0.429,0.077,0
+"MGP",0,2.35886107426051,0.707,0.178,0
+"IGFBP6",0,2.32348070236816,0.515,0.105,0
+"DCN",0,2.31379725539251,0.38,0.007,0
+"IFI27",0,2.20757404198392,0.424,0.033,0
+"MT1A",0,2.20743898939655,0.336,0.031,0
+"TIMP1",0,2.17577995338573,0.864,0.693,0
+"CSF3",0,2.12390991586269,0.348,0.016,0
+"LGALS1",0,2.07717174859661,0.818,0.194,0
+"CXCL2",0,2.05804809463236,0.377,0.14,0
+"TPM2",0,2.04592836769388,0.475,0.183,0
+"STC1",0,1.88561607702683,0.26,0.005,0
+"ADAMTS4",0,1.81500599991667,0.564,0.007,0
+"AKAP12",0,1.80327333175128,0.599,0.051,0
+"GEM",0,1.79996977665522,0.475,0.094,0
+"PLPP3",0,1.69957895148618,0.613,0.05,0
+"LUM",0,1.66670206288439,0.271,0.005,0
+"SRGN",0,1.64344531928405,0.483,0.016,0
+"CREM",0,1.60448971960675,0.593,0.155,0
+"SERPINE1",0,1.53907665601399,0.397,0.043,0
+"MT2A",0,1.4799735243476,0.807,0.61,0
+"SPARC",0,1.47829443640837,0.616,0.045,0
+"HLA-DRB1",0,1.47634274469489,0.394,0.069,0
+"A2M",0,1.45799667776449,0.495,0.004,0
+"PMP22",0,1.44794368173077,0.553,0.014,0
+"ADAMTS9",0,1.44495270614977,0.574,0.164,0
+"CLDN5",0,1.44050806195018,0.303,0.004,0
+"CRISPLD2",0,1.43726540805598,0.406,0.022,0
+"PTN",0,1.42623318419868,0.298,0.012,0
+"TFPI",0,1.42503244810105,0.522,0.016,0
+"COL6A2",0,1.39466732816361,0.471,0.017,0
+"C1S",0,1.38628102492775,0.403,0.036,0
+"C1R",0,1.3692177726174,0.431,0.093,0
+"SPRY1",0,1.3639582174392,0.328,0.035,0
+"IGFBP4",0,1.35101177234523,0.665,0.217,0
+"SOCS3",0,1.30902910056725,0.418,0.181,0
+"GSN",0,1.30506520995541,0.703,0.387,0
+"SERPING1",0,1.28834521910818,0.557,0.133,0
+"S100A4",0,1.27948497386243,0.353,0.061,0
+"GNG11",0,1.25187116035782,0.47,0.027,0
+"ICAM1",0,1.25103868390613,0.446,0.039,0
+"HLA-DRA",0,1.2259993006124,0.349,0.084,0
+"SLC2A3",0,1.21183184009103,0.427,0.007,0
+"TCF4",0,1.20734785319568,0.454,0.079,0
+"ADAMTS1",0,1.19384763998005,0.395,0.051,0
+"GYPC",0,1.1673645902117,0.432,0.012,0
+"COL4A1",0,1.13947001893179,0.471,0.018,0
+"MFAP4",0,1.13829254663562,0.276,0.002,0
+"CD93",0,1.12773696486979,0.311,0.004,0
+"GPX3",0,1.12278424381216,0.486,0.168,0
+"MFGE8",0,1.11186494379527,0.4,0.066,0
+"FTL",0,1.10570201052532,0.998,0.996,0
+"IFITM2",0,1.09622088605487,0.76,0.361,0
+"SOD3",0,1.09468773550915,0.434,0.141,0
+"PKIG",0,1.07015872616231,0.478,0.037,0
+"MYLK",0,1.06946804501044,0.302,0.036,0
+"BNIP3L",0,1.06788042106125,0.433,0.19,0
+"BGN",0,1.06276175727964,0.313,0.003,0
+"TSC22D1",0,1.05168004930845,0.686,0.481,0
+"MMP2",0,1.03460951598224,0.281,0.03,0
+"SELM",0,1.02476214699384,0.757,0.449,0
+"MAP1B",0,1.01356950057548,0.446,0.092,0
+"CD200",0,1.00409776872784,0.307,0.037,0
+"RCAN1",0,1.00170028016025,0.304,0.057,0
+"THBD",0,0.980596462419037,0.257,0.033,0
+"IFITM3",0,0.974068058325107,0.926,0.681,0
+"INSIG1",0,0.960355420020766,0.503,0.186,0
+"PLVAP",0,0.952720084540191,0.257,0.002,0
+"PCAT19",0,0.952181434680814,0.312,0.006,0
+"EDNRB",0,0.931344504753404,0.282,0.003,0
+"CALCRL",0,0.930942471056838,0.282,0.004,0
+"CST3",0,0.929672005124908,0.88,0.765,0
+"BST2",0,0.913124402829383,0.385,0.049,0
+"NNMT",0,0.908560912811799,0.285,0.025,0
+"CDKN1A",0,0.906912920184886,0.741,0.508,0
+"HLA-E",0,0.894902609452439,0.847,0.677,0
+"ARID5A",0,0.894653770761093,0.432,0.106,0
+"TMSB4X",0,0.890780468436511,0.994,0.933,0
+"PNP",0,0.871669283948557,0.438,0.16,0
+"HLA-DPA1",0,0.868784894532554,0.277,0.033,0
+"HLA-DRB5",0,0.856338051000458,0.293,0.032,0
+"CSRP2",0,0.856307944468502,0.462,0.187,0
+"PRRX1",0,0.850329911778928,0.267,0.002,0
+"EPAS1",0,0.846723163830484,0.452,0.184,0
+"CTSL",0,0.831629591236177,0.426,0.168,0
+"MSN",0,0.825510160656912,0.508,0.187,0
+"CLIC4",0,0.823840293995555,0.542,0.185,0
+"LDHA",0,0.820439830453995,0.854,0.658,0
+"LMCD1",0,0.816340194922396,0.278,0.054,0
+"HLA-B",0,0.815462136912527,0.897,0.851,0
+"NR4A2",0,0.811533094858348,0.29,0.072,0
+"ISG15",0,0.806543148248116,0.318,0.104,0
+"PTMA",0,0.806243172762274,0.999,0.995,0
+"SOD2",0,0.802390117820088,0.867,0.727,0
+"ADGRL4",0,0.790049027802065,0.27,0.001,0
+"HLA-A",0,0.787853857294099,0.942,0.881,0
+"AEBP1",0,0.785610185559771,0.296,0.026,0
+"KLF9",0,0.778492702325455,0.42,0.13,0
+"TUBB6",0,0.772256008730784,0.452,0.133,0
+"B2M",0,0.769814019730839,0.999,0.993,0
+"COL6A1",0,0.763727402726993,0.303,0.025,0
+"TAGLN2",0,0.763119639179336,0.782,0.596,0
+"TIMP2",0,0.75568361353686,0.323,0.026,0
+"LMO4",0,0.742279783424695,0.342,0.115,0
+"ANKRD28",0,0.735829733099667,0.331,0.074,0
+"HLA-DPB1",0,0.729023816843719,0.316,0.085,0
+"UPP1",0,0.725307402202424,0.289,0.062,0
+"MGLL",0,0.721964801625337,0.296,0.034,0
+"ITM2A",0,0.721630260940231,0.271,0.032,0
+"PNRC1",0,0.717757180341393,0.871,0.744,0
+"LIMS1",0,0.713087383931869,0.433,0.191,0
+"ZEB1",0,0.705878855482179,0.298,0.009,0
+"PDLIM3",0,0.705015400914034,0.263,0.025,0
+"RDX",0,0.702942722577951,0.404,0.158,0
+"SLC4A7",0,0.700038612371655,0.423,0.152,0
+"NR2F2",0,0.693158207033491,0.275,0.058,0
+"SDCBP",2.46573538682373e-303,0.725006527999333,0.769,0.618,5.73283477436517e-299
+"RHOQ",1.26201125468556e-297,0.74817983114089,0.301,0.101,2.93417616714393e-293
+"RHOB",1.04471468902897e-288,1.10062146709578,0.37,0.149,2.42896165199236e-284
+"ADIRF",1.98505986794133e-285,0.969182689910121,0.615,0.361,4.6152641929636e-281
+"CFD",2.38155931175815e-265,2.39969795139114,0.33,0.14,5.53712539983769e-261
+"PTGS2",4.62549512629227e-263,1.7060512398562,0.304,0.113,1.07542761686295e-258
+"DNAJB9",6.80794908033878e-263,0.88797779440846,0.488,0.264,1.58284816117877e-258
+"EMP1",1.48913957056734e-237,0.763723324457966,0.708,0.506,3.46224950156906e-233
+"NR4A1",1.22718049755861e-229,0.837831820630746,0.383,0.18,2.85319465682378e-225
+"NFKBIA",4.82553449692386e-210,0.914208640247266,0.824,0.74,1.1219367705348e-205
+"CALD1",1.72500904923064e-204,1.14154292862704,0.617,0.442,4.01064603946125e-200
+"CD74",3.88565437377328e-179,1.20813744245922,0.453,0.288,9.03414641902287e-175
+"CEBPB",1.36300247365197e-172,0.956025111624211,0.617,0.501,3.16898075124083e-168
+"GADD45B",1.00971788613334e-170,1.48685101121296,0.545,0.401,2.34759408526002e-166
+"ID2",2.87216712605345e-170,0.775127853168569,0.335,0.162,6.67778856807426e-166
+"FBLN1",9.23575305864446e-163,2.05188484165657,0.358,0.218,2.14731258613484e-158
+"PDK4",1.00167849804243e-161,1.53851073742064,0.434,0.272,2.32890250794865e-157
+"JUNB",7.54008368734433e-160,0.901090221151883,0.757,0.649,1.75306945730756e-155
+"RHOBTB3",6.82827318365995e-155,0.860102156319912,0.323,0.171,1.58757351520094e-150
+"THBS1",3.25534197878508e-127,0.764440348204278,0.329,0.182,7.56867010067531e-123
+"NDRG1",4.20625936420683e-126,0.745475396464599,0.486,0.354,9.77955302178088e-122
+"JUN",2.70455477103472e-109,0.721844399479531,0.693,0.597,6.28808984265572e-105
+"CRYAB",9.73661536133703e-68,0.778831474614523,0.491,0.391,2.26376307151086e-63
+"MEG3",1.29729904607994e-67,0.934605755066499,0.449,0.378,3.01622028213587e-63
+"IER3",2.0785905969469e-65,1.36964112412111,0.635,0.627,4.83272313790153e-61
+"TAGLN",7.14527016840783e-56,1.7655497331943,0.375,0.296,1.66127531415482e-51
+"ID3",7.68784962332514e-41,0.694930881048569,0.371,0.289,1.78742503742309e-36
+"FOS",8.18615180064779e-39,0.743251405524629,0.524,0.448,1.90328029365061e-34
+"TPM1",2.32360816854733e-35,0.992495037939129,0.432,0.386,5.40238899187254e-31
+"SERPINF1",6.56023844543821e-29,0.857942886733171,0.341,0.303,1.52525543856438e-24
+"ID4",2.26329976161942e-17,0.889562772727801,0.266,0.227,5.26217194576515e-13
+"MYL9",1.91656138962639e-13,1.52224573026194,0.403,0.42,4.45600523088136e-09
+"G0S2",2.70363404946342e-13,1.52837835729027,0.287,0.255,6.28594916500245e-09
+"DNAJB1",5.01436604406916e-11,0.785501506000992,0.461,0.463,1.16584010524608e-06
diff --git a/genesets/genes.deg.Stress.csv b/genesets/genes.deg.Stress.csv
index b50b35177ee1f209190f93d972ce16ff9c6cf168..281cf366c38b6f4030a4aa1d066eeed5d617c3a9 100644
--- a/genesets/genes.deg.Stress.csv
+++ b/genesets/genes.deg.Stress.csv
@@ -1,18 +1,13 @@
