Add in analysis for spikein normalized data.

README.md

@@ -27,6 +27,9 @@ PARP-1 interacting snoRNA and DDX21
 
 ## Analysis of RNA-seq
 - spike_in_correlation.py: Script to look at Spike-in counts to correlation
+- spike_in_correlation.sh: Script to analyze spike-ins
+- RNA-seq.Rmd: RNA-seq of data analysis regardless of spike-ins
+
 
 
 ## General Analysis

RNA-seq_spikein.Rmd

+DDX21 RNA-seq Analsysis Spike-in
+=====================================
+
+## Setup and Imports
+```{r init}
+source("http://bioconductor.org/biocLite.R")
+biocLite("RUVSeq")
+install.packages("stringr")
+install.packages("ggplot2")
+install.packages("VennDiagram")
+install.packages("reshape")
+install.packages("eulerr")
+install.packages("gplots")
+install.packages("multcompView")
+library(eulerr)
+library(RUVSeq)
+library(RColorBrewer)
+library(edgeR)
+library(gplots)
+library(multcompView)
+```
+
+
+## Read in data
+```{r spikein}
+ddx21kd_rep1 <- read.csv("/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/DDX21_1KD-1.counts", header=F, sep='\t',col.names=c("GeneId", "DDX21KD_rep1"))
+ddx21kd_rep2 <- read.csv("/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/DDX21_1KD-2.counts", header=F, sep='\t',col.names=c("GeneId", "DDX21KD_rep2"))
+mut_ddx21_rep1 <- read.csv("/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/DDX21_1KD_pos_Mut_DDX21-1.counts", header=F, sep='\t',col.names=c("GeneId", "MUT_DDX21_rep1"))
+mut_ddx21_rep2 <- read.csv("/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/DDX21_1KD_pos_Mut_DDX21-2.counts", header=F, sep='\t',col.names=c("GeneId", "MUT_DDX21_rep2"))
+wt_ddx21_rep1 <- read.csv("/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/DDX21_1KD_pos_WT_DDX21-1.counts", header=F, sep='\t',col.names=c("GeneId", "WT_DDX21_rep1"))
+wt_ddx21_rep2 <- read.csv("/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/DDX21_1KD_pos_WT_DDX21-2.counts", header=F, sep='\t',col.names=c("GeneId", "WT_DDX21_rep2"))
+ddx21_rep1 <- read.csv("/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/LucKD-1.counts", header=F, sep='\t',col.names=c("GeneId", "DDX21_rep1"))
+ddx21_rep2 <- read.csv("/Volumes/project/GCRB/Lee_Lab/s163035/MCF7_DDX21_inducibile_kd_Daeseok/htseq_counts/LucKD-2.counts", header=F, sep='\t',col.names=c("GeneId", "DDX21_rep2"))
+
+merged_spikein <- Reduce(function(x, y) merge(x, y, all=TRUE),
+                 list(ddx21_rep1, ddx21_rep2, ddx21kd_rep1, ddx21kd_rep2, mut_ddx21_rep1, mut_ddx21_rep2, wt_ddx21_rep1, wt_ddx21_rep2))
+rownames(merged_spikein) <- merged_spikein$GeneId
+merged_spikein_genes <- merged_spikein[grep("__", rownames(merged_spikein),invert = T),!(names(merged_spikein) %in% c('GeneId'))]
+
+mapping <- read.csv("reference_annotations/mapping.txt", header=F, sep=',')
