gRNA resEdgeR_QLF result
Last updated: 2019-03-22
Checks: 5 1
Knit directory: cropseq/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 5b26d50 | simingz | 2019-03-14 | empirical p |
| html | 5b26d50 | simingz | 2019-03-14 | empirical p |
| Rmd | ce584ed | simingz | 2019-03-11 | gRNA-qqplot |
| html | ce584ed | simingz | 2019-03-11 | gRNA-qqplot |
| Rmd | ca1b0d7 | simingz | 2019-03-06 | gRNA-box-plot |
| html | ca1b0d7 | simingz | 2019-03-06 | gRNA-box-plot |
| html | f306625 | simingz | 2019-03-05 | gRNA-DE |
| Rmd | 6283eea | simingz | 2019-03-04 | stricter filtering for gRNA |
| html | 6283eea | simingz | 2019-03-04 | stricter filtering for gRNA |
| html | 811d97b | simingz | 2019-03-01 | gNNA-de |
| html | c912143 | simingz | 2019-03-01 | gRNA-de |
| html | 9809320 | simingz | 2019-02-28 | gRNA_edgeR-QLF |
| Rmd | 0dffd41 | simingz | 2019-02-28 | gRNA_edgeR-QLF |
| html | 0dffd41 | simingz | 2019-02-28 | gRNA_edgeR-QLF |
| Rmd | 2fd9ad6 | simingz | 2019-02-28 | gRNA_edgeR-QLF |
| html | 2fd9ad6 | simingz | 2019-02-28 | gRNA_edgeR-QLF |
| Rmd | a9f9f26 | simingz | 2019-02-27 | gRNA-de |
| html | a9f9f26 | simingz | 2019-02-27 | gRNA-de |
This summarizes results obtained from running module load R; Rscript code/gRNA_edgeR-QLF_run.R from shell.
library(Matrix)
load("data/DE_input.Rd")
source("code/qq-plot.R")
gRNAdm0 <- dm[(dim(dm)[1]-75):dim(dm)[1],]Using only cells with negative control gRNA as controls
source("code/empiricalFDR.R")
pbins <- 10** (-4:-10)
for (gRNAfile in list.files("data/gRNA_edgeR-QLF/", "*edgeR-qlf_Neg1.Rd")){
print(gRNAfile)
gRNA <- strsplit(gRNAfile, "_edgeR")[[1]][1]
gRNAlocus <- strsplit(gRNA, split = "_")[[1]][1]
load(paste0("data/gRNA_edgeR-QLF/", gRNAfile))
fdrmetricall <- empiricalFDR(res1$table$PValue, res1$table$PValue, unlist(lapply(permres1, function(x) x$table$PValue)))
empiricalPall <- empiricalPvalue(res1$table$PValue, unlist(lapply(permres1, function(x) x$table$PValue)))
empiricalPfdrall <- p.adjust(empiricalPall, method="BH")
resEmpiricalp <- cbind(res1$table, fdrmetricall,empiricalPall,empiricalPfdrall)
save(resEmpiricalp, file=paste0("data/gRNA_edgeR-QLF/", gRNA,"_edgeR-qlf_Neg1_Empricialp.Rd"))
outpvalues <- c(res1$table[1:10,"PValue"], pbins)
outpbins <- matrix(NA, nrow=length(pbins), ncol=dim(res1$table)[2])
rownames(outpbins) <- pbins
colnames(outpbins) <- colnames(res1$table)
outm <- rbind(res1$table[1:10,], outpbins)
fdrmetric <- empiricalFDR(outpvalues, res1$table$PValue, unlist(lapply(permres1, function(x) x$table$PValue)))