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
-"JUN",0,3.0758001039643,0.988,0.573,0
-"FOS",0,3.00733901143765,0.954,0.416,0
-"GADD45B",0,2.50525260858546,0.833,0.379,0
-"EGR1",0,2.459952490935,0.868,0.286,0
-"ATF3",0,2.43352318601894,0.94,0.306,0
-"JUNB",0,2.29781033404575,0.97,0.621,0
-"IER2",0,2.13633541210568,0.895,0.571,0
-"ZFP36",0,2.11876291057998,0.956,0.61,0
-"HES1",0,1.94886819710079,0.686,0.276,0
-"RHOB",0,1.85215527020016,0.777,0.159,0
-"NR4A1",0,1.84065143007834,0.79,0.188,0
-"DUSP1",0,1.83426334801917,0.876,0.534,0
-"DNAJB1",0,1.83415300875228,0.906,0.445,0
-"BTG2",0,1.6855166291728,0.793,0.321,0
-"ID1",0,1.65678103354601,0.741,0.416,0
-"UBC",0,1.65097277593505,0.993,0.917,0
-"DDIT3",0,1.6226073481499,0.623,0.122,0
+"JUN",0,2.78514474389602,0.953,0.609,0
+"FOS",0,2.6180888667142,0.843,0.459,0
+"EGR1",0,2.27744499658095,0.827,0.313,0
+"ATF3",0,2.24777061964067,0.877,0.331,0
+"JUNB",0,1.97088620438955,0.899,0.663,0
+"GADD45B",0,1.92104125732309,0.72,0.423,0
+"IER2",0,1.88242169361821,0.806,0.625,0
+"ZFP36",0,1.86471330757214,0.93,0.655,0
+"DNAJB1",0,1.81462475826555,0.91,0.467,0
+"RHOB",0,1.70021664456101,0.72,0.179,0
+"NR4A1",0,1.63532584305745,0.727,0.208,0
+"UBC",0,1.6303655140661,0.991,0.936,0
diff --git a/r.scripts/sc-TissueMapper.R b/r.scripts/sc-TissueMapper.R
index db19abd99e8bccf2b00fc2a888d773b5a4f022e4..53b6d5874a9435b026be315a74d9c02dea0805bc 100644
--- a/r.scripts/sc-TissueMapper.R
+++ b/r.scripts/sc-TissueMapper.R
@@ -491,14 +491,19 @@ scQuSAGE <- function(sc10x,gs,res.use=0.1,ds=25000,nm="Lin",folder="lin"){
number.clusters <- length(unique(sc10x@ident))
labels <- paste0("Cluster_",as.vector(factor(sc10x@ident)))
- if ((ncol(sc10x@data)>ds & ds!=0)){
- rnd <- sample(1:ncol(sc10x@data),ds)
- data <- sc10x@data[,rnd]
- labels <- labels[rnd]
- } else {
- data <- sc10x@data
+
+ cell.sample <- NULL
+ for (i in 1:number.clusters){
+ cell <- names(sc10x@ident[sc10x@ident==i])
+ if (length(cell)>ds & ds!=0){
+ rnd <- sample(1:length(cell),ds)
+ cell <- cell[rnd]
+ }
+ cell.sample <- c(cell.sample,cell)
}
+ data <- sc10x@data[,colnames(sc10x@data) %in% cell.sample]
data <- as.data.frame(as.matrix(data))
+ labels <- labels[colnames(sc10x@data) %in% cell.sample]
#Make labels for QuSAGE
clust <- list()
@@ -541,7 +546,7 @@ scQuSAGE <- function(sc10x,gs,res.use=0.1,ds=25000,nm="Lin",folder="lin"){
if (max(results.cor[results.cor[,4]==i,][,2])>=0){
results.clust.id <- rbind(results.clust.id,results.cor[results.cor[,4]==i,][which.max(results.cor[results.cor[,4]==i,][,2]),])
} else {
- results.clust.id <- rbind(results.clust.id,c("Unknown",0,0,i))
+ results.clust.id <- rbind(results.clust.id,data.frame(pathway.name="Unknown",log.fold.change=0,FDR=0,Cluster=i))
}
}
rownames(results.clust.id) <- NULL
@@ -554,9 +559,10 @@ scQuSAGE <- function(sc10x,gs,res.use=0.1,ds=25000,nm="Lin",folder="lin"){
qs <- get(paste0("results.",i))
if (max(qs$path.mean)>max.x.rg){
max.x.rg <- max(qs$path.mean)
- if (min(qs$path.mean)<min.x.rg){
- min.x.rg <- min(qs$path.mean)
- }}
+ }
+ if (min(qs$path.mean)<min.x.rg){
+ min.x.rg <- min(qs$path.mean)
+ }
if (max(qs$path.PDF)>max.y.rg){
max.y.rg <- max(qs$path.PDF)
}}
@@ -601,7 +607,7 @@ scQuSAGE <- function(sc10x,gs,res.use=0.1,ds=25000,nm="Lin",folder="lin"){
merge.cluster <- c(merge.cluster,"Unknown")
}}
sc10x@ident <- plyr::mapvalues(x=sc10x@ident,from=1:number.clusters,to=merge.cluster)
- sc10x@ident <- factor(sc10x@ident,levels=names(gs))
+ sc10x@ident <- factor(sc10x@ident,levels=c(names(gs),"Unknown"))
sc10x <- StashIdent(object=sc10x,save.name=nm)
postscript(paste0("./analysis/tSNE/",folder,"/tSNE_",nm,".eps"))
@@ -638,14 +644,20 @@ scQuSAGEsm <- function(sc10x,gs,ds=25000,nm="Lin",folder="lin"){
clusters <- unique(sc10x@ident)
labels <- as.vector(factor(sc10x@ident))
- if ((ncol(sc10x@data)>ds & ds!=0)){
- rnd <- sample(1:ncol(sc10x@data),ds)
- data <- sc10x@data[,rnd]
- labels <- labels[rnd]
- } else {
- data <- sc10x@data
+
+ cell.sample <- NULL
+ for (i in clusters){
+ cell <- names(sc10x@ident[sc10x@ident==i])
+ if (length(cell)>ds & ds!=0){
+ rnd <- sample(1:length(cell),ds)
+ cell <- cell[rnd]
+ }
+ cell.sample <- c(cell.sample,cell)
}
+ data <- sc10x@data[,colnames(sc10x@data) %in% cell.sample]
data <- as.data.frame(as.matrix(data))
+ labels <- labels[colnames(sc10x@data) %in% cell.sample]
+
#Make labels for QuSAGE
clust <- list()
@@ -683,9 +695,10 @@ scQuSAGEsm <- function(sc10x,gs,ds=25000,nm="Lin",folder="lin"){
qs <- get(paste0("results.",i))
if (max(qs$path.mean)>max.x.rg){
max.x.rg <- max(qs$path.mean)
- if (min(qs$path.mean)<min.x.rg){
- min.x.rg <- min(qs$path.mean)
- }}
+ }
+ if (min(qs$path.mean)<min.x.rg){
+ min.x.rg <- min(qs$path.mean)
+ }
if (max(qs$path.PDF)>max.y.rg){
max.y.rg <- max(qs$path.PDF)
}}
@@ -744,14 +757,19 @@ scQuSAGElg <- function(sc10x,gs,ds=25000,nm="Lin",folder="lin"){
clusters <- unique(sc10x@ident)
labels <- as.vector(factor(sc10x@ident))
- if ((ncol(sc10x@data)>ds & ds!=0)){
- rnd <- sample(1:ncol(sc10x@data),ds)
- data <- sc10x@data[,rnd]
- labels <- labels[rnd]
- } else {
- data <- sc10x@data
+
+ cell.sample <- NULL
+ for (i in clusters){
+ cell <- names(sc10x@ident[sc10x@ident==i])
+ if (length(cell)>ds & ds!=0){
+ rnd <- sample(1:length(cell),ds)
+ cell <- cell[rnd]
+ }
+ cell.sample <- c(cell.sample,cell)
}
+ data <- sc10x@data[,colnames(sc10x@data) %in% cell.sample]
data <- as.data.frame(as.matrix(data))
+ labels <- labels[colnames(sc10x@data) %in% cell.sample]
#Make labels for QuSAGE
clust <- list()
@@ -1071,41 +1089,17 @@ scCCA <- function(sc10x.1,sc10x.2,nm.1="D17",nm.2="D27",cc=FALSE){
}
-sc3CCA <- function(sc10x.1,sc10x.2,sc10x.3,nm.1="D17",nm.2="D27",nm.3="D35",cc=FALSE,cca=25,acca=15){
- gc()
- if (cc==TRUE){
- sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
- } else {
- sc10x.1 <- ScaleData(object=sc10x.1,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45)
- }
- gc()
-
- gc()
- if (cc==TRUE){
- sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
- } else {
- sc10x.2 <- ScaleData(object=sc10x.2,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45)
- }
- gc()
-
- gc()
- if (cc==TRUE){
- sc10x.3 <- ScaleData(object=sc10x.3,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
- } else {
- sc10x.3 <- ScaleData(object=sc10x.3,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45)
- }
- gc()
-
- sc10x.1 <- FindVariableGenes(sc10x.1,do.plot=FALSE)
- sc10x.2 <- FindVariableGenes(sc10x.2,do.plot=FALSE)
- sc10x.3 <- FindVariableGenes(sc10x.3,do.plot=FALSE)
- genes.hvg.1 <- head(rownames(sc10x.1@hvg.info),2000)
- genes.hvg.2 <- head(rownames(sc10x.2@hvg.info),2000)
- genes.hvg.3 <- head(rownames(sc10x.3@hvg.info),2000)
+sc3CCA <- function(sc10x.1,sc10x.2,sc10x.3,nm.1="D17",nm.2="D27",nm.3="D35",cc=FALSE,cca=25,acca=15,lx=0.15,hx=3.5,ly=0.75){
+ sc10x.1 <- FindVariableGenes(object=sc10x.1,mean.function=ExpMean,dispersion.function=LogVMR,x.low.cutoff=lx,x.high.cutoff=hx,y.cutoff=ly,do.plot=FALSE)
+ sc10x.2 <- FindVariableGenes(object=sc10x.2,mean.function=ExpMean,dispersion.function=LogVMR,x.low.cutoff=lx,x.high.cutoff=hx,y.cutoff=ly,do.plot=FALSE)
+ sc10x.3 <- FindVariableGenes(object=sc10x.3,mean.function=ExpMean,dispersion.function=LogVMR,x.low.cutoff=lx,x.high.cutoff=hx,y.cutoff=ly,do.plot=FALSE)
+ genes.hvg.1 <- sc10x.1@var.genes
+ genes.hvg.2 <- sc10x.2@var.genes
+ genes.hvg.3 <- sc10x.3@var.genes
genes.hvg.Comb <- unique(c(genes.hvg.1,genes.hvg.2,genes.hvg.3))
- genes.hvg.Comb <- intersect(genes.hvg.Comb,rownames(sc10x.1@scale.data))
- genes.hvg.Comb <- intersect(genes.hvg.Comb,rownames(sc10x.2@scale.data))
- genes.hvg.Comb <- intersect(genes.hvg.Comb,rownames(sc10x.3@scale.data))
+ genes.hvg.Comb <- intersect(genes.hvg.Comb,rownames(sc10x.1@data))
+ genes.hvg.Comb <- intersect(genes.hvg.Comb,rownames(sc10x.2@data))
+ genes.hvg.Comb <- intersect(genes.hvg.Comb,rownames(sc10x.3@data))
sc10x.1@meta.data$patient <- nm.1