+colnames(mapping) <- c("GeneId", "TranscriptId","GeneName","TranscriptName")
+mapping_tmp <- data.frame(mapping$GeneId,mapping$GeneName)
+mapping_genes <- mapping_tmp[!duplicated(mapping_tmp[,c('mapping.GeneId','mapping.GeneName')]),]
+colnames(mapping_genes) <- c("GeneId", "GeneName")
+rownames(mapping_genes) <- mapping_genes$GeneId
+```
+
+
+# Differential analysis setup
+```{r setup}
+# Filter out of at least 25 reads in at least 2 samples
+filter <- apply(merged_spikein_genes, 1, function(x) length(x[x>25])>=2)
+filtered <- merged_spikein_genes[filter,]
+genes <- rownames(filtered)[grep("ENS", rownames(filtered))]
+spikes <- rownames(filtered)[grep("gSpikein_ERC", rownames(filtered))]
+
+x <- as.factor(rep(c("DDX21", "DDX21KD", "MUT_DDX21", "WT_DDX21"), each=2))
+set <- newSeqExpressionSet(as.matrix(filtered), phenoData = data.frame(x, row.names=colnames(filtered)))
+
+set1 <- RUVg(set, spikes, k=3)
+pData(set1)
+colors <- brewer.pal(4, "Set2")
+plotRLE(set1, outline=FALSE, ylim=c(-1, 1), col=colors[x])
+plotPCA(set1, col=colors[x], cex=1.2)
+```
+
+# Differential Analysis
+```{r diff_analysis}
+design <- model.matrix(~x + W_1, data=pData(set1))
+y <- DGEList(counts=counts(set1), group=x)
+y <- calcNormFactors(y, method="upperquartile")
+y <- estimateGLMCommonDisp(y, design)
+y <- estimateGLMTagwiseDisp(y, design)
+
+fit <- glmFit(y, design)
+
+# Differential Analysis 5% FDR
+
+# Differential Analysis between groups KD and WT
+lrt_kd <- glmLRT(fit, coef=2)
+table_kd <- merge(topTags(lrt_kd, n=Inf)$table,mapping_genes,by="row.names")
+det_kd <- decideTests(lrt_kd)
+table_kd_up <- table_kd[det_kd == 1,]
+table_kd_down <- table_kd[det_kd == -1,]
+table_kd_up_down <- table_kd[det_kd != 0,]
+write.table(table_kd_up, "tables/kd_up_genes_spikein.csv",sep=",", row.names = FALSE)
+write.table(table_kd_down, "tables/kd_down_genes_spikein.csv",sep=",", row.names = FALSE)
+
+
+# Differential Analysis between groups KD and MUT
+lrt_mut <- glmLRT(fit, coef=3)
+table_mut <- merge(topTags(lrt_mut, n=Inf)$table,mapping_genes,by="row.names")
+det_mut  <- decideTests(lrt_mut)
+table_mut_up <- table_mut[det_mut == 1,]
+table_mut_down <- table_mut[det_mut == -1,]
+table_mut_up_down <- table_mut[det_mut != 0,]
+write.table(table_mut_up, "tables/mut_up_genes_spikein.csv",sep=",", row.names = FALSE)
+write.table(table_mut_down, "tables/mut_down_genes_spikein.csv",sep=",", row.names = FALSE)
+
+# Differential Analysis between groups KD and WT rexpression
+lrt_wt <- glmLRT(fit, coef=4)
+table_wt <- merge(topTags(lrt_wt, n=Inf)$table,mapping_genes,by="row.names")
+det_wt  <- decideTests(lrt_wt)
+table_wt_up <- table_wt[det_wt == 1,]
+table_wt_down <- table_wt[det_wt == -1,]