empiricalP <- c(empiricalPall[1:10], rep(NA,length(pbins)))
empiricalP.FDR <- c(empiricalPfdrall[1:10], rep(NA,length(pbins)))
outm <- cbind(outm,empiricalP,empiricalP.FDR, fdrmetric)
outm$logFC <- -outm$logFC
print(signif(outm,2))
plotgn <- rownames(outm[1:10,][outm[1:10, "EmpiricalFDR"] <0.2,])
if (length(plotgn)!=0){
for (gn in plotgn){
gcount <- dm[gn, gRNAdm0[gRNA,] >0 & colSums(gRNAdm0[rownames(gRNAdm0) != gRNA,]) == 0]
ncount1 <- dm[gn, colnames(dm1dfagg)[dm1dfagg["neg",] >0 & nlocus==1]]
a <- rbind(cbind(gcount,1),cbind(ncount1,2))
colnames(a) <- c("count","categ")
par(mfrow=c(1,3))
boxplot(count ~categ, data = a, lwd = 2, main=paste(gRNA, gn, sep=":"), outcol="white")
stripchart(count ~categ, data=a, vertical = TRUE, method = "jitter", add = TRUE, pch = 21, cex=2, col = 'blue')
qqplot( -log10(unlist(lapply(permres1, function(x) x$table$PValue))),-log10(res1$table$PValue), xlab="permuted (-log10 pvalue)", ylab="observed (-log10 pvalue)")
abline(a=0, b=1, col="red")
grid()
qqplot(-log10(runif(length(empiricalPall))),-log10(empiricalPall))
abline(a=0, b=1, col="red")
grid()
}
}
}[1] "BAG5_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -2.90 7.5 17.0 5.4e-05 0.34 0.00031 1 1
LIX1 1.10 6.7 12.0 6.2e-04 1.00 0.00110 1 2
FIZ1 -1.30 6.6 12.0 7.4e-04 1.00 0.00130 1 3
HEXIM1 0.98 6.6 11.0 9.2e-04 1.00 0.00150 1 4
BTG2 -1.30 7.1 11.0 1.2e-03 1.00 0.00180 1 5
CCND1 -0.77 8.0 11.0 1.2e-03 1.00 0.00190 1 6
CCNE2 -1.40 6.6 10.0 1.8e-03 1.00 0.00260 1 7
PCF11 -1.20 6.7 10.0 1.8e-03 1.00 0.00270 1 8
ARF4 -0.72 8.4 9.9 1.9e-03 1.00 0.00280 1 9
UFM1 -0.97 7.1 9.5 2.4e-03 1.00 0.00330 1 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 2.00 2.0
LIX1 7.10 3.5
FIZ1 8.30 2.8
HEXIM1 9.80 2.5
BTG2 12.00 2.3
CCND1 12.00 2.0
CCNE2 17.00 2.4
PCF11 17.00 2.1
ARF4 18.00 1.9
UFM1 21.00 2.1
1e-04 2.60 2.6
1e-05 0.99 Inf
1e-06 0.43 Inf
1e-07 0.30 Inf
1e-08 0.23 Inf
1e-09 0.17 Inf
1e-10 0.17 Inf
[1] "BAG5_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -3.00 7.5 18 3.7e-05 0.21 0.00020 0.94 1
CCNE2 -1.80 6.5 17 6.8e-05 0.21 0.00030 0.94 2
NIN 1.10 6.9 15 1.6e-04 0.33 0.00051 0.99 3
EPS15 -1.60 6.4 17 3.2e-04 0.50 0.00078 0.99 4
RAB32 -1.60 6.7 13 4.0e-04 0.51 0.00096 0.99 5
MALAT1 0.60 14.0 13 4.8e-04 0.51 0.00110 0.99 6
ARFGAP1 1.00 6.6 12 5.9e-04 0.54 0.00120 0.99 7
SYMPK 0.98 6.7 11 8.8e-04 0.63 0.00170 0.99 8
SLC39A9 -1.40 6.5 13 9.0e-04 0.63 0.00170 0.99 9
FKBP5 -1.30 6.5 11 1.4e-03 0.71 0.00230 0.99 10
1e-04 NA NA NA NA NA NA NA 2