sc10x.2@meta.data$patient <- nm.2
@@ -1161,10 +1155,14 @@ sc3CCA <- function(sc10x.1,sc10x.2,sc10x.3,nm.1="D17",nm.2="D27",nm.3="D35",cc=
sctSNECustCol <- function(sc10x,i,bl,rd,file){
sc10x <- SetAllIdent(object=sc10x,id=i)
- sc10x@ident <- factor(sc10x@ident,levels=c(bl,rd))
+ sc10x@ident <- factor(sc10x@ident,levels=c(bl,rd,"Unknown"))
postscript(paste0("./analysis/diy/tSNE_",file,".",i,".CustCol.eps"))
if (length(bl)==1 & length(rd)==1){
- plot <- TSNEPlot(object=sc10x,pt.size=2.5,do.label=FALSE,label.size=10,do.return=TRUE,vector.friendly=FALSE,colors.use=c(brewer.pal(5,"Blues")[5],brewer.pal(5,"Reds")[5]))
+ if (length(sc10x@ident[sc10x@ident=="Unknown"])>0){
+ plot <- TSNEPlot(object=sc10x,pt.size=2.5,do.label=FALSE,label.size=10,do.return=TRUE,vector.friendly=FALSE,colors.use=c(brewer.pal(5,"Blues")[5],brewer.pal(5,"Reds")[5],"grey50"))
+ } else {
+ plot <- TSNEPlot(object=sc10x,pt.size=2.5,do.label=FALSE,label.size=10,do.return=TRUE,vector.friendly=FALSE,colors.use=c(brewer.pal(5,"Blues")[5],brewer.pal(5,"Reds")[5]))
+ }
plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
plot(plot)
@@ -1183,6 +1181,7 @@ sctSNECustCol <- function(sc10x,i,bl,rd,file){
sctSNEbwCol <- function(sc10x,i,file,files){
sc10x <- SetAllIdent(object=sc10x,id=i)
+ sc10x@ident <- factor(sc10x@ident,levels=c("Epi","BE","LE","OE1","OE_SCGB","OE2","OE_KRT13","St","Fib","SM","Endo","Leu","Unknown",1:50))
postscript(paste0("./analysis/diy/tSNE_",files,".",file,"_",i,".bwCol.eps"))
plot <- TSNEPlot(object=sc10x,pt.size=2.5,do.label=FALSE,label.size=10,do.return=TRUE,vector.friendly=FALSE,colors.use=colorRampPalette(c("white","black"))(length(unique(sc10x@ident))+2)[3:(length(unique(sc10x@ident))+2)])
plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
@@ -1238,10 +1237,10 @@ scPseudotime <- function(sc10x,i,ds){
scMonocle <- reduceDimension(scMonocle,method='DDRTree')
scMonocle <- orderCells(scMonocle)
postscript(paste0("./analysis/pseudotime/Trajectory.State.eps"),paper="special",width=10,height=10,horizontal=FALSE)
- plot_cell_trajectory(scMonocle,color_by="State")
+ plot(plot_cell_trajectory(scMonocle,color_by="State"))
dev.off()
postscript(paste0("./analysis/pseudotime/Trajectory.",i,".eps"),paper="special",width=10,height=10,horizontal=FALSE)
- plot_cell_trajectory(scMonocle,color_by=i)
+ plot(plot_cell_trajectory(scMonocle,color_by=i))
dev.off()
my_pseudotime_de <- differentialGeneTest(scMonocle,fullModelFormulaStr = "~sm.ns(Pseudotime)",cores=50)
@@ -1249,17 +1248,17 @@ scPseudotime <- function(sc10x,i,ds){
my_pseudotime_gene <- my_pseudotime_gene$gene_short_name
my_pseudotime_gene <- as.character(my_pseudotime_gene)
postscript(paste0("./analysis/pseudotime/Genes.State.eps"),paper="special",width=10,height=10,horizontal=FALSE)
- plot_genes_branched_pseudotime(scMonocle[my_pseudotime_gene,],color_by="State")
+ plot(plot_genes_branched_pseudotime(scMonocle[my_pseudotime_gene,],color_by="State"))
dev.off()
postscript(paste0("./analysis/pseudotime/Genes.",i,".eps"),paper="special",width=10,height=10,horizontal=FALSE)
- plot_genes_branched_pseudotime(scMonocle[my_pseudotime_gene,],color_by=i)
+ plot(plot_genes_branched_pseudotime(scMonocle[my_pseudotime_gene,],color_by=i))
dev.off()
my_pseudotime_de %>% arrange(qval) %>% head(50) %>% select(gene_short_name) -> gene_to_cluster
gene_to_cluster <- gene_to_cluster$gene_short_name
postscript(paste0("./analysis/pseudotime/Heatmap.eps"),paper="special",width=10,height=10,horizontal=FALSE)
- my_pseudotime_cluster <- plot_pseudotime_heatmap(scMonocle[gene_to_cluster,],show_rownames=TRUE,return_heatmap=TRUE)
+ my_pseudotime_cluster <- plot_pseudotime_heatmap(scMonocle[gene_to_cluster,],show_rownames=TRUE,return_heatmap=TRUE)
dev.off()
#BEAM_res <- BEAM(scMonocle,branch_point=1,cores=50)
diff --git a/r.scripts/sc-TissueMapper_RUN.D17_FACS.R b/r.scripts/sc-TissueMapper_RUN.D17_FACS.R
new file mode 100644
index 0000000000000000000000000000000000000000..7812cd1180f5bd6ac6604f8cd4d15fd8bdae8992
--- /dev/null
+++ b/r.scripts/sc-TissueMapper_RUN.D17_FACS.R
@@ -0,0 +1,357 @@
+gc()
+library(methods)
+library(optparse)
+library(Seurat)
+library(readr)
+library(fBasics)
+library(pastecs)
+library(qusage)
+library(RColorBrewer)
+library(monocle)
+library(dplyr)
+library(viridis)
+
+source("../r.scripts/sc-TissueMapper.R")
+
+#Create folder structure
+setwd("../")
+if (!dir.exists("./analysis")){
+ dir.create("./analysis")
+}
+if (!dir.exists("./analysis/qc")){
+ dir.create("./analysis/qc")
+}
+if (!dir.exists("./analysis/qc/cc")){
+ dir.create("./analysis/qc/cc")
+}
+if (!dir.exists("./analysis/tSNE")){
+ dir.create("./analysis/tSNE")
+}
+if (!dir.exists("./analysis/tSNE/pre.stress")){
+ dir.create("./analysis/tSNE/pre.stress")
+}
+if (!dir.exists("./analysis/pca")){
+ dir.create("./analysis/pca")
+}
+if (!dir.exists("./analysis/pca/stress")){
+ dir.create("./analysis/pca/stress")
+}
+if (!dir.exists("./analysis/violin")){
+ dir.create("./analysis/violin")
+}
+if (!dir.exists("./analysis/violin/stress")){
+ dir.create("./analysis/violin/stress")
+}
+if (!dir.exists("./analysis/table")){
+ dir.create("./analysis/table")
+}
+if (!dir.exists("./analysis/tSNE/post.stress")){
+ dir.create("./analysis/tSNE/post.stress")
+}
+if (!dir.exists("./analysis/cor")){
+ dir.create("./analysis/cor")
+}
+if (!dir.exists("./analysis/tSNE/lin")){
+ dir.create("./analysis/tSNE/lin")
+}
+if (!dir.exists("./analysis/tSNE/epi")){
+ dir.create("./analysis/tSNE/epi")
+}
+if (!dir.exists("./analysis/tSNE/st")){
+ dir.create("./analysis/tSNE/st")
+}
+if (!dir.exists("./analysis/tSNE/merge")){
+ dir.create("./analysis/tSNE/merge")
+}
+if (!dir.exists("./analysis/pca/ne")){
+ dir.create("./analysis/pca/ne")
+}
+if (!dir.exists("./analysis/tSNE/ne")){
+ dir.create("./analysis/tSNE/ne")
+}
+if (!dir.exists("./analysis/violin/ne")){
+ dir.create("./analysis/violin/ne")
+}
+if (!dir.exists("./analysis/tSNE/FINAL")){
+ dir.create("./analysis/tSNE/FINAL")
+}
+if (!dir.exists("./analysis/deg")){
+ dir.create("./analysis/deg")
+}
+if (!dir.exists("./analysis/cca")){
+ dir.create("./analysis/cca")
+}
+if (!dir.exists("./analysis/diy")){
+ dir.create("./analysis/diy")
+}
+if (!dir.exists("./analysis/pseudotime")){
+ dir.create("./analysis/pseudotime")
+}
+
+#Retrieve command-line options
+option_list=list(
+ make_option("--p",action="store",default="DPrF",type='character',help="Project Name"),
+ make_option("--g",action="store",default="ALL",type='character',help="Group To analyze"),
+ make_option("--lg",action="store",default=500,type='integer',help="Threshold for cells with minimum genes"),
+ make_option("--hg",action="store",default=3000,type='integer',help="Threshold for cells with maximum genes"),
+ make_option("--lm",action="store",default=0,type='numeric',help="Threshold for cells with minimum %mito genes"),
+ make_option("--hm",action="store",default=0.1,type='numeric',help="Threshold for cells with maximum %mito genes"),
+ make_option("--lx",action="store",default=0.2,type='numeric',help="x low threshold for hvg selection"),
+ make_option("--hx",action="store",default=5,type='numeric',help="x high threshold for hvg selection"),
+ make_option("--ly",action="store",default=1,type='numeric',help="y low threshold for hvg selection"),
+ make_option("--cc",action="store",default=TRUE,type='logical',help="Scale cell cycle?"),
+ make_option("--cca",action="store",default=50,type='integer',help="Number of CCAs to cacluate"),
+ make_option("--acca",action="store",default=30,type='integer',help="Number of CCAs to align"),
+ make_option("--pc",action="store",default=50,type='integer',help="Number of PCs to cacluate"),
+ make_option("--res.prestress",action="store",default=1,type='numeric',help="Resolution to cluster, pre-stress"),
+ make_option("--st",action="store",default=TRUE,type='logical',help="Remove stressed cells?"),
