Commit 25690b09 authored by Gervaise H. Henry's avatar Gervaise H. Henry 🤠

Merge branch 'develop' into 'master'

Merge develop into master

See merge request sc-TissueMapper_Pr!2
parents 0f46f0cd 8ca3e573
......@@ -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)
......
#!/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
#!/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
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
......
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,,
This diff is collapsed.
"","p_val","avg_logFC","pct.1","pct.2","p_val_adj"
"DST",0,1.85116698511768,0.704,0.243,0
"KRT14",0,1.80428824047279,0.343,0.072,0
"KRT15",0,1.50308322534141,0.773,0.4,0
"CYR61",0,1.35696343675258,0.507,0.206,0
"TAGLN",0,1.33204335317379,0.339,0.086,0
"KRT5",0,1.30816605835336,0.756,0.237,0
"RGCC",0,1.26574870899703,0.534,0.272,0
"CAV1",0,1.23202605189523,0.523,0.131,0
"TIMP3",0,1.2112303712643,0.498,0.183,0
"KRT17",0,1.08143798036746,0.958,0.709,0
"MYC",0,1.0606340744712,0.681,0.322,0
"PHLDA1",0,0.993665431208041,0.649,0.354,0
"S100A2",0,0.993122961615973,0.844,0.579,0
"MYL9",0,0.967070863488437,0.482,0.113,0
"ZFP36L2",0,0.914287122805166,0.692,0.416,0
"PALLD",0,0.897043580599764,0.581,0.253,0
"SERPINF1",0,0.829751044031732,0.342,0.071,0
"HSPA1A",0,0.813115857159925,0.762,0.644,0
"CAV2",0,0.74764879480185,0.547,0.277,0
"MEG3",0,0.743473702955259,0.427,0.124,0
"FHL2",0,0.708667289843018,0.736,0.543,0
"CALD1",3.48077374277518e-297,0.716403475296559,0.482,0.216,7.97549687682077e-293
"EDN1",2.48101591357511e-290,0.947518819849994,0.444,0.201,5.68475176277465e-286
"CLU",4.79943286551763e-288,0.76070898008182,0.575,0.34,1.09969405247605e-283
"HBEGF",4.57124849208229e-252,0.77667024224929,0.548,0.333,1.04741016699081e-247
"HSPA1B",6.65879417959476e-225,0.720007512013583,0.702,0.599,1.52572951037055e-220
"IGFBP2",7.60747902277488e-213,0.695287462978635,0.506,0.326,1.74310166848841e-208
"F3",3.36862783841994e-187,0.712186405961584,0.57,0.409,7.71853696617161e-183
"DEFB1",1.90414473394983e-151,0.77338012556503,0.426,0.274,4.36296682889924e-147
"DKK1",2.06237131334032e-124,1.0809959494317,0.311,0.167,4.72551139025668e-120
"CRYAB",2.82290237400476e-64,0.859327395531967,0.396,0.299,6.4681162095571e-60
"DST",0,1.81727872364378,0.72,0.279,0
"KRT14",0,1.80661115311404,0.364,0.092,0
"KRT15",0,1.42745869762371,0.791,0.453,0
"CYR61",0,1.32029104527785,0.52,0.235,0
"TAGLN",0,1.29224633209788,0.361,0.107,0
"RGCC",0,1.26265400419006,0.549,0.295,0
"KRT5",0,1.24866930427906,0.793,0.274,0
"TIMP3",0,1.23238910939631,0.521,0.205,0
"CAV1",0,1.17499933161214,0.548,0.163,0
"MYC",0,1.07235433849672,0.709,0.352,0
"KRT17",0,1.04365352461911,0.965,0.747,0
"PHLDA1",0,1.03665390322501,0.672,0.364,0
"MYL9",0,0.942251653106022,0.517,0.135,0
"S100A2",0,0.941599789389682,0.878,0.666,0
"PALLD",0,0.917555621348643,0.616,0.283,0
"ZFP36L2",0,0.910932922088037,0.716,0.464,0
"HSPA1A",0,0.862724850863177,0.767,0.665,0
"MEG3",0,0.813360356034023,0.461,0.134,0
"SERPINF1",0,0.800315549779026,0.374,0.096,0
"CLU",0,0.772601189643244,0.618,0.381,0
"FHL2",0,0.762684015113309,0.753,0.563,0
"CAV2",0,0.719852335454528,0.592,0.332,0
"STK17A",0,0.701486572186172,0.667,0.451,0
"CALD1",0,0.69740206160408,0.509,0.245,0
"CSRP1",0,0.69624763307282,0.511,0.261,0
"HBEGF",1.86620346756631e-294,0.804717806059973,0.578,0.36,4.33892306209168e-290
"EDN1",2.91179342061972e-292,0.900546173165856,0.454,0.219,6.76991970294085e-288
"F3",1.05478125285573e-222,0.75116792786021,0.591,0.424,2.45236641288958e-218
"HSPA1B",3.75167349033879e-210,0.713867344731702,0.707,0.631,8.72264086503768e-206
"DEFB1",4.71225000347581e-186,0.848686903097786,0.47,0.316,1.09559812580813e-181
"DKK1",3.60249040468869e-124,1.05782564420798,0.326,0.188,8.37579019090121e-120
"CRYAB",3.56780411383671e-58,0.958711314555255,0.412,0.331,8.29514456467036e-54
This diff is collapsed.
"","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