+table_wt_up_down <- table_wt[det_wt != 0,]
+write.table(table_wt_up, "tables/wt_up_genes_spikein.csv",sep=",", row.names = FALSE)
+write.table(table_wt_down, "tables/wt_down_genes_spikein.csv",sep=",", row.names = FALSE)
+
+
+# Expression of genes found to be regulated by knockdown of DDX21
+sample_cpm <- cpm(fit$fitted.values)
+sample_cpm_kd <- sample_cpm[det_kd != 0,]
+sample_cpm_kd_order_fc <- sample_cpm_kd[cluster$order,]
+
+# Expression of DDX21 across replicates
+jpeg('figures/ddx21_expression_cpm.jpg')
+barplot(sample_cpm_kd_order_fc[58,], main="DDX21 Expression", xlab="Sample", ylab="CPM", names.arg=c("LUC 1", "LUC 2", "KD 1", "KD 2", "MUT 1", "MUT 2", "WT 1", "WT 2"),
+col=c("red","red","black", "black", "dimgrey", "dimgrey", "lightgrey", "lightgrey"), ylim=c(0,300),cex.axis=1,las=2,lwd=4)
+dev.off()
+
+# Heat Map Fold Change Affected by KD and not affected for WT
+ddx21_fc <- table_kd[(det_kd != 0 & det_wt == 0),]$logFC
+wt_fc <- table_wt[(det_kd != 0 & det_wt == 0),]$logFC
+mut_fc <- table_mut[(det_kd != 0 & det_wt == 0),]$logFC
+fold_change <- data.frame(rownames(table_kd[(det_kd != 0 & det_wt == 0),]),table_kd[(det_kd != 0 & det_wt == 0),]$GeneId,table_kd[(det_kd != 0 & det_wt == 0),]$GeneName,ddx21_fc,wt_fc,mut_fc)
+fold_change$max <- apply(abs(fold_change[,4:6]),1,max)
+fold_change_max_abs_scale <- fold_change[,1:3]
+fold_change_max_abs_scale$"LUCKD" <- 0
+fold_change_max_abs_scale$"DDX21 KD" <- fold_change$ddx21_fc/fold_change$max
+fold_change_max_abs_scale$"WT" <- fold_change$wt_fc/fold_change$max
+fold_change_max_abs_scale$"MUT"  <- fold_change$mut_fc/fold_change$max
+names(fold_change_max_abs_scale) <- c("GID", "YORF", "NAME", "LUCKD", "DDX21KD", "WT", "MUT")
+d <- dist(fold_change_max_abs_scale[,4:6], method = "euclidean")
+fold_change_max_abs_scale_cluster  <- hclust(d, "ward.D")
+fold_change_max_abs_scale_cluster_sorted <- fold_change_max_abs_scale[fold_change_max_abs_scale_cluster$order,]
+write.table(fold_change_max_abs_scale_cluster_sorted, "figures/DDX21_regulated_genes.cdt", sep="\t", row.names = FALSE)
+
+
+tri.to.squ<-function(x)
+{
+    rn<-row.names(x)
+    cn<-colnames(x)
+    an<-unique(c(cn,rn))
+    myval<-x[!is.na(x)]
+    mymat<-matrix(1,nrow=length(an),ncol=length(an),dimnames=list(an,an))
+    for(ext in 1:length(cn))
+    {
+        for(int in 1:length(rn))
+        {
+            if(is.na(x[row.names(x)==rn[int],colnames(x)==cn[ext]])) next
+            mymat[row.names(mymat)==rn[int],colnames(mymat)==cn[ext]]<-x[row.names(x)==rn[int],colnames(x)==cn[ext]]
+            mymat[row.names(mymat)==cn[ext],colnames(mymat)==rn[int]]<-x[row.names(x)==rn[int],colnames(x)==cn[ext]]
+        }
+
+    }
+    return(mymat)
+}
+