+ make_option("--stg",action="store",default="dws",type='character',help="Geneset to use for stress ID"),
+ make_option("--cut.stress",action="store",default=0.9,type='numeric',help="Cutoff for stress score"),
+ make_option("--res.poststress",action="store",default=0.5,type='numeric',help="Resolution to cluster, post-stress"),
+ make_option("--cut.ne",action="store",default=0.999,type='numeric',help="Cutoff for NE score")
+)
+opt=parse_args(OptionParser(option_list=option_list))
+rm(option_list)
+if (opt$lm==0){opt$lm=-Inf}
+
+sc10x <- scLoad("D17_FACS")
+
+if (opt$cc==TRUE){
+ results <- scCellCycle(sc10x)
+ sc10x <- results[[1]]
+ genes.s <- results[[2]]
+ genes.g2m <- results[[3]]
+ rm(results)
+} else {
+ genes.s=""
+ genes.g2m=""
+}
+
+results <- scQC(sc10x,lg=opt$lg,hg=opt$hg,lm=opt$lm,hm=opt$hm)
+sc10x <- results[[1]]
+counts.cell.raw <- results[[2]]
+counts.gene.raw <- results[[3]]
+counts.cell.filtered <- results[[4]]
+counts.gene.filtered <- results[[5]]
+rm(results)
+
+gc()
+if (opt$cc==TRUE){
+ sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
+} else {
+ sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45)
+}
+gc()
+
+results <- scPC(sc10x,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=50,hpc=0.85,file="pre.stress",cca=FALSE)
+sc10x <- results[[1]]
+genes.hvg.prestress <- results[[2]]
+pc.use.prestress <- results[[3]]
+rm(results)
+
+sc10x <- scCluster(sc10x,pc.use=pc.use.prestress,res.use=opt$res.prestress,folder="pre.stress",red="pca")
+
+if (opt$st==TRUE){
+ results <- scStress(sc10x,stg=opt$stg,res.use=opt$res.prestress,cut=opt$cut.stress)
+ sc10x <- results[[1]]
+ counts.cell.filtered.stress <- results[[2]]
+ sc10x.Stress <- results[[3]]
+ rm(results)
+
+ results <- scPC(sc10x,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=50,hpc=0.85,file="post.stress",cca=FALSE)
+ sc10x <- results[[1]]
+ genes.hvg.poststress <- results[[2]]
+ pc.use.poststress <- results[[3]]
+ rm(results)
+
+ sc10x <- scCluster(sc10x,pc.use=pc.use.poststress,res.use=0.5,folder="post.stress",red="pca")
+}
+
+gene.set1 <- read_delim("./genesets/genes.deg.Epi.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "Epi"
+gene.set <- c(gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.St.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "St"
+gene.set <- c(gene.set,gene.set1)
+rm(gene.set1)
+gc()
+min.all <- min(table(sc10x@meta.data[,paste0("res",opt$res.poststress)]))
+results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=min.all,nm="Lin",folder="lin")
+sc10x <- results[[1]]
+results.cor.Lin <- results[[2]]
+results.clust.Lin.id <- results[[3]]
+rm(results)
+rm(gene.set)
+
+sc10x <- SetAllIdent(object=sc10x,id="Lin")
+sc10x.Epi <- scSubset(sc10x,i="Lin",g="Epi")
+if (any(levels(sc10x@ident)=="Unknown")){
+ sc10x.St <- scSubset(sc10x,i="Lin",g=c("St","Unknown"))
+} else {
+ sc10x.St <- scSubset(sc10x,i="Lin",g="St")
+}
+sc10x.Epi <- SetAllIdent(object=sc10x.Epi,id=paste0("res",opt$res.poststress))
+sc10x.Epi <- BuildClusterTree(sc10x.Epi,do.reorder=TRUE,reorder.numeric=TRUE,do.plot=FALSE)
+sc10x.Epi <- StashIdent(object=sc10x.Epi,save.name=paste0("res",opt$res.poststress))
+sc10x.St <- SetAllIdent(object=sc10x.St,id=paste0("res",opt$res.poststress))
+sc10x.St <- BuildClusterTree(sc10x.St,do.reorder=TRUE,reorder.numeric=TRUE,do.plot=FALSE)
+sc10x.St <- StashIdent(object=sc10x.St,save.name=paste0("res",opt$res.poststress))
+
+sc10x.Epi <- RunTSNE(object=sc10x.Epi,reduction.use="pca",dims.use=1:pc.use.poststress,do.fast=TRUE)
+postscript(paste0("./analysis/tSNE/epi/tSNE_Sample.eps"))
+plot <- TSNEPlot(object=sc10x.Epi,group.by="samples",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+postscript(paste0("./analysis/tSNE/epi/tSNE_res",opt$res.poststress,".eps"))
+plot <- TSNEPlot(object=sc10x.Epi,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+rm(plot)
+
+sc10x.St <- RunTSNE(object=sc10x.St,reduction.use="pca",dims.use=1:pc.use.poststress,do.fast=TRUE)
+postscript(paste0("./analysis/tSNE/st/tSNE_Sample.eps"))
+plot <- TSNEPlot(object=sc10x.St,group.by="samples",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+postscript(paste0("./analysis/tSNE/st/tSNE_res",opt$res.poststress,".eps"))
+plot <- TSNEPlot(object=sc10x.St,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+rm(plot)
+
+gene.set1 <- read_delim("./genesets/genes.deg.BE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "BE"
+gene.set <- c(gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.LE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "LE"
+gene.set <- c(gene.set,gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.OE1.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "OE_SCGB"
+gene.set <- c(gene.set,gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.OE2.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "OE_KRT13"
+gene.set <- c(gene.set,gene.set1)
+rm(gene.set1)
+gc()
+min.epi <- min(table(sc10x.Epi@meta.data[,paste0("res",opt$res.poststress)]))
+results <- scQuSAGE(sc10x.Epi,gs=gene.set,res.use=opt$res.poststress,ds=min.epi,nm="Epi.dws.sc",folder="epi")
+sc10x.Epi <- results[[1]]
+results.cor.Epi.dws <- results[[2]]
+results.clust.Epi.dws.id <- results[[3]]
+rm(results)
+rm(gene.set)
+
+gene.set1 <- read_delim("./genesets/genes.deg.Endo.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "Endo"
+gene.set <- c(gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.SM.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "SM"
+gene.set <- c(gene.set,gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.Fib.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "Fib"
+gene.set <- c(gene.set,gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.Leu.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "Leu"
+gene.set <- c(gene.set,gene.set1)
+rm(gene.set1)
+gc()
+min.st <- min(table(sc10x.St@meta.data[,paste0("res",opt$res.poststress)]))
+results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=opt$res.poststress,ds=min.st,nm="St.dws.sc",folder="st")
+sc10x.St <- results[[1]]
+results.cor.St.go <- results[[2]]
+results.clust.St.go.id <- results[[3]]
+rm(results)
+rm(gene.set)
+
+sc10x.Epi.NE <- scNE(sc10x.Epi,neg="dws",cut=opt$cut.ne)
+
+sc10x <- scMerge(sc10x,sc10x.Epi,sc10x.St,i.1="Epi.dws.sc",i.2="St.dws.sc",nm="Merge_Epi.dws.sc_St.dws.sc")
+
+sc10x <- scMerge(sc10x,sc10x,sc10x.Epi.NE,i.1="Merge_Epi.dws.sc_St.dws.sc",i.2="NE",nm="Merge_Epi.dws.sc_St.dws.sc_NE")
+
+sc10x.Epi <- scMerge(sc10x.Epi,sc10x.Epi,sc10x.Epi.NE,i.1="Epi.dws.sc",i.2="NE",nm="Epi.dws.sc_NE")
+
+sc10x <- SetAllIdent(object=sc10x,id="Merge_Epi.dws.sc_St.dws.sc")
+sc10x@ident <- factor(sc10x@ident,levels=c("BE","LE","OE_SCGB","OE_KRT13","Fib","SM","Endo","Leu"))
+postscript("./analysis/tSNE/FINAL/tSNE_FINAL.eps")
+plot <- TSNEPlot(object=sc10x,pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+
+scTables(sc10x,i.1="samples",i.2="Merge_Epi.dws.sc_St.dws.sc")
+scTables(sc10x,i.1="samples",i.2="Merge_Epi.dws.sc_St.dws.sc_NE")
+scTables(sc10x,i.1="Merge_Epi.dws.sc_St.dws.sc_NE",i.2="Merge_Epi.dws.sc_St.dws.sc")
+
+sctSNECustCol(sc10x,i="Lin",bl="Epi",rd="St",file="D17")
+sctSNECustCol(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",bl=c("BE","LE","OE_SCGB","OE_KRT13"),rd=c("Fib","SM","Endo","Leu"),file="D17")
+sctSNECustCol(sc10x.Epi,i="Epi.dws.sc",bl=c("BE","LE","OE_SCGB","OE_KRT13"),rd="",file="D17")
+sctSNECustCol(sc10x.St,i="St.dws.sc",bl="",rd=c("Fib","SM","Endo","Leu"),file="D17")
+
+sctSNEbwCol(sc10x,i=paste0("res",opt$res.poststress),file="ALL",files="D17")
+sctSNEbwCol(sc10x.Epi,i=paste0("res",opt$res.poststress),file="Epi",files="D17")
+sctSNEbwCol(sc10x.St,i=paste0("res",opt$res.poststress),file="St",files="D17")
+sctSNEbwCol(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",file="ALL",files="D17")
+sctSNEbwCol(sc10x.Epi,i="Epi.dws.sc",file="Epi",files="D17")
+sctSNEbwCol(sc10x.St,i="St.dws.sc",file="St",files="D17")
+
+for (g in c("Epi","St","Unknown")){