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 1.300 1.30
CCNE2 1.900 0.94
NIN 3.200 1.10
EPS15 5.000 1.20
RAB32 6.100 1.20
MALAT1 6.900 1.10
ARFGAP1 7.800 1.10
SYMPK 11.000 1.30
SLC39A9 11.000 1.20
FKBP5 15.000 1.50
1e-04 2.300 1.20
1e-05 0.790 Inf
1e-06 0.460 Inf
1e-07 0.300 Inf
1e-08 0.099 Inf
1e-09 0.099 Inf
1e-10 0.099 Inf
[1] "BAG5_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
CDKN3 1.20 7.0 15 0.00012 0.55 0.00044 0.95 1
RACGAP1 1.20 6.6 14 0.00027 0.55 0.00071 0.95 2
BIN3 -1.30 6.8 13 0.00047 0.55 0.00100 0.95 3
RASSF7 -1.60 6.4 15 0.00052 0.55 0.00110 0.95 4
ASCL1 -1.70 6.9 12 0.00058 0.55 0.00120 0.95 5
KIF2C 1.20 6.7 12 0.00060 0.55 0.00120 0.95 6
MYC -2.40 7.5 12 0.00061 0.55 0.00120 0.95 7
CDKN1A -1.50 7.9 12 0.00081 0.57 0.00150 0.95 8
DFFA 0.78 7.2 11 0.00096 0.57 0.00160 0.95 9
ARL6IP1 0.84 7.9 11 0.00097 0.57 0.00160 0.95 10
1e-04 NA NA NA NA NA NA NA 0
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
CDKN3 2.800 2.8
RACGAP1 4.500 2.3
BIN3 6.600 2.2
RASSF7 6.900 1.7
ASCL1 7.400 1.5
KIF2C 7.600 1.3
MYC 7.800 1.1
CDKN1A 9.200 1.2
DFFA 10.000 1.1
ARL6IP1 10.000 1.0
1e-04 2.400 Inf
1e-05 0.760 Inf
1e-06 0.400 Inf
1e-07 0.130 Inf
1e-08 0.099 Inf
1e-09 0.099 Inf
1e-10 0.099 Inf
[1] "BCL11B_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
PRR11 1.5 6.7 14 0.00026 0.79 0.00073 0.98 1
ARL6IP1 1.1 7.9 12 0.00070 0.79 0.00140 0.98 2
MLXIP -2.3 6.5 13 0.00071 0.79 0.00140 0.98 3
POMGNT2 -2.2 6.5 12 0.00089 0.79 0.00170 0.98 4
PTPN18 -2.2 6.5 12 0.00089 0.79 0.00170 0.98 5
SFT2D2 -2.2 6.5 11 0.00100 0.79 0.00200 0.98 6
UNG -2.2 6.9 11 0.00140 0.79 0.00250 0.98 7
FAM111B -2.3 6.5 10 0.00160 0.79 0.00280 0.98 8
UXS1 -2.0 6.8 10 0.00160 0.79 0.00290 0.98 9
IMPA2 -2.1 6.8 10 0.00170 0.79 0.00300 0.98 10
1e-04 NA NA NA NA NA NA NA 0
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
PRR11 4.60 4.6
ARL6IP1 9.00 4.5
MLXIP 9.00 3.0
POMGNT2 11.00 2.7
PTPN18 11.00 2.2
SFT2D2 12.00 2.1
UNG 16.00 2.3
FAM111B 18.00 2.2
UXS1 18.00 2.0
IMPA2 19.00 1.9
1e-04 3.00 Inf
1e-05 1.30 Inf
1e-06 0.70 Inf
1e-07 0.47 Inf
1e-08 0.33 Inf
1e-09 0.30 Inf
1e-10 0.30 Inf
[1] "BCL11B_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
RGS5 1.5 6.7 24 1.7e-06 0.010 8.4e-05 0.32 1
PHLDA1 1.5 7.1 23 3.2e-06 0.010 1.2e-04 0.32 2
CEBPD 1.4 6.8 18 3.8e-05 0.077 3.0e-04 0.32 3
JAG1 1.4 7.0 17 4.8e-05 0.077 3.3e-04 0.32 4
RPRML -1.6 6.7 15 1.5e-04 0.130 5.9e-04 0.32 5
RMI2 -1.5 6.7 15 1.5e-04 0.130 6.0e-04 0.32 6
CDC6 -1.6 6.9 15 1.7e-04 0.130 6.4e-04 0.32 7
ATAD2 -1.6 6.7 14 2.2e-04 0.130 7.0e-04 0.32 8