+# Fold change Boxplots
+ddx21_fc_up <- table_kd[(det_kd == 1 & det_wt == 0),]$logFC
+wt_fc_up <- table_wt[(det_kd == 1 & det_wt == 0),]$logFC
+mut_fc_up <- table_mut[(det_kd == 1 & det_wt == 0),]$logFC
+fold_change_up <- data.frame(table_kd[(det_kd == 1 & det_wt == 0),]$GeneId,table_kd[(det_kd == 1 & det_wt == 0),]$GeneName,ddx21_fc_up,wt_fc_up,mut_fc_up)
+colnames(fold_change_up) <- c("GeneID", "NAME", "ddx21_fc", "wt_fc", "mut_fc")
+up_not_recovered <- fold_change_up[which(fold_change_up$mut_fc > .25),]
+up_moderatley_recovered <- fold_change_up[which(fold_change_up$mut_fc < .25),]
+jpeg('figures/boxplot_ddx21_up_regulated_not_recovered_genes.jpg')
+boxplot(2^up_not_recovered[,3:5], col=(c("yellow","yellow","yellow")), main="DDX21 Mut Not Recovered", ylab="Fold Change",outline=FALSE, notch=FALSE, names=c("KD", "WT", "MUT"),ylim = c(1,2.2),yaxt="n", cex.axis=1,las=2,lwd=4,lty=1)
+axis(2, at=seq(1,2.2,.2))
+dev.off()
+jpeg('figures/boxplot_ddx21_up_regulated_moderatley_recovered_genes.jpg')
+boxplot(2^up_moderatley_recovered[,3:5], col=(c("yellow","yellow","yellow")), main="DDX21 Mut Recovered", ylab="Fold Change",outline=FALSE, notch=FALSE, names=c("KD", "WT", "MUT"),ylim = c(0.6,2.2),yaxt="n", cex.axis=1,las=2,lwd=4,lty=1)
+axis(2, at=seq(0.6,2.2,.2))
+dev.off()
+
+# Wilcox Rank Test
+# Significance  0.05
+up_not_recovered_df <- melt(up_not_recovered[,3:5])
+mw <- pairwise.wilcox.test(up_not_recovered_df$value, up_not_recovered_df$variable, paired=TRUE, p.adj = "bonf")
+mymat<-tri.to.squ(mw$p.value)
+myletters<-multcompLetters(mymat,compare="<=",threshold=0.05,Letters=letters)
+
+
+ddx21_fc_down <- table_kd[(det_kd == -1 & det_wt == 0),]$logFC
+wt_fc_down <- table_wt[(det_kd == -1 & det_wt == 0),]$logFC
+mut_fc_down <- table_mut[(det_kd == -1 & det_wt == 0),]$logFC
+fold_change_down <- data.frame(table_kd[(det_kd == -1 & det_wt == 0),]$GeneId,table_kd[(det_kd == -1 & det_wt == 0),]$GeneName,ddx21_fc_down,wt_fc_down,mut_fc_down)
+colnames(fold_change_down) <- c("GeneID", "NAME", "ddx21_fc", "wt_fc", "mut_fc")
+down_not_recovered <- fold_change_down[which(fold_change_down$mut_fc < -.5),]
+down_moderatley_recovered <- fold_change_down[which(fold_change_down$mut_fc >= -.5),]
+jpeg('figures/boxplot_ddx21_down_regulated_not_recovered_genes.jpg')
+boxplot(2^down_not_recovered[,3:5], col=(c("cyan","cyan","cyan")), main="DDX21 Mut Not Recovered", ylab="Fold Change",outline=FALSE, notch=FALSE, names=c("KD", "WT", "MUT"),ylim = c(0.4,1.2),yaxt="n", cex.axis=1,las=2,lwd=4,lty=1)
+axis(2, at=seq(0.4,1.2,.2))
+dev.off()
+jpeg('figures/boxplot_ddx21_down_regulated_moderatley_recovered_genes.jpg')