+ sctSNEHighlight(sc10x,i="Lin",g=g,file="D17")
+}
+for (g in c("BE","LE","OE_SCGB","OE_KRT13")){
+ sctSNEHighlight(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",g=g,file="D17")
+ sctSNEHighlight(sc10x.Epi,i="Epi.dws.c",g=g,file="D17")
+}
+sctSNEHighlight(sc10x.Epi.NE,i="NE",g="NE",file="D17")
+for (g in c("Fib","SM","Endo","Leu")){
+ sctSNEHighlight(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",g=g,file="D17")
+ sctSNEHighlight(sc10x.St,i="St.dws.sc",g=g,file="D17")
+}
+for (g in c("D17PrPzF_BE","D17PrPzF_LE","D17PrPzF_OE","D17PrPzF_FMSt")){
+ sctSNEHighlight(sc10x,i="samples",g=g,file="D17")
+}
+rm(i)
+rm(g)
+
+postscript(paste0("./analysis/diy/Feature.eps"))
+FeaturePlot(sc10x,features.plot=c("PECAM1","CD200","PDPN","EPCAM","DPP4","PSCA","VIM","KRT5","KLK3"),cols.use=c("grey","darkred"),reduction.use="tsne")
+dev.off()
+
+save(list=ls(pattern="sc10x.Stress"),file="./analysis/sc10x.Stress.Rda")
+rm(list=ls(pattern="sc10x.Stress"))
+save(list=ls(pattern="sc10x.Epi"),file="./analysis/sc10x.Epi.Rda")
+rm(list=ls(pattern="^sc10x.Epi"))
+save(list=ls(pattern="sc10x.St"),file="./analysis/sc10x.St.Rda")
+rm(list=ls(pattern="sc10x.St"))
+save(list=ls(pattern="^sc10x"),file="./analysis/sc10x.Rda")
+rm(list=ls(pattern="^sc10x"))
+save.image(file="./analysis/Data.RData")
diff --git a/r.scripts/sc-TissueMapper_RUN.D27_FACS.R b/r.scripts/sc-TissueMapper_RUN.D27_FACS.R
new file mode 100644
index 0000000000000000000000000000000000000000..61cadc9c0da54b927d49f81fb35f9f76986d82e8
--- /dev/null
+++ b/r.scripts/sc-TissueMapper_RUN.D27_FACS.R
@@ -0,0 +1,362 @@
+gc()
+library(methods)
+library(optparse)
+library(Seurat)
+library(readr)
+library(fBasics)
+library(pastecs)
+library(qusage)
+library(RColorBrewer)
+library(monocle)
+library(dplyr)
+library(viridis)
+
+source("../r.scripts/sc-TissueMapper.R")
+
+#Create folder structure
+setwd("../")
+if (!dir.exists("./analysis")){
+ dir.create("./analysis")
+}
+if (!dir.exists("./analysis/qc")){
+ dir.create("./analysis/qc")
+}
+if (!dir.exists("./analysis/qc/cc")){
+ dir.create("./analysis/qc/cc")
+}
+if (!dir.exists("./analysis/tSNE")){
+ dir.create("./analysis/tSNE")
+}
+if (!dir.exists("./analysis/tSNE/pre.stress")){
+ dir.create("./analysis/tSNE/pre.stress")
+}
+if (!dir.exists("./analysis/pca")){
+ dir.create("./analysis/pca")
+}
+if (!dir.exists("./analysis/pca/stress")){
+ dir.create("./analysis/pca/stress")
+}
+if (!dir.exists("./analysis/violin")){
+ dir.create("./analysis/violin")
+}
+if (!dir.exists("./analysis/violin/stress")){
+ dir.create("./analysis/violin/stress")
+}
+if (!dir.exists("./analysis/table")){
+ dir.create("./analysis/table")
+}
+if (!dir.exists("./analysis/tSNE/post.stress")){
+ dir.create("./analysis/tSNE/post.stress")
+}
+if (!dir.exists("./analysis/cor")){
+ dir.create("./analysis/cor")
+}
+if (!dir.exists("./analysis/tSNE/lin")){
+ dir.create("./analysis/tSNE/lin")
+}
+if (!dir.exists("./analysis/tSNE/epi")){
+ dir.create("./analysis/tSNE/epi")
+}
+if (!dir.exists("./analysis/tSNE/st")){
+ dir.create("./analysis/tSNE/st")
+}
+if (!dir.exists("./analysis/tSNE/merge")){
+ dir.create("./analysis/tSNE/merge")
+}
+if (!dir.exists("./analysis/pca/ne")){
+ dir.create("./analysis/pca/ne")
+}
+if (!dir.exists("./analysis/tSNE/ne")){
+ dir.create("./analysis/tSNE/ne")
+}
+if (!dir.exists("./analysis/violin/ne")){
+ dir.create("./analysis/violin/ne")
+}
+if (!dir.exists("./analysis/tSNE/FINAL")){
+ dir.create("./analysis/tSNE/FINAL")
+}
+if (!dir.exists("./analysis/deg")){
+ dir.create("./analysis/deg")
+}
+if (!dir.exists("./analysis/cca")){
+ dir.create("./analysis/cca")
+}
+if (!dir.exists("./analysis/diy")){
+ dir.create("./analysis/diy")
+}
+if (!dir.exists("./analysis/pseudotime")){
+ dir.create("./analysis/pseudotime")
+}
+
+#Retrieve command-line options
+option_list=list(
+ make_option("--p",action="store",default="DPrF",type='character',help="Project Name"),
+ make_option("--g",action="store",default="ALL",type='character',help="Group To analyze"),
+ make_option("--lg",action="store",default=500,type='integer',help="Threshold for cells with minimum genes"),
+ make_option("--hg",action="store",default=3000,type='integer',help="Threshold for cells with maximum genes"),
+ make_option("--lm",action="store",default=0,type='numeric',help="Threshold for cells with minimum %mito genes"),
+ make_option("--hm",action="store",default=0.1,type='numeric',help="Threshold for cells with maximum %mito genes"),
+ make_option("--lx",action="store",default=0.2,type='numeric',help="x low threshold for hvg selection"),
+ make_option("--hx",action="store",default=5,type='numeric',help="x high threshold for hvg selection"),
+ make_option("--ly",action="store",default=1,type='numeric',help="y low threshold for hvg selection"),
+ make_option("--cc",action="store",default=TRUE,type='logical',help="Scale cell cycle?"),
+ make_option("--cca",action="store",default=50,type='integer',help="Number of CCAs to cacluate"),
+ make_option("--acca",action="store",default=30,type='integer',help="Number of CCAs to align"),
+ make_option("--pc",action="store",default=50,type='integer',help="Number of PCs to cacluate"),
+ make_option("--res.prestress",action="store",default=1,type='numeric',help="Resolution to cluster, pre-stress"),
+ make_option("--st",action="store",default=TRUE,type='logical',help="Remove stressed cells?"),
+ make_option("--stg",action="store",default="dws",type='character',help="Geneset to use for stress ID"),
+ make_option("--cut.stress",action="store",default=0.9,type='numeric',help="Cutoff for stress score"),
+ make_option("--res.poststress",action="store",default=0.5,type='numeric',help="Resolution to cluster, post-stress"),
+ make_option("--cut.ne",action="store",default=0.999,type='numeric',help="Cutoff for NE score")
+)
+opt=parse_args(OptionParser(option_list=option_list))
+rm(option_list)
+if (opt$lm==0){opt$lm=-Inf}
+
+sc10x <- scLoad("D27_FACS")
+
+if (opt$cc==TRUE){
+ results <- scCellCycle(sc10x)
+ sc10x <- results[[1]]
+ genes.s <- results[[2]]
+ genes.g2m <- results[[3]]
+ rm(results)
+} else {
+ genes.s=""
+ genes.g2m=""
+}
+
+results <- scQC(sc10x,lg=opt$lg,hg=opt$hg,lm=opt$lm,hm=opt$hm)
+sc10x <- results[[1]]
+counts.cell.raw <- results[[2]]
+counts.gene.raw <- results[[3]]
+counts.cell.filtered <- results[[4]]
+counts.gene.filtered <- results[[5]]
+rm(results)
+
+gc()
+if (opt$cc==TRUE){
+ sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
+} else {
+ sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45)
+}
+gc()
+
+results <- scPC(sc10x,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=50,hpc=0.85,file="pre.stress",cca=FALSE)
+sc10x <- results[[1]]
+genes.hvg.prestress <- results[[2]]
+pc.use.prestress <- results[[3]]
+rm(results)
+
+sc10x <- scCluster(sc10x,pc.use=pc.use.prestress,res.use=opt$res.prestress,folder="pre.stress",red="pca")
+
+if (opt$st==TRUE){
+ results <- scStress(sc10x,stg=opt$stg,res.use=opt$res.prestress,cut=opt$cut.stress)
+ sc10x <- results[[1]]
+ counts.cell.filtered.stress <- results[[2]]
+ sc10x.Stress <- results[[3]]
+ rm(results)
+
+ results <- scPC(sc10x,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=50,hpc=0.85,file="post.stress",cca=FALSE)
+ sc10x <- results[[1]]
+ genes.hvg.poststress <- results[[2]]
+ pc.use.poststress <- results[[3]]
+ rm(results)
+
+ sc10x <- scCluster(sc10x,pc.use=pc.use.poststress,res.use=0.5,folder="post.stress",red="pca")
+}
+
+gene.set1 <- read_delim("./genesets/genes.deg.Epi.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "Epi"
+gene.set <- c(gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.St.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "St"
+gene.set <- c(gene.set,gene.set1)
+rm(gene.set1)
+gc()
+min.all <- min(table(sc10x@meta.data[,paste0("res",opt$res.poststress)]))
+results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=min.all,nm="Lin",folder="lin")