GAP43 1.1 8.1 14 2.4e-04 0.130 7.2e-04 0.32 9
SCML1 -1.5 6.7 14 2.4e-04 0.130 7.2e-04 0.32 10
1e-04 NA NA NA NA NA NA NA 4
1e-05 NA NA NA NA NA NA NA 2
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
RGS5 0.54 0.54
PHLDA1 0.74 0.37
CEBPD 1.90 0.64
JAG1 2.10 0.53
RPRML 3.70 0.75
RMI2 3.80 0.64
CDC6 4.10 0.58
ATAD2 4.50 0.56
GAP43 4.60 0.51
SCML1 4.60 0.46
1e-04 2.70 0.69
1e-05 0.87 0.43
1e-06 0.43 Inf
1e-07 0.37 Inf
1e-08 0.23 Inf
1e-09 0.13 Inf
1e-10 0.10 Inf
[1] "BCL11B_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
NOP2 -2.3 6.5 12 0.00073 1 0.0010 1 1
TLK2 1.4 6.6 12 0.00074 1 0.0010 1 2
SPEN -2.3 6.5 12 0.00076 1 0.0010 1 3
DUSP1 -2.6 6.8 11 0.00100 1 0.0014 1 4
DKK3 1.2 6.8 11 0.00110 1 0.0015 1 5
MFSD3 -2.2 6.5 12 0.00120 1 0.0017 1 6
TP53I11 -2.2 6.5 11 0.00130 1 0.0018 1 7
ZNF48 1.2 6.7 11 0.00140 1 0.0019 1 8
MGRN1 -2.1 6.5 11 0.00150 1 0.0021 1 9
DTNA -2.1 6.5 10 0.00170 1 0.0024 1 10
1e-04 NA NA NA NA NA NA NA 0
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
NOP2 6.50 6.5
TLK2 6.50 3.2
SPEN 6.50 2.2
DUSP1 8.60 2.1
DKK3 9.70 1.9
MFSD3 11.00 1.8
TP53I11 12.00 1.6
ZNF48 12.00 1.5
MGRN1 13.00 1.5
DTNA 15.00 1.5
1e-04 1.20 Inf
1e-05 0.50 Inf
1e-06 0.30 Inf
1e-07 0.13 Inf
1e-08 0.00 NaN
1e-09 0.00 NaN
1e-10 0.00 NaN
[1] "CHRNA3_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MT-ND4 1.4 11.0 12.0 0.00064 0.8 0.00062 0.76 1
SEPN1 2.2 6.5 12.0 0.00065 0.8 0.00062 0.76 2
FBXW11 2.1 6.5 11.0 0.00100 0.8 0.00088 0.76 3
ABHD17A 2.0 6.7 11.0 0.00120 0.8 0.00100 0.76 4
RGS5 2.1 6.6 10.0 0.00180 0.8 0.00130 0.76 5
ACVR2B 1.9 6.6 9.7 0.00220 0.8 0.00160 0.76 6
BTBD7 2.0 6.5 9.6 0.00230 0.8 0.00160 0.76 7
PREPL 1.9 6.5 9.6 0.00230 0.8 0.00170 0.76 8
SCAMP3 -3.6 7.0 9.0 0.00310 0.8 0.00210 0.76 9
AP1S2 -2.8 7.4 9.0 0.00320 0.8 0.00220 0.76 10
1e-04 NA NA NA NA NA NA NA 0
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MT-ND4 4.000 4.0
SEPN1 4.000 2.0
FBXW11 5.600 1.9
ABHD17A 6.400 1.6
RGS5 8.500 1.7
ACVR2B 9.900 1.7
BTBD7 10.000 1.5
PREPL 10.000 1.3
SCAMP3 13.000 1.5
AP1S2 14.000 1.4
1e-04 1.600 Inf
1e-05 0.730 Inf
1e-06 0.400 Inf
1e-07 0.300 Inf
1e-08 0.170 Inf
1e-09 0.067 Inf
1e-10 0.067 Inf
[1] "CHRNA3_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR
RP11-46C20.1 1.40 6.6 17 5.6e-05 0.35 0.00029 1
FIZ1 -1.80 6.6 15 1.9e-04 0.41 0.00062 1
RCAN1 1.40 6.8 14 2.1e-04 0.41 0.00065 1
PKMYT1 -1.80 6.7 14 2.6e-04 0.41 0.00072 1
ARFGAP3 -1.70 6.5 13 4.0e-04 0.51 0.00095 1
SERPINE2 1.30 6.7 13 5.1e-04 0.54 0.00110 1
MKNK1 -1.60 6.5 12 6.7e-04 0.57 0.00130 1