"DEFB1",0,1.21793929553001,0.391,0.052,0
"EDN1",0,1.20545333899665,0.388,0.049,0
"PHLDA2",0,1.16749998951287,0.78,0.374,0
"CLDN7",0,1.15674806046914,0.477,0.052,0
"S100A16",0,1.09657537591032,0.832,0.359,0
"CLDN1",0,1.08747914067975,0.423,0.057,0
"HBEGF",0,1.08719426210414,0.498,0.172,0
"EHF",0,1.06412944685902,0.498,0.046,0
"SERPINB5",0,1.06125761656886,0.427,0.037,0
"LIMA1",0,1.06050250259071,0.61,0.164,0
"EZR",0,1.05086798241258,0.717,0.248,0
"ANXA2",0,1.02858668096986,0.982,0.816,0
"LAMB3",0,1.01690102884403,0.485,0.054,0
"ACTB",0,1.01481951337827,0.99,0.856,0
"MPZL2",0,1.01463073435289,0.605,0.13,0
"PLAU",0,0.997401291150059,0.521,0.185,0
"ANXA1",0,0.988403350379077,0.843,0.501,0
"CEACAM1",0,0.987709477461549,0.462,0.077,0
"TSTD1",0,0.963988434657716,0.549,0.079,0
"S100A11",0,0.948370328131872,0.988,0.845,0
"SLC14A1",0,0.928826382545563,0.415,0.051,0
"CD9",0,0.928446508700755,0.942,0.572,0
"STK17A",0,0.90725533158024,0.585,0.209,0
"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
"TNFRSF12A",0,0.860586965605445,0.876,0.431,0
"MAST4",0,0.860437490667748,0.636,0.206,0
"ALDH1A3",0,0.858442811276262,0.427,0.103,0
"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
"ANXA11",0,0.70806704116464,0.546,0.187,0
"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
"LCN2",6.86012777899797e-285,1.81070164381097,0.387,0.095,1.5718610780018e-280
"SDC1",3.46966812339611e-283,0.704031385942233,0.316,0.038,7.9500505711375e-279
"LAMC2",6.53450403154877e-283,0.725072009545453,0.387,0.088,1.49725090874877e-278
"FAM110C",2.49755656570217e-280,0.79725608442184,0.298,0.027,5.72265135899337e-276
"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
"LMO7",7.41833306546289e-257,0.749292731646457,0.301,0.04,1.69976265528951e-252
"ID1",4.66741976631916e-255,0.879974872976305,0.455,0.167,1.06944589105671e-250
"GPX2",2.80582778756736e-241,0.801513915439008,0.292,0.042,6.42899320965308e-237
"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
"CLDN4",0,2.33798655274461,0.83,0.229,0
"S100A2",0,2.14736694057859,0.824,0.336,0
"SFN",0,2.14188708633312,0.849,0.126,0
"KRT15",0,2.13730992361203,0.705,0.122,0
"KRT8",0,1.98122977079159,0.878,0.156,0
"SLPI",0,1.97212133924044,0.609,0.126,0
"KRT23",0,1.9475241025607,0.647,0.109,0
"KRT7",0,1.85832624877284,0.762,0.135,0
"WFDC2",0,1.82603184536208,0.706,0.142,0
"AQP3",0,1.75707702047555,0.714,0.138,0
"KLF5",0,1.72630607453798,0.808,0.128,0
"KRT18",0,1.65532949882324,0.889,0.214,0
"FXYD3",0,1.61927290958347,0.793,0.123,0
"DST",0,1.61622963903937,0.608,0.203,0
"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
"SPINT2",0,1.39239631839613,0.792,0.11,0
"AREG",0,1.3786787337354,0.444,0.097,0
"ACTG1",0,1.37293440601088,0.992,0.839,0
"DEFB1",0,1.34503533365797,0.431,0.055,0
"ANXA1",0,1.30604259801877,0.86,0.505,0
"F3",0,1.30192501208712,0.549,0.139,0
"S100A14",0,1.29343286078518,0.589,0.071,0
"FHL2",0,1.26558560397518,0.705,0.222,0
"CLDN7",0,1.23141144972301,0.523,0.056,0
"CXCL17",0,1.21533791862415,0.375,0.051,0
"PHLDA2",0,1.19530647532187,0.808,0.394,0
"GADD45A",0,1.18964097065961,0.83,0.473,0
"EZR",0,1.15296351442262,0.754,0.253,0
"CLDN1",0,1.11410745865298,0.457,0.064,0
"EDN1",0,1.10942157265544,0.394,0.057,0
"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
"LAMB3",0,1.07163577834265,0.532,0.055,0
"HBEGF",0,1.06681378224294,0.522,0.201,0
"LIMA1",0,1.0513260826661,0.647,0.19,0
"ACTB",0,1.05079544839747,0.992,0.9,0
"VAMP8",0,1.02255596752927,0.607,0.073,0
"PLAU",0,1.01992439702576,0.555,0.196,0
"TSTD1",0,1.01749694576366,0.602,0.078,0
"S100A11",0,1.0047767484748,0.991,0.879,0
"ANXA2",0,1.0000025381118,0.987,0.867,0
"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
"GSTP1",0,0.869236837206919,0.935,0.801,0
"IRF6",0,0.857811859218995,0.471,0.038,0
"PRSS22",0,0.855291125992551,0.367,0.028,0
"MAST4",0,0.847336115298592,0.678,0.235,0
"TSPAN1",0,0.832731564261921,0.392,0.04,0
"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