+sc10x <- results[[1]]
+results.cor.Lin <- results[[2]]
+results.clust.Lin.id <- results[[3]]
+rm(results)
+rm(gene.set)
+
+sc10x <- SetAllIdent(object=sc10x,id="Lin")
+sc10x.Epi <- scSubset(sc10x,i="Lin",g="Epi")
+if (any(levels(sc10x@ident)=="Unknown")){
+ sc10x.St <- scSubset(sc10x,i="Lin",g=c("St","Unknown"))
+} else {
+ sc10x.St <- scSubset(sc10x,i="Lin",g="St")
+}
+sc10x.Epi <- SetAllIdent(object=sc10x.Epi,id=paste0("res",opt$res.poststress))
+sc10x.Epi <- BuildClusterTree(sc10x.Epi,do.reorder=TRUE,reorder.numeric=TRUE,do.plot=FALSE)
+sc10x.Epi <- StashIdent(object=sc10x.Epi,save.name=paste0("res",opt$res.poststress))
+sc10x.St <- SetAllIdent(object=sc10x.St,id=paste0("res",opt$res.poststress))
+sc10x.St <- BuildClusterTree(sc10x.St,do.reorder=TRUE,reorder.numeric=TRUE,do.plot=FALSE)
+sc10x.St <- StashIdent(object=sc10x.St,save.name=paste0("res",opt$res.poststress))
+
+sc10x.Epi <- RunTSNE(object=sc10x.Epi,reduction.use="pca",dims.use=1:pc.use.poststress,do.fast=TRUE)
+postscript(paste0("./analysis/tSNE/epi/tSNE_Sample.eps"))
+plot <- TSNEPlot(object=sc10x.Epi,group.by="samples",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+postscript(paste0("./analysis/tSNE/epi/tSNE_res",opt$res.poststress,".eps"))
+plot <- TSNEPlot(object=sc10x.Epi,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+rm(plot)
+
+sc10x.St <- RunTSNE(object=sc10x.St,reduction.use="pca",dims.use=1:pc.use.poststress,do.fast=TRUE)
+postscript(paste0("./analysis/tSNE/st/tSNE_Sample.eps"))
+plot <- TSNEPlot(object=sc10x.St,group.by="samples",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+postscript(paste0("./analysis/tSNE/st/tSNE_res",opt$res.poststress,".eps"))
+plot <- TSNEPlot(object=sc10x.St,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+rm(plot)
+
+gene.set1 <- read_delim("./genesets/genes.deg.BE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "BE"
+gene.set <- c(gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.LE.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "LE"
+gene.set <- c(gene.set,gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.OE1.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "OE_SCGB"
+gene.set <- c(gene.set,gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.OE2.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "OE_KRT13"
+gene.set <- c(gene.set,gene.set1)
+rm(gene.set1)
+gc()
+min.epi <- min(table(sc10x.Epi@meta.data[,paste0("res",opt$res.poststress)]))
+results <- scQuSAGE(sc10x.Epi,gs=gene.set,res.use=opt$res.poststress,ds=min.epi,nm="Epi.dws.sc",folder="epi")
+sc10x.Epi <- results[[1]]
+results.cor.Epi.dws <- results[[2]]
+results.clust.Epi.dws.id <- results[[3]]
+rm(results)
+rm(gene.set)
+
+gene.set1 <- read_delim("./genesets/genes.deg.Endo.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "Endo"
+gene.set <- c(gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.SM.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "SM"
+gene.set <- c(gene.set,gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.Fib.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "Fib"
+gene.set <- c(gene.set,gene.set1)
+gene.set1 <- read_delim("./genesets/genes.deg.Leu.csv",",",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- gene.set1[1]
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "Leu"
+gene.set <- c(gene.set,gene.set1)
+rm(gene.set1)
+gc()
+min.st <- min(table(sc10x.St@meta.data[,paste0("res",opt$res.poststress)]))
+results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=opt$res.poststress,ds=min.st,nm="St.dws.sc",folder="st")
+sc10x.St <- results[[1]]
+results.cor.St.go <- results[[2]]
+results.clust.St.go.id <- results[[3]]
+rm(results)
+rm(gene.set)
+
+sc10x.Epi.NE <- scNE(sc10x.Epi,neg="dws",cut=opt$cut.ne)
+
+sc10x <- scMerge(sc10x,sc10x.Epi,sc10x.St,i.1="Epi.dws.sc",i.2="St.dws.sc",nm="Merge_Epi.dws.sc_St.dws.sc")
+
+sc10x <- scMerge(sc10x,sc10x,sc10x.Epi.NE,i.1="Merge_Epi.dws.sc_St.dws.sc",i.2="NE",nm="Merge_Epi.dws.sc_St.dws.sc_NE")
+
+sc10x.Epi <- scMerge(sc10x.Epi,sc10x.Epi,sc10x.Epi.NE,i.1="Epi.dws.sc",i.2="NE",nm="Epi.dws.sc_NE")
+
+sc10x <- SetAllIdent(object=sc10x,id="samples")
+sc10x <- SetIdent(object=sc10x,cells.use=names(sc10x@ident[sc10x@ident %in% c("D27PrTzF_StPDPNn","D27PrTzF_StPDPNp")]),ident.use="St")
+sc10x <- StashIdent(object=sc10x,save.name="msamples")
+
+sc10x <- SetAllIdent(object=sc10x,id="Merge_Epi.dws.sc_St.dws.sc")
+sc10x@ident <- factor(sc10x@ident,levels=c("BE","LE","OE_SCGB","OE_KRT13","Fib","SM","Endo","Leu"))
+postscript("./analysis/tSNE/FINAL/tSNE_FINAL.eps")
+plot <- TSNEPlot(object=sc10x,pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+
+scTables(sc10x,i.1="samples",i.2="Merge_Epi.dws.sc_St.dws.sc")
+scTables(sc10x,i.1="samples",i.2="Merge_Epi.dws.sc_St.dws.sc_NE")
+scTables(sc10x,i.1="Merge_Epi.dws.sc_St.dws.sc_NE",i.2="Merge_Epi.dws.sc_St.dws.sc")
+
+sctSNECustCol(sc10x,i="Lin",bl="Epi",rd="St",file="D27")
+sctSNECustCol(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",bl=c("BE","LE","OE_SCGB","OE_KRT13"),rd=c("Fib","SM","Endo","Leu"),file="D27")
+sctSNECustCol(sc10x.Epi,i="Epi.dws.sc",bl=c("BE","LE","OE_SCGB","OE_KRT13"),rd="",file="D27")
+sctSNECustCol(sc10x.St,i="St.dws.sc",bl="",rd=c("Fib","SM","Endo","Leu"),file="D27")
+
+sctSNEbwCol(sc10x,i=paste0("res",opt$res.poststress),file="ALL",files="D27")
+sctSNEbwCol(sc10x.Epi,i=paste0("res",opt$res.poststress),file="Epi",files="D27")
+sctSNEbwCol(sc10x.St,i=paste0("res",opt$res.poststress),file="St",files="D27")
+sctSNEbwCol(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",file="ALL",files="D27")
+sctSNEbwCol(sc10x.Epi,i="Epi.dws.sc",file="Epi",files="D27")
+sctSNEbwCol(sc10x.St,i="St.dws.sc",file="St",files="D27")
+
+for (g in c("Epi","St","Unknown")){
+ sctSNEHighlight(sc10x,i="Lin",g=g,file="D27")
+}
+for (g in c("BE","LE","OE_SCGB","OE_KRT13")){
+ sctSNEHighlight(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",g=g,file="D27")
+ sctSNEHighlight(sc10x.Epi,i="Epi.dws.c",g=g,file="D27")
+}
+sctSNEHighlight(sc10x.Epi.NE,i="NE",g="NE",file="D27")
+for (g in c("Fib","SM","Endo","Leu")){
+ sctSNEHighlight(sc10x,i="Merge_Epi.dws.sc_St.dws.sc",g=g,file="D27")
+ sctSNEHighlight(sc10x.St,i="St.dws.sc",g=g,file="D27")
+}
+for (g in c("D27PrTzF_BE","D27PrTzF_LE","D27PrTzF_OE","D27PrTzF_Edn","D27PrTzF_StPDPNn","D27PrTzF_StPDPNp")){
+ sctSNEHighlight(sc10x,i="samples",g=g,file="D27")
+}
+sctSNEHighlight(sc10x,i="msamples",g=c("St"),file="D27")
+rm(i)
+rm(g)
+
+postscript(paste0("./analysis/diy/Feature.eps"))
+FeaturePlot(sc10x,features.plot=c("PECAM1","CD200","PDPN","EPCAM","DPP4","PSCA","VIM","KRT5","KLK3"),cols.use=c("grey","darkred"),reduction.use="tsne")
+dev.off()
+
+save(list=ls(pattern="sc10x.Stress"),file="./analysis/sc10x.Stress.Rda")
+rm(list=ls(pattern="sc10x.Stress"))
+save(list=ls(pattern="sc10x.Epi"),file="./analysis/sc10x.Epi.Rda")
+rm(list=ls(pattern="^sc10x.Epi"))
+save(list=ls(pattern="sc10x.St"),file="./analysis/sc10x.St.Rda")
+rm(list=ls(pattern="sc10x.St"))
+save(list=ls(pattern="^sc10x"),file="./analysis/sc10x.Rda")
+rm(list=ls(pattern="^sc10x"))
+save.image(file="./analysis/Data.RData")
diff --git a/r.scripts/sc-TissueMapper_RUN.Pd.R b/r.scripts/sc-TissueMapper_RUN.Pd.R
index 295db929e35772d887c229f1db37813f555df44b..2b76a12cf783845896c1e4cf532c3380aea995b6 100644
--- a/r.scripts/sc-TissueMapper_RUN.Pd.R
+++ b/r.scripts/sc-TissueMapper_RUN.Pd.R
@@ -3,7 +3,6 @@ library(methods)
library(optparse)
library(Seurat)
library(readr)
-library(readxl)
library(fBasics)
library(pastecs)
library(qusage)
@@ -94,28 +93,21 @@ option_list=list(
make_option("--p",action="store",default="DPrF",type='character',help="Project Name"),
make_option("--g",action="store",default="ALL",type='character',help="Group To analyze"),
make_option("--lg",action="store",default=500,type='integer',help="Threshold for cells with minimum genes"),