SLC25A26 -1.50 6.7 12 7.2e-04 0.57 0.00140 1
PRDX1 0.44 9.5 11 1.2e-03 0.68 0.00200 1
SNAPC1 1.20 6.7 11 1.2e-03 0.68 0.00200 1
1e-04 NA NA NA NA NA NA NA
1e-05 NA NA NA NA NA NA NA
1e-06 NA NA NA NA NA NA NA
1e-07 NA NA NA NA NA NA NA
1e-08 NA NA NA NA NA NA NA
1e-09 NA NA NA NA NA NA NA
1e-10 NA NA NA NA NA NA NA
#in_real #in_perm EmpiricalFDR
RP11-46C20.1 1 1.90 1.9
FIZ1 2 3.90 2.0
RCAN1 3 4.10 1.4
PKMYT1 4 4.50 1.1
ARFGAP3 5 6.00 1.2
SERPINE2 6 7.00 1.2
MKNK1 7 8.50 1.2
SLC25A26 8 8.80 1.1
PRDX1 9 13.00 1.4
SNAPC1 10 13.00 1.3
1e-04 1 2.80 2.8
1e-05 0 0.93 Inf
1e-06 0 0.56 Inf
1e-07 0 0.46 Inf
1e-08 0 0.26 Inf
1e-09 0 0.23 Inf
1e-10 0 0.20 Inf
[1] "CHRNA3_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
CDC42EP3 1.8 6.8 23 4.0e-06 0.025 0.00013 0.56 1
VGF 1.9 6.9 19 2.6e-05 0.083 0.00022 0.56 2
RRP9 1.3 7.1 18 3.9e-05 0.083 0.00027 0.56 3
OXR1 -2.4 6.5 17 7.7e-05 0.120 0.00038 0.56 4
GLIPR1 1.5 6.7 15 1.3e-04 0.160 0.00044 0.56 5
AKAP12 1.2 7.4 15 1.7e-04 0.180 0.00056 0.56 6
TTC28 -2.3 6.5 14 2.4e-04 0.210 0.00069 0.56 7
PRR11 1.4 6.7 14 2.8e-04 0.210 0.00075 0.56 8
NANS 1.2 7.1 14 3.0e-04 0.210 0.00079 0.56 9
LPP 1.3 6.8 13 4.3e-04 0.270 0.00100 0.64 10
1e-04 NA NA NA NA NA NA NA 4
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
CDC42EP3 0.84 0.84
VGF 1.40 0.69
RRP9 1.70 0.57
OXR1 2.40 0.60
GLIPR1 2.80 0.56
AKAP12 3.60 0.59
TTC28 4.40 0.63
PRR11 4.80 0.60
NANS 5.00 0.56
LPP 6.40 0.64
1e-04 2.70 0.66
1e-05 1.00 1.00
1e-06 0.54 Inf
1e-07 0.40 Inf
1e-08 0.30 Inf
1e-09 0.27 Inf
1e-10 0.23 Inf
[1] "DPYD_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR
CTD-2006C1.2 1.90 7.2 47 1.2e-10 7.6e-07 7.3e-05 0.46
DUSP4 1.20 6.8 20 1.1e-05 3.4e-02 2.4e-04 0.46
CTSD 0.99 7.4 19 2.6e-05 5.6e-02 3.1e-04 0.46
NQO1 1.30 7.5 18 3.6e-05 5.7e-02 3.6e-04 0.46
MYC -2.50 7.5 17 5.7e-05 7.2e-02 4.4e-04 0.46
TACC1 1.20 6.6 16 8.8e-05 8.1e-02 5.7e-04 0.46
NTRK2 -1.20 7.1 16 8.9e-05 8.1e-02 5.7e-04 0.46
ADIPOR2 -1.40 6.5 16 1.5e-04 1.1e-01 7.6e-04 0.46
TUBA1C 1.20 7.0 15 1.7e-04 1.1e-01 8.1e-04 0.46
NCAPH -1.40 6.5 15 1.7e-04 1.1e-01 8.3e-04 0.46
1e-04 NA NA NA NA NA NA NA
1e-05 NA NA NA NA NA NA NA
1e-06 NA NA NA NA NA NA NA
1e-07 NA NA NA NA NA NA NA
1e-08 NA NA NA NA NA NA NA
1e-09 NA NA NA NA NA NA NA
1e-10 NA NA NA NA NA NA NA
#in_real #in_perm EmpiricalFDR
CTD-2006C1.2 1 0.46 0.46
DUSP4 2 1.50 0.76
CTSD 3 2.00 0.66
NQO1 4 2.30 0.57
MYC 5 2.80 0.56
TACC1 6 3.60 0.61
NTRK2 7 3.60 0.52
ADIPOR2 8 4.80 0.60
TUBA1C 9 5.10 0.57
NCAPH 10 5.30 0.53
1e-04 7 4.00 0.57