+boxplot(2^down_moderatley_recovered[,3:5], col=(c("cyan","cyan","cyan")), main="DDX21 Mut Recovered", ylab="Fold Change",outline=FALSE, notch=FALSE, names=c("KD", "WT", "MUT"),ylim = c(0.4,1.2),yaxt="n", cex.axis=1,las=2,lwd=4,lty=1)
+axis(2, at=seq(0.4,1.2,.2))
+dev.off()
+
+# Wilcox Rank Test
+# Significance  0.05
+down_not_recovered_df <- melt(down_not_recovered[,3:5])
+mw <- pairwise.wilcox.test(down_not_recovered_df$value, down_not_recovered_df$variable)
+mymat<-tri.to.squ(mw$p.value)
+myletters<-multcompLetters(mymat,compare="<=",threshold=0.05,Letters=letters)
+
+```

figures/DDX21_regulated_genes.cdt

+"GID"	"YORF"	"NAME"	"LUCKD"	"DDX21KD"	"WT"	"MUT"
+"6575"	"ENSG00000148303.12"	"RPL7A"	0	-1	-0.259291629899229	-0.449506630852822
+"10470"	"ENSG00000184949.11"	"FAM227A"	0	-1	-0.256510773847042	-0.283375490758114
+"373"	"ENSG00000033327.8"	"GAB2"	0	-1	-0.239354847680858	-0.560144654856979
+"11660"	"ENSG00000204628.7"	"GNB2L1"	0	-1	-0.246815671182654	-0.572680416856648
+"12493"	"ENSG00000234857.2"	"HNRNPUL2-BSCL2"	0	-1	-0.178004667273657	-0.160229776096772
+"2024"	"ENSG00000102317.13"	"RBM3"	0	-1	-0.211193891137497	-0.590586756495283
+"11977"	"ENSG00000215030.4"	"RPL13P12"	0	-1	-0.20685825263711	-0.341402192505837
+"9513"	"ENSG00000175061.13"	"C17orf76-AS1"	0	-1	-0.329497605226728	-0.266769167961129
+"12660"	"ENSG00000241370.1"	"RPP21"	0	-1	-0.32390386292658	-0.195820643510665
+"13378"	"ENSG00000265681.2"	"RPL17"	0	-1	-0.321321315917947	-0.0681730650201384
+"5575"	"ENSG00000138175.8"	"ARL3"	0	-1	-0.292833258659547	0.00402248791976751
+"10210"	"ENSG00000182628.8"	"SKA2"	0	-1	-0.296782782410002	-0.614289760133776
+"6726"	"ENSG00000150540.9"	"HNMT"	0	-1	-0.308854208925129	-0.269274497394847
+"6702"	"ENSG00000149806.6"	"FAU"	0	-1	-0.303362046093514	-0.259572955021615
+"11617"	"ENSG00000204387.8"	"C6orf48"	0	-1	-0.302564025712188	-0.230638405521634
+"12589"	"ENSG00000237883.1"	"DGUOK-AS1"	0	-1	-0.355647780891432	-0.371456206230603
+"12359"	"ENSG00000230989.2"	"HSBP1"	0	-1	-0.37042811757272	-0.475704424134617
+"12731"	"ENSG00000243678.7"	"NME1-NME2"	0	-1	-0.365078803091647	-0.325081366484849
+"13286"	"ENSG00000261485.1"	"PAN3-AS1"	0	-0.958749062606917	-0.393404539403541	-1
+"4577"	"ENSG00000130255.8"	"RPL36"	0	-1	-0.420254497097943	-0.36805256119101
+"10856"	"ENSG00000188483.6"	"IER5L"	0	-1	-0.396998465220999	-0.735883249907464
+"10069"	"ENSG00000181019.8"	"NQO1"	0	-1	0.702246043804737	0.198263566163276
+"2930"	"ENSG00000111341.5"	"MGP"	0	-1	0.075051473736394	-0.665905748214854
+"7326"	"ENSG00000158427.10"	"TMSB15B"	0	-1	-0.0388351634481664	-0.319828397870383
+"8256"	"ENSG00000165732.8"	"DDX21"	0	-1	-0.0612472237433242	-0.0322143784991788
+"3610"	"ENSG00000118181.6"	"RPS25"	0	-1	-0.442736428130959	-0.00437386232622415
+"12301"	"ENSG00000229117.4"	"RPL41"	0	-1	-0.438193803703272	-0.05103739584508