- make_option("--hg",action="store",default=2500,type='integer',help="Threshold for cells with maximum genes"),
+ make_option("--hg",action="store",default=3000,type='integer',help="Threshold for cells with maximum genes"),
make_option("--lm",action="store",default=0,type='numeric',help="Threshold for cells with minimum %mito genes"),
make_option("--hm",action="store",default=0.1,type='numeric',help="Threshold for cells with maximum %mito genes"),
- make_option("--lx",action="store",default=0.0125,type='numeric',help="x low threshold for hvg selection"),
- make_option("--hx",action="store",default=3.5,type='numeric',help="x high threshold for hvg selection"),
- make_option("--ly",action="store",default=0.5,type='numeric',help="y low threshold for hvg selection"),
+ make_option("--lx",action="store",default=0.2,type='numeric',help="x low threshold for hvg selection"),
+ make_option("--hx",action="store",default=5,type='numeric',help="x high threshold for hvg selection"),
+ make_option("--ly",action="store",default=1,type='numeric',help="y low threshold for hvg selection"),
make_option("--cc",action="store",default=TRUE,type='logical',help="Scale cell cycle?"),
make_option("--cca",action="store",default=50,type='integer',help="Number of CCAs to cacluate"),
make_option("--acca",action="store",default=30,type='integer',help="Number of CCAs to align"),
- make_option("--pc",action="store",default=25,type='integer',help="Number of PCs to cacluate"),
- make_option("--hpc",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, pre-stress"),
+ make_option("--pc",action="store",default=50,type='integer',help="Number of PCs to cacluate"),
make_option("--res.prestress",action="store",default=1,type='numeric',help="Resolution to cluster, pre-stress"),
make_option("--st",action="store",default=TRUE,type='logical',help="Remove stressed cells?"),
- make_option("--stg",action="store",default="dws",type='character',help="Geneset to use for stress ID"),
+ make_option("--stg",action="store",default="go",type='character',help="Geneset to use for stress ID"),
make_option("--cut.stress",action="store",default=0.9,type='numeric',help="Cutoff for stress score"),
- #make_option("--hpc.poststress",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, post-stress"),
- make_option("--res.poststress",action="store",default=0.15,type='numeric',help="Resolution to cluster, post-stress"),
- make_option("--ds",action="store",default=10000,type='integer',help="Number of cells to downsample"),
- #make_option("--hpc.epi",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, Epi"),
- make_option("--res.epi",action="store",default=0.15,type='numeric',help="Resolution to cluster, Epi"),
- #make_option("--hpc.st",action="store",default=0.85,type='numeric',help="Max variance cutoff for PCs to use, St"),
- make_option("--res.st",action="store",default=0.15,type='numeric',help="Resolution to cluster, St"),
+ make_option("--res.poststress",action="store",default=0.2,type='numeric',help="Resolution to cluster, post-stress"),
make_option("--cut.ne",action="store",default=0.999,type='numeric',help="Cutoff for NE score")
)
opt=parse_args(OptionParser(option_list=option_list))
@@ -143,64 +135,85 @@ counts.cell.filtered <- results[[4]]
counts.gene.filtered <- results[[5]]
rm(results)
+gc()
+if (opt$cc==TRUE){
+ sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito","S.Score","G2M.Score"),display.progress=FALSE,do.par=TRUE,num.cores=45)
+} else {
+ sc10x <- ScaleData(object=sc10x,vars.to.regress=c("nUMI","percent.mito"),display.progress=FALSE,do.par=TRUE,num.cores=45)
+}
+gc()
+
sc10x.D17 <- scSubset(sc10x,"D17","D17")
sc10x.D27 <- scSubset(sc10x,"D27","D27")
sc10x.D35 <- scSubset(sc10x,"D35","D35")
-results <- sc3CCA(sc10x.D17,sc10x.D27,sc10x.D35,"D17","D27","D35",cc=opt$cc,cca=opt$cca,acca=opt$acca)
+results <- sc3CCA(sc10x.D17,sc10x.D27,sc10x.D35,"D17","D27","D35",cc=opt$cc,cca=opt$cca,acca=opt$acca,lx=opt$lx,hx=opt$hx,ly=opt$ly)
sc10x <- results[[1]]
genes.hvg.cca <- results[[2]]
rm(results)
-#results <- scPC(sc10xlx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=opt$pc,hpc=opt$hpc,file="pre.stress",cca=TRUE)
-#sc10x <- results[[1]]
-#genes.hvg.prestress <- results[[2]]
-#pc.use.prestress <- results[[3]]
-#rm(results)
+rm(sc10x.D17)
+rm(sc10x.D27)
+rm(sc10x.D35)
sc10x <- scCluster(sc10x,pc.use=opt$acca,res.use=opt$res.prestress,folder="pre.stress",red="cca.aligned")
if (opt$st==TRUE){
- results <- scStress(sc10x,stg=opt$stg,res.use=opt$res.prestress,pc.use=pc.use.prestress,cut=opt$cut.stress)
+ results <- scStress(sc10x,stg=opt$stg,res.use=opt$res.prestress,cut=opt$cut.stress)
sc10x <- results[[1]]
counts.cell.filtered.stress <- results[[2]]
sc10x.Stress <- results[[3]]
rm(results)
- #results <- scPC(sc10x,lx=opt$lx,hx=opt$hx,ly=opt$ly,cc=opt$cc,pc=opt$pc,hpc=opt$hpc,file="post.stress",cca=TRUE)
- #sc10x <- results[[1]]
- #genes.hvg.poststress <- results[[2]]
- #pc.use.poststress <- results[[3]]
- #rm(results)
-
sc10x <- scCluster(sc10x,pc.use=opt$acca,res.use=opt$res.poststress,folder="post.stress",red="cca.aligned")
}
-gene.set1 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
-gene.set1 <- as.list(gene.set1)
-names(gene.set1) <- "St"
-gene.set <- c(gene.set1)
gene.set1 <- read_delim("./genesets/DEG_Epi_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
names(gene.set1) <- "Epi"
+gene.set <- c(gene.set1)
+gene.set1 <- read_delim("./genesets/DEG_FMSt_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
+gene.set1 <- as.list(gene.set1)
+names(gene.set1) <- "St"
gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
-results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=opt$ds,nm="Lin",folder="lin")
+min.all <- min(table(sc10x@meta.data[,paste0("res",opt$res.poststress)]))
+results <- scQuSAGE(sc10x,gs=gene.set,res.use=opt$res.poststress,ds=min.all,nm="Lin",folder="lin")
sc10x <- results[[1]]
results.cor.Lin <- results[[2]]
results.clust.Lin.id <- results[[3]]
rm(results)
rm(gene.set)
+sc10x <- SetAllIdent(object=sc10x,id="Lin")
sc10x.Epi <- scSubset(sc10x,i="Lin",g="Epi")
if (any(levels(sc10x@ident)=="Unknown")){
sc10x.St <- scSubset(sc10x,i="Lin",g=c("St","Unknown"))
} else {
sc10x.St <- scSubset(sc10x,i="Lin",g="St")
}
+sc10x.Epi <- SetAllIdent(object=sc10x.Epi,id=paste0("res",opt$res.poststress))
+sc10x.Epi <- BuildClusterTree(sc10x.Epi,do.reorder=TRUE,reorder.numeric=TRUE,do.plot=FALSE)
+sc10x.Epi <- StashIdent(object=sc10x.Epi,save.name=paste0("res",opt$res.poststress))
+sc10x.St <- SetAllIdent(object=sc10x.St,id=paste0("res",opt$res.poststress))
+sc10x.St <- BuildClusterTree(sc10x.St,do.reorder=TRUE,reorder.numeric=TRUE,do.plot=FALSE)
+sc10x.St <- StashIdent(object=sc10x.St,save.name=paste0("res",opt$res.poststress))
-sc10x.Epi <- scCluster(sc10x.Epi,pc.use=opt$acca,res.use=opt$res.epi,folder="epi",red="cca.aligned")
+sc10x.Epi <- RunTSNE(object=sc10x.Epi,reduction.use="cca.aligned",dims.use=1:opt$acca,do.fast=TRUE)
+postscript(paste0("./analysis/tSNE/epi/tSNE_Sample.eps"))
+plot <- TSNEPlot(object=sc10x.Epi,group.by="samples",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+postscript(paste0("./analysis/tSNE/epi/tSNE_res",opt$res.poststress,".eps"))
+plot <- TSNEPlot(object=sc10x.Epi,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+rm(plot)
gene.set1 <- read_delim("./genesets/DEG_BE_5FC.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=FALSE)
gene.set1 <- as.list(gene.set1)
@@ -216,14 +229,15 @@ names(gene.set1) <- "OE"
gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
gc()
-results <- scQuSAGE(sc10x.Epi,gs=gene.set,res.use=0.15,ds=opt$ds,nm="Epi.dws",folder="epi")
+min.epi <- min(table(sc10x.Epi@meta.data[,paste0("res",opt$res.poststress)]))
+results <- scQuSAGE(sc10x.Epi,gs=gene.set,res.use=opt$res.poststress,ds=min.epi,nm="Epi.dws",folder="epi")
sc10x.Epi <- results[[1]]
results.cor.Epi.dws <- results[[2]]
results.clust.Epi.dws.id <- results[[3]]
rm(results)