1e-05 1 1.50 1.50
1e-06 1 0.73 0.73
1e-07 1 0.53 0.53
1e-08 1 0.50 0.50
1e-09 1 0.50 0.50
1e-10 0 0.46 Inf
[1] "DPYD_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR
MYC -2.70 7.3 35 1.3e-08 8.6e-05 8.4e-05 0.53
RGS5 1.40 6.8 25 1.3e-06 4.2e-03 1.9e-04 0.61
MEG3 0.97 7.8 14 2.0e-04 4.3e-01 6.4e-04 0.93
CLN8 -0.97 6.6 13 3.6e-04 5.6e-01 8.0e-04 0.93
KCTD10 0.86 6.6 12 5.3e-04 5.7e-01 1.0e-03 0.93
CSRP1 0.97 7.3 12 6.2e-04 5.7e-01 1.2e-03 0.93
LRRC45 -1.00 6.4 15 6.3e-04 5.7e-01 1.2e-03 0.93
NKAIN1 -0.91 6.6 12 8.0e-04 5.8e-01 1.4e-03 0.93
SPAG7 0.38 8.2 11 9.7e-04 5.8e-01 1.6e-03 0.93
RP11-995C19.3 -0.88 6.7 11 9.8e-04 5.8e-01 1.6e-03 0.93
1e-04 NA NA NA NA NA NA NA
1e-05 NA NA NA NA NA NA NA
1e-06 NA NA NA NA NA NA NA
1e-07 NA NA NA NA NA NA NA
1e-08 NA NA NA NA NA NA NA
1e-09 NA NA NA NA NA NA NA
1e-10 NA NA NA NA NA NA NA
#in_real #in_perm EmpiricalFDR
MYC 1 0.53 0.53
RGS5 2 1.20 0.61
MEG3 3 4.10 1.40
CLN8 4 5.10 1.30
KCTD10 5 6.60 1.30
CSRP1 6 7.70 1.30
LRRC45 7 7.70 1.10
NKAIN1 8 8.80 1.10
SPAG7 9 10.00 1.10
RP11-995C19.3 10 10.00 1.00
1e-04 2 2.90 1.50
1e-05 2 1.60 0.78
1e-06 1 1.20 1.20
1e-07 1 0.80 0.80
1e-08 0 0.50 Inf
1e-09 0 0.27 Inf
1e-10 0 0.23 Inf
[1] "DPYD_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -3.4 7.5 18 2.8e-05 0.18 0.00023 1 1
NEAT1 -1.7 8.2 17 7.2e-05 0.23 0.00039 1 2
PRR11 1.1 6.7 13 3.2e-04 0.67 0.00082 1 3
TP53I11 -1.6 6.5 13 5.2e-04 0.71 0.00120 1 4
RAB32 -1.7 6.7 12 5.6e-04 0.71 0.00120 1 5
EMC9 1.0 6.8 12 8.0e-04 0.79 0.00170 1 6
CEP164 -1.4 6.6 11 1.0e-03 0.79 0.00200 1 7
SKA3 1.0 6.6 11 1.2e-03 0.79 0.00230 1 8
VWA1 -1.4 6.5 11 1.4e-03 0.79 0.00250 1 9
ANKRD9 -1.4 6.5 13 1.4e-03 0.79 0.00250 1 10
1e-04 NA NA NA NA NA NA NA 2
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 1.50 1.5
NEAT1 2.50 1.2
PRR11 5.20 1.7
TP53I11 7.40 1.8
RAB32 7.70 1.5
EMC9 11.00 1.8
CEP164 13.00 1.8
SKA3 14.00 1.8
VWA1 16.00 1.7
ANKRD9 16.00 1.6
1e-04 2.80 1.4
1e-05 0.83 Inf
1e-06 0.53 Inf
1e-07 0.30 Inf
1e-08 0.27 Inf
1e-09 0.20 Inf
1e-10 0.17 Inf
[1] "GALNT10_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -2.8 7.5 20 1.6e-05 0.086 0.00020 0.71 1
CDKN1C 1.6 7.1 19 2.7e-05 0.086 0.00022 0.71 2
RPRD2 -1.5 6.5 17 2.6e-04 0.460 0.00077 1.00 3
PDK2 -1.5 6.4 17 2.9e-04 0.460 0.00086 1.00 4
FAM104B -1.1 6.9 13 4.0e-04 0.510 0.00100 1.00 5
DECR1 -1.2 6.9 12 5.9e-04 0.580 0.00130 1.00 6
AKAP13 -1.2 6.6 12 6.4e-04 0.580 0.00140 1.00 7
ASRGL1 -1.0 7.0 11 8.6e-04 0.680 0.00170 1.00 8
IGFBP5 -1.6 6.6 11 1.0e-03 0.730 0.00190 1.00 9