+"4183"	"ENSG00000125356.6"	"NDUFA1"	0	-1	-0.457022249174771	-0.440331604432744
+"7385"	"ENSG00000159199.9"	"ATP5G1"	0	-1	-0.467628416573922	-0.537289769429211
+"6303"	"ENSG00000144935.10"	"TRPC1"	0	-0.946185459993292	-0.527526432642783	-1
+"8917"	"ENSG00000170091.6"	"NSG2"	0	-0.942311136078745	-0.505382647495403	-1
+"9590"	"ENSG00000175768.8"	"TOMM5"	0	-1	-0.539887572938722	-0.476311267933874
+"5473"	"ENSG00000137563.7"	"GGH"	0	-1	-0.525947656702851	-0.482734753801642
+"12946"	"ENSG00000251928.1"	"RNU6-585P"	0	-1	-0.519218284051912	-0.613134214673837
+"1689"	"ENSG00000100142.10"	"POLR2F"	0	-1	-0.487627696420955	-0.290721803356872
+"7182"	"ENSG00000156482.6"	"RPL30"	0	-1	-0.484677068221715	-0.438063056438316
+"12489"	"ENSG00000234741.3"	"GAS5"	0	-1	-0.483432615922367	-0.262784574086306
+"2563"	"ENSG00000107223.8"	"EDF1"	0	-1	-0.495359772187569	-0.60534137629071
+"9589"	"ENSG00000175764.10"	"TTLL11"	0	-1	-0.503604371065877	-0.354138381805198
+"10174"	"ENSG00000182240.11"	"BACE2"	0	-1	-0.506376781112603	-0.960120699618985
+"10957"	"ENSG00000189403.10"	"HMGB1"	0	-1	-0.571087477535587	-0.526002102651654
+"11952"	"ENSG00000214595.7"	"EML6"	0	-1	-0.567210844129215	-0.499783242280499
+"10383"	"ENSG00000184194.5"	"GPR173"	0	-1	-0.578897803270124	-0.708692810265114
+"1339"	"ENSG00000087245.8"	"MMP2"	0	-1	-0.589179914997358	0.658329932332413
+"6089"	"ENSG00000143222.7"	"UFC1"	0	-1	-0.584578560020082	-0.43482430906772
+"7882"	"ENSG00000163644.10"	"PPM1K"	0	-1	-0.586066257157298	-0.943404281974684
+"4160"	"ENSG00000124813.16"	"RUNX2"	0	-0.942062123305916	-0.599400807055966	-1
+"3377"	"ENSG00000115758.8"	"ODC1"	0	-0.974887643481951	-0.609289186726763	-1
+"11606"	"ENSG00000204316.8"	"MRPL38"	0	-1	-0.601020540887356	-0.451969125552638
+"12357"	"ENSG00000230873.4"	"STMND1"	0	-1	-0.609021778149115	-0.475548021318145
+"3920"	"ENSG00000122026.6"	"RPL21"	0	-0.991828550600218	-0.617281303035962	-1
+"10871"	"ENSG00000188612.7"	"SUMO2"	0	-1	-0.61911873328624	-0.545532799769525
+"9225"	"ENSG00000172428.6"	"MYEOV2"	0	-1	-0.82524903969743	-0.497935572661993
+"2034"	"ENSG00000102543.10"	"CDADC1"	0	-1	-0.766329452584357	0.0517729658707944
+"11303"	"ENSG00000198034.6"	"RPS4X"	0	-1	-0.733246531821575	-0.906774728553396
+"11289"	"ENSG00000197958.8"	"RPL12"	0	-1	-0.699903349006058	-0.975199043997027
+"2338"	"ENSG00000105329.5"	"TGFB1"	0	-1	-0.697058167326636	-0.803809322744816
+"10731"	"ENSG00000187109.9"	"NAP1L1"	0	-1	-0.697851309558922	-0.931129738072123
+"13502"	"ENSG00000269858.1"	"EGLN2"	0	-1	-0.676345336463788	-0.543540081749014
+"5436"	"ENSG00000137267.5"	"TUBB2A"	0	-1	-0.68167983628864	-0.522987187204123
+"7841"	"ENSG00000163479.9"	"SSR2"	0	-1	-0.684285515098785	-0.367057886007922