rm(gene.set)
-sc10x.Epi <- SetAllIdent(object=sc10x.Epi,id=paste0("res",opt$res.epi))
+sc10x.Epi <- SetAllIdent(object=sc10x.Epi,id=paste0("res",opt$res.poststress))
OE <- levels(factor(sc10x.Epi@ident[sc10x.Epi@meta.data$Epi.dws=="OE"]))
OE.cells <- NULL
for (i in 1:length(OE)){
@@ -243,6 +257,7 @@ dev.off()
rm(plot)
rm(OE)
rm(OE.cells)
+rm(i)
gene.set1 <- read_csv("./genesets/Basal cells-signature-genes.csv")
gene.set1 <- gene.set1[,2]
@@ -261,11 +276,68 @@ names(gene.set1) <- "CGC"
gene.set<- c(gene.set,gene.set1)
rm(gene.set1)
gc()
-results.cor.Epi.lgea <- scQuSAGEsm(sc10x.Epi,gs=gene.set,ds=opt$ds,nm="Epi.dws.sub",folder="lgea")
+results.cor.Epi.lgea <- scQuSAGEsm(sc10x.Epi,gs=gene.set,ds=min.epi,nm="Epi.dws.sub",folder="lgea")
rm(gene.set)
+sc10x.St <- RunTSNE(object=sc10x.St,reduction.use="cca.aligned",dims.use=1:opt$acca,do.fast=TRUE)
+postscript(paste0("./analysis/tSNE/st/tSNE_Sample.eps"))
+plot <- TSNEPlot(object=sc10x.St,group.by="samples",pt.size=2.5,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+postscript(paste0("./analysis/tSNE/st/tSNE_res",opt$res.poststress,".eps"))
+plot <- TSNEPlot(object=sc10x.St,pt.size=5,do.label=TRUE,label.size=10,do.return=TRUE,vector.friendly=FALSE)
+plot <- plot+theme(axis.text.x=element_text(size=20),axis.text.y=element_text(size=20),axis.title.x=element_text(size=20),axis.title.y=element_text(size=20),legend.text=element_text(size=20))
+plot <- plot+guides(colour=guide_legend(override.aes=list(size=10)))
+plot(plot)
+dev.off()
+rm(plot)
+
+gene.set1 <- read_delim("./genesets/DEG_C5.BP.M11704.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- as.list(gene.set1[-1,])
+names(gene.set1) <- "Endo"
+gene.set <- c(gene.set1)
+gene.set1 <- read_delim("./genesets/DEG_C5.BP.M10794.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- as.list(gene.set1[-1,])
+names(gene.set1) <- "SM"
+gene.set <- c(gene.set,gene.set1)
+gene.set1 <- read_delim("./genesets/DEG_C5.BP.M13024.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- as.list(gene.set1[-1,])
+names(gene.set1) <- "Fib"
+gene.set <- c(gene.set,gene.set1)
+gene.set1 <- read_delim("./genesets/DEG_C5.BP.M10124.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
+gene.set1 <- as.list(gene.set1[-1,])
+names(gene.set1) <- "Leu"
+gene.set <- c(gene.set,gene.set1)
+rm(gene.set1)
+gc()
+min.st <- min(table(sc10x.Epi@meta.data[,paste0("res",opt$res.poststress)]))
+results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=0.2,ds=min.st,nm="St.go",folder="st")
+sc10x.St <- results[[1]]
+results.cor.St.go <- results[[2]]
+results.clust.St.go.id <- results[[3]]
+rm(results)
+rm(gene.set)
+
+sc10x.Epi.NE <- scNE(sc10x.Epi,neg="EurUro",cut=opt$cut.ne)
+
+sc10x.Epi <- scMergeSubClust(sc10x.Epi,i="Epi.dws.sub",g=c("BE","LE"),nm="Merge")
+
+sc10x.St <- scMergeSubClust(sc10x.St,i="St.go",g=c("Endo","SM","Fib","Leu"),nm="Merge")
+
+sc10x <- scMerge(sc10x,sc10x.Epi,sc10x.St,i.1="Merge",i.2="Merge",nm="Merge_Epi.dws_St.go")
+
+sc10x <- scMerge(sc10x,sc10x,sc10x.Epi.NE,i.1="Merge_Epi.dws_St.go",i.2="NE",nm="Merge_Epi.dws_St.go_NE")
+
+sc10x.Epi <- scMerge(sc10x.Epi,sc10x.Epi,sc10x.Epi.NE,i.1="Epi.dws.sub",i.2="NE",nm="Epi.dws.sub_NE")
+
+sc10x <- SetAllIdent(object=sc10x,id="Lin")
+sc10x <- SetIdent(object=sc10x,cells.use=names(sc10x@ident[sc10x@ident %in% c("St","Unknown")]),ident.use="St")
+sc10x <- StashIdent(object=sc10x,save.name="mLin")
+
gene.orthog <- read.delim("./genesets/Ensemble.mus-hum.txt")
-gene.set1 <- read_excel("./genesets/SupTab3_Consensus_Sigs.xlsx",skip=5)
+gene.set1 <- read_csv("./genesets/SupTab3_Consensus_Sigs.csv",skip=6)
gene.set2 <- as.data.frame(gene.set1$Basal[!is.na(gene.set1$Basal)])
colnames(gene.set2) <- "genes"
gene.set2 <- as.data.frame(merge(gene.set2,gene.orthog,by.x="genes",by.y="Gene.name")[,4])
@@ -303,7 +375,7 @@ gene.set2 <- as.list(gene.set2)
names(gene.set2) <- "Ionocyte"
gene.set <- c(gene.set,gene.set2)
rm(gene.set2)
-gene.set1 <- read_excel("./genesets/SupTab6_Krt13_Hillock.xlsx",skip=5)
+gene.set1 <- read_csv("./genesets/SupTab6_Krt13_Hillock.csv",skip=6)
gene.set1 <- gene.set1[gene.set1$FDR<=0.05 & gene.set1$'log2 fold-change (MAST)'>=1.5,1]
colnames(gene.set1) <- "genes"
gene.set1 <- as.data.frame(merge(gene.set1,gene.orthog,by.x="genes",by.y="Gene.name")[,4])
@@ -313,48 +385,11 @@ gene.set <- c(gene.set,gene.set1)
rm(gene.set1)
rm(gene.orthog)
gene.set <- lapply(gene.set,droplevels)
-results.cor.Epi.MusLungHierarchy <- scQuSAGEsm(sc10x.Epi,gs=gene.set,ds=opt$ds,nm="Epi.dws.sub",folder="MusLungHierarchy")
-rm(gene.set)
-
-sc10x.St <- scCluster(sc10x.St,pc.use=opt$acca,res.use=opt$res.st,folder="st",red="cca.aligned")
-
-gene.set1 <- read_delim("./genesets/DEG_C5.BP.M11704.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- as.list(gene.set1[-1,])
-names(gene.set1) <- "Endo"
-gene.set <- c(gene.set1)
-gene.set1 <- read_delim("./genesets/DEG_C5.BP.M10794.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- as.list(gene.set1[-1,])
-names(gene.set1) <- "SM"
-gene.set <- c(gene.set,gene.set1)
-gene.set1 <- read_delim("./genesets/DEG_C5.BP.M13024.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- as.list(gene.set1[-1,])
-names(gene.set1) <- "Fib"
-gene.set <- c(gene.set,gene.set1)
-gene.set1 <- read_delim("./genesets/DEG_C5.BP.M10124.txt","\t",escape_double=FALSE,trim_ws=TRUE,col_names=TRUE)
-gene.set1 <- as.list(gene.set1[-1,])
-names(gene.set1) <- "Leu"
-gene.set <- c(gene.set,gene.set1)
-rm(gene.set1)
-gc()
-results <- scQuSAGE(sc10x.St,gs=gene.set,res.use=0.15,ds=opt$ds,nm="St.go",folder="st")
-sc10x.St <- results[[1]]
-results.cor.St.go <- results[[2]]
-results.clust.St.go.id <- results[[3]]
-rm(results)
+results.cor.Epi.MusLungHierarchy <- scQuSAGEsm(sc10x.Epi,gs=gene.set,ds=min.epi,nm="Epi.dws.sub_NE",folder="MusLungHierarchy")
rm(gene.set)
-sc10x.Epi.NE <- scNE(sc10x.Epi,neg="EurUro",cut=opt$cut.ne)
-
-sc10x.Epi <- scMergeSubClust(sc10x.Epi,i="Epi.dws.sub",g=c("BE","LE"),nm="Merge")
-
-sc10x.St <- scMergeSubClust(sc10x.St,i="St.go",g=c("Endo","SM","Fib","Leu"),nm="Merge")
-
-sc10x <- scMerge(sc10x,sc10x.Epi,sc10x.St,i.1="Merge",i.2="Merge",nm="Merge_Epi.dws_St.go")
-
-sc10x <- scMerge(sc10x,sc10x,sc10x.Epi.NE,i.1="Merge_Epi.dws_St.go",i.2="NE",nm="Merge_Epi.dws_St.go_NE")
-
gene.set.c2.all <- read.gmt("./genesets/c2.all.v6.1.symbols.gmt")
-results.cor.c2.ALL <- scQuSAGElg(sc10x,gs=gene.set.c2.all,ds=opt$ds,nm="Merge_Epi.dws_St.go",folder="c2.all")
+results.cor.c2.ALL <- scQuSAGElg(sc10x,gs=gene.set.c2.all,ds=min.all,nm="Merge_Epi.dws_St.go",folder="c2.all")
rm(gene.set.c2.all)
sc10x <- SetAllIdent(object=sc10x,id="Merge_Epi.dws_St.go")
@@ -448,6 +483,7 @@ for (i in ls(pattern="^genes.deg")){
}
sctSNECustCol(sc10x,i="Lin",bl="Epi",rd="St",file="D")
+sctSNECustCol(sc10x,i="mLin",bl="Epi",rd="St",file="D")
sctSNECustCol(sc10x,i="Merge_Epi.dws_St.go",bl=c("BE","LE","OE1","OE2"),rd=c("Fib","SM","Endo","Leu"),file="D")
sctSNECustCol(sc10x.Epi,i="Epi.dws.sub",bl=c("BE","LE","OE1","OE2"),rd="",file="D")
sctSNECustCol(sc10x.St,i="St.go",bl="",rd=c("Fib","SM","Endo","Leu"),file="D")
@@ -459,9 +495,10 @@ sctSNEbwCol(sc10x,i="Merge_Epi.dws_St.go",file="ALL",files="D")
sctSNEbwCol(sc10x.Epi,i="Epi.dws.sub",file="Epi",files="D")
sctSNEbwCol(sc10x.St,i="St.go",file="St",files="D")
-for (g in c("Epi","St")){
+for (g in c("Epi","St","Unknown")){
sctSNEHighlight(sc10x,i="Lin",g=g,file="D")
}
+sctSNEHighlight(sc10x,i="mLin",g=c("St"),file="D")
for (g in c("BE","LE","OE1","OE2")){
sctSNEHighlight(sc10x,i="Merge_Epi.dws_St.go",g=g,file="D")
sctSNEHighlight(sc10x.Epi,i="Epi.dws.sub",g=g,file="D")
@@ -476,6 +513,7 @@ for (g in c("D17","D27","D35")){
}
sctSNEHighlight(sc10x,i="Pz",g="Pz",file="D")
sctSNEHighlight(sc10x,i="Tz",g="Tz",file="D")
+rm(i)
rm(g)
scCustHeatmap(sc10x.Epi,i="Epi.dws.sub",gs=c(genes.deg.BE.unique,genes.deg.LE.unique,genes.deg.OE1.unique,genes.deg.OE2.unique),g=c("BE","LE","OE1","OE2"))