SCAF8 -1.2 6.5 13 1.2e-03 0.730 0.00210 1.00 10
1e-04 NA NA NA NA NA NA NA 2
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 1.30 1.30
CDKN1C 1.40 0.71
RPRD2 4.90 1.60
PDK2 5.40 1.40
FAM104B 6.60 1.30
DECR1 8.40 1.40
AKAP13 8.80 1.30
ASRGL1 11.00 1.30
IGFBP5 12.00 1.30
SCAF8 14.00 1.40
1e-04 2.70 1.40
1e-05 1.10 Inf
1e-06 0.43 Inf
1e-07 0.23 Inf
1e-08 0.20 Inf
1e-09 0.20 Inf
1e-10 0.20 Inf
[1] "GALNT10_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
RGS5 1.40 6.7 21 8.4e-06 0.053 0.00013 0.57 1
MYC -2.90 7.5 19 1.7e-05 0.054 0.00018 0.57 2
RACGAP1 1.20 6.6 16 7.6e-05 0.160 0.00030 0.62 3
DBNDD1 -1.40 6.5 14 3.2e-04 0.500 0.00073 1.00 4
ST7L 0.98 6.6 13 4.3e-04 0.540 0.00087 1.00 5
SYPL1 -0.91 7.1 11 1.0e-03 1.000 0.00170 1.00 6
PUS3 -1.10 6.7 11 1.3e-03 1.000 0.00210 1.00 7
FZD3 0.54 7.6 11 1.3e-03 1.000 0.00210 1.00 8
IGF1R 0.93 6.6 10 1.5e-03 1.000 0.00220 1.00 9
REV3L -1.30 6.5 12 1.6e-03 1.000 0.00230 1.00 10
1e-04 NA NA NA NA NA NA NA 3
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
RGS5 0.800 0.80
MYC 1.100 0.57
RACGAP1 1.900 0.62
DBNDD1 4.600 1.20
ST7L 5.500 1.10
SYPL1 11.000 1.80
PUS3 13.000 1.90
FZD3 13.000 1.60
IGF1R 14.000 1.60
REV3L 15.000 1.50
1e-04 2.200 0.72
1e-05 0.900 0.90
1e-06 0.330 Inf
1e-07 0.130 Inf
1e-08 0.130 Inf
1e-09 0.067 Inf
1e-10 0.033 Inf
[1] "GALNT10_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
STMN2 -2.80 7.1 26 6.6e-07 0.0034 0.00012 0.47 1
MYC -2.70 7.4 25 1.1e-06 0.0034 0.00015 0.47 2
NEAT1 1.30 8.8 20 1.1e-05 0.0170 0.00030 0.47 3
RGS5 1.30 6.7 20 1.1e-05 0.0170 0.00030 0.47 4
EML1 -1.40 6.5 19 4.8e-05 0.0610 0.00043 0.55 5
SLAIN2 -1.30 6.4 19 1.3e-04 0.1400 0.00061 0.58 6
TADA1 -1.30 6.4 17 1.8e-04 0.1600 0.00069 0.58 7
ZNF512 0.89 6.7 14 2.0e-04 0.1600 0.00073 0.58 8
SPOCK1 1.00 6.7 14 2.9e-04 0.2100 0.00087 0.61 9
ELMO1 -1.20 6.5 13 5.0e-04 0.2900 0.00120 0.61 10
1e-04 NA NA NA NA NA NA NA 5
1e-05 NA NA NA NA NA NA NA 2
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
STMN2 0.76 0.76
MYC 0.95 0.48
NEAT1 1.90 0.63
RGS5 1.90 0.47
EML1 2.70 0.55
SLAIN2 3.90 0.64
TADA1 4.30 0.62
ZNF512 4.60 0.58
SPOCK1 5.50 0.61
ELMO1 7.40 0.74
1e-04 3.40 0.68
1e-05 1.80 0.92
1e-06 0.95 0.95
1e-07 0.33 Inf
1e-08 0.20 Inf
1e-09 0.16 Inf
1e-10 0.16 Inf
[1] "KCTD13_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
TUBA1C -2.9 6.8 26 9.4e-07 0.006 3.1e-05 0.20 1
MYC -3.4 7.5 18 3.1e-05 0.097 1.9e-04 0.59 2
SHPRH -1.6 6.6 16 9.9e-05 0.210 3.3e-04 0.67 3
CTTNBP2NL -1.6 6.5 15 2.2e-04 0.290 5.4e-04 0.67 4
SLC20A2 -1.6 6.6 14 2.3e-04 0.290 5.6e-04 0.67 5