+"8370"	"ENSG00000166441.8"	"RPL27A"	0	-1	-0.635062720624566	-0.848853066427527
+"4245"	"ENSG00000125835.13"	"SNRPB"	0	-1	-0.633759791490139	-0.845257062866378
+"6653"	"ENSG00000149260.10"	"CAPN5"	0	-1	-0.633627467891963	-0.567557163075033
+"7772"	"ENSG00000163041.5"	"H3F3A"	0	-1	-0.642452217688981	-0.853918662632115
+"7862"	"ENSG00000163584.13"	"RPL22L1"	0	-1	-0.639582897673436	-0.799340749898383
+"6973"	"ENSG00000153574.8"	"RPIA"	0	-1	-0.667498886320712	-0.793493511046235
+"3634"	"ENSG00000118515.7"	"SGK1"	0	-1	-0.657521287809424	-0.791648246237144
+"5737"	"ENSG00000139579.8"	"NABP2"	0	-1	-0.648917278129512	-0.573552165061392
+"251"	"ENSG00000013583.4"	"HEBP1"	0	0.591073727672592	0.47531479873542	1
+"6883"	"ENSG00000152409.8"	"JMY"	0	1	0.41341022244312	0.545572578809404
+"4072"	"ENSG00000124098.9"	"FAM210B"	0	1	0.445027391385085	0.366894844293312
+"12671"	"ENSG00000241781.2"	"AL161626.1"	0	1	0.440499292816783	0.858725306002536
+"6110"	"ENSG00000143367.11"	"TUFT1"	0	1	0.456568782908754	0.549690868979347
+"12692"	"ENSG00000242299.1"	"RP11-234A1.1"	0	1	0.466761662514677	0.509501467232065
+"4689"	"ENSG00000131069.15"	"ACSS2"	0	0.901535815117477	0.475396904913733	1
+"7573"	"ENSG00000161202.13"	"DVL3"	0	0.95635062679373	0.466507805802869	1
+"9542"	"ENSG00000175265.13"	"GOLGA8A"	0	1	0.522205455885712	0.506343180653645
+"4844"	"ENSG00000132561.9"	"MATN2"	0	1	0.495315235608566	0.0739617650233378
+"12055"	"ENSG00000220842.5"	"RP11-572P18.1"	0	1	0.508612694369989	0.0297101345510955
+"13094"	"ENSG00000257084.1"	"U47924.27"	0	1	0.506313233083149	0.451550383331052
+"1720"	"ENSG00000100276.9"	"RASL10A"	0	1	0.56612216218496	0.738404052261622
+"585"	"ENSG00000057294.9"	"PKP2"	0	1	0.572009540465615	0.297243493726589
+"1462"	"ENSG00000090581.5"	"GNPTG"	0	1	0.573455896057002	0.722435540667495
+"6066"	"ENSG00000143061.13"	"IGSF3"	0	1	0.542755063249404	0.635347635714383
+"6331"	"ENSG00000145348.12"	"TBCK"	0	1	0.546214724915017	0.797498941364701
+"7404"	"ENSG00000159348.8"	"CYB5R1"	0	1	0.554920124322913	0.75885831924491
+"8188"	"ENSG00000165288.10"	"BRWD3"	0	1	0.559920332751134	0.435188732587294
+"921"	"ENSG00000072274.8"	"TFRC"	0	1	0.675252938963592	0.783395355254841
+"1096"	"ENSG00000078114.14"	"NEBL"	0	1	0.649378960211372	0.867935570369383
+"12176"	"ENSG00000225791.2"	"TRAM2-AS1"	0	1	0.644213223679953	0.731071903819352
+"6357"	"ENSG00000145685.9"	"LHFPL2"	0	1	0.637188852452039	0.703828909721836
+"11224"	"ENSG00000197563.5"	"PIGN"	0	1	0.631661820520365	0.904497272701011
+"9275"	"ENSG00000172869.10"	"DMXL1"	0	0.944838189382231	0.60411240666733	1
+"4263"	"ENSG00000125952.14"	"MAX"	0	1	0.597417850789008	0.690864504646611
+"7168"	"ENSG00000156273.11"	"BACH1"	0	1	0.622135789520344	0.697017935366309
+"6642"	"ENSG00000149177.8"	"PTPRJ"	0	1	0.616735185428519	0.705112826115606
+"11176"	"ENSG00000197265.4"	"GTF2E2"	0	1	0.615314921996045	0.89161530739901
+"3708"	"ENSG00000119574.8"	"ZBTB45"	0	1	0.715610523345718	0.222061506202278
+"118"	"ENSG00000006831.9"	"ADIPOR2"	0	1	0.74071479675078	0.834789826525939
+"1954"	"ENSG00000101639.14"	"CEP192"	0	1	0.728095800585357	0.969218261558476
+"5869"	"ENSG00000140905.5"	"GCSH"	0	1	0.733764136897481	0.26433116101688
+"3057"	"ENSG00000112414.10"	"GPR126"	0	0.926649233108986	0.790117863227818	1
+"6254"	"ENSG00000144455.9"	"SUMF1"	0	1	0.813957898386459	0.739629528750039
+"6365"	"ENSG00000145736.10"	"GTF2H2"	0	1	0.780407116267696	0.807047660498584
+"4701"	"ENSG00000131171.8"	"SH3BGRL"	0	1	-0.838995008612552	-0.343922528330215
+"12547"	"ENSG00000236824.1"	"BCYRN1"	0	0.730981858140711	-0.353095135742429	-1
+"4075"	"ENSG00000124126.9"	"PREX1"	0	1	-0.446668445616761	0.0244508293888281
+"9336"	"ENSG00000173391.4"	"OLR1"	0	1	-0.469588846495123	0.198763622567183
+"9437"	"ENSG00000174307.5"	"PHLDA3"	0	1	-0.45843290638089	-0.190505463820357
+"9766"	"ENSG00000177606.5"	"JUN"	0	1	-0.11451285797351	-0.0457354291035481
+"1964"	"ENSG00000101825.7"	"MXRA5"	0	1	-0.0549250691348075	0.0916066230917265
+"4148"	"ENSG00000124762.9"	"CDKN1A"	0	1	-0.0486070893147965	-0.122787494853853
+"6777"	"ENSG00000151240.11"	"DIP2C"	0	1	0.348128418047094	0.318603640507497
+"2747"	"ENSG00000109099.9"	"PMP22"	0	1	0.280169235294298	0.986716267717722
+"6714"	"ENSG00000150093.14"	"ITGB1"	0	1	0.30492351589521	0.639295211711425
+"7780"	"ENSG00000163083.5"	"INHBB"	0	1	0.0638345729609293	0.38984919936399
+"4362"	"ENSG00000127415.8"	"IDUA"	0	1	0.197321504752081	0.302555404350811
+"10406"	"ENSG00000184363.5"	"PKP3"	0	1	0.201538414259564	0.609634615646393

figures/DDX21_regulated_genes.jtv

+<DocumentConfig><UrlExtractor/><ArrayUrlExtractor/><Views><View type="Dendrogram" dock="1"><ColorExtractor contrast="1.4" logtransform="0"><ColorSet up="#FEF437" down="#2CFCF5"/></ColorExtractor><ArrayDrawer/><GlobalXMap current="Fill"><FixedMap type="Fixed" scale="44.0"/><FillMap type="Fill"/><NullMap type="Null"/></GlobalXMap><GlobalYMap current="Fill"><FixedMap type="Fixed" scale="7.0"/><FillMap type="Fill"/><NullMap type="Null"/></GlobalYMap><ZoomXMap current="Fill"><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></ZoomXMap><ZoomYMap current="Fill"><FixedMap type="Fixed"/><FillMap type="Fill"/><NullMap type="Null"/></ZoomYMap><TextView><TextView><GeneSummary/></TextView><TextView><GeneSummary/></TextView><TextView><GeneSummary/></TextView></TextView><ArrayNameView><ArraySummary included="0"/></ArrayNameView><AtrSummary/><GtrSummary/></View></Views></DocumentConfig>
\ No newline at end of file