BEX2 -1.8 6.7 13 3.6e-04 0.340 7.5e-04 0.67 6
HES6 1.1 9.1 13 4.1e-04 0.340 8.4e-04 0.67 7
CWC25 1.0 6.8 13 4.7e-04 0.340 9.2e-04 0.67 8
ADGRL2 1.1 6.7 13 4.9e-04 0.340 9.5e-04 0.67 9
NRSN2 -1.4 6.6 12 7.6e-04 0.450 1.2e-03 0.72 10
1e-04 NA NA NA NA NA NA NA 3
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
TUBA1C 0.200 0.20
MYC 1.200 0.59
SHPRH 2.100 0.69
CTTNBP2NL 3.400 0.85
SLC20A2 3.600 0.71
BEX2 4.800 0.80
HES6 5.300 0.76
CWC25 5.800 0.73
ADGRL2 6.000 0.67
NRSN2 7.800 0.78
1e-04 2.100 0.70
1e-05 0.660 0.66
1e-06 0.200 0.20
1e-07 0.033 Inf
1e-08 0.000 NaN
1e-09 0.000 NaN
1e-10 0.000 NaN
[1] "KCTD13_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
RCAN1 -2.1 6.6 21 7.4e-06 0.047 0.00014 0.76 1
MYC -3.0 7.5 17 4.8e-05 0.130 0.00035 0.76 2
CMTM8 -1.9 6.6 16 8.3e-05 0.130 0.00048 0.76 3
KRT8 -2.4 7.0 16 8.4e-05 0.130 0.00048 0.76 4
IGFBP5 -2.2 6.6 15 1.4e-04 0.170 0.00060 0.76 5
NINJ1 -1.3 7.0 14 2.9e-04 0.300 0.00091 0.89 6
SLC20A2 -1.5 6.6 13 3.3e-04 0.300 0.00099 0.89 7
EFCC1 -1.5 6.5 14 7.1e-04 0.570 0.00170 1.00 8
PPP1R14C -1.7 6.8 11 1.1e-03 0.690 0.00230 1.00 9
PGAM5 -1.2 6.6 11 1.4e-03 0.690 0.00290 1.00 10
1e-04 NA NA NA NA NA NA NA 4
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
RCAN1 0.90 0.90
MYC 2.20 1.10
CMTM8 3.00 1.00
KRT8 3.00 0.76
IGFBP5 3.80 0.76
NINJ1 5.80 0.96
SLC20A2 6.30 0.89
EFCC1 11.00 1.30
PPP1R14C 14.00 1.60
PGAM5 18.00 1.80
1e-04 3.30 0.81
1e-05 1.00 1.00
1e-06 0.53 Inf
1e-07 0.30 Inf
1e-08 0.23 Inf
1e-09 0.17 Inf
1e-10 0.17 Inf
[1] "KCTD13_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
IGFBP5 2.0 6.9 17 7.1e-05 0.30 0.00015 0.53 1
TLE4 1.4 6.9 16 9.4e-05 0.30 0.00017 0.53 2
GEMIN2 1.4 6.9 15 1.7e-04 0.36 0.00028 0.58 3
IPO9 1.1 7.1 12 7.2e-04 0.72 0.00110 0.94 4
PYCRL -2.1 6.5 13 7.6e-04 0.72 0.00120 0.94 5
PPIL2 -2.1 6.5 14 7.6e-04 0.72 0.00120 0.94 6
GINM1 -2.0 6.6 11 8.7e-04 0.72 0.00140 0.94 7
QRICH1 1.3 6.6 11 9.1e-04 0.72 0.00140 0.94 8
ALDH1B1 1.2 6.6 11 1.2e-03 0.74 0.00200 0.94 9
SLC20A1 1.1 6.7 10 1.8e-03 0.74 0.00260 0.94 10
1e-04 NA NA NA NA NA NA NA 2
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
IGFBP5 0.960 0.96
TLE4 1.100 0.53
GEMIN2 1.800 0.58
IPO9 7.200 1.80
PYCRL 7.600 1.50
PPIL2 7.600 1.30
GINM1 8.600 1.20
QRICH1 9.000 1.10
ALDH1B1 12.000 1.40
SLC20A1 17.000 1.70
1e-04 1.200 0.58
1e-05 0.560 Inf
1e-06 0.430 Inf
1e-07 0.260 Inf
1e-08 0.170 Inf
1e-09 0.170 Inf
1e-10 0.099 Inf
[1] "KMT2E_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
EXOC6 1.5 6.6 14.0 0.00025 0.98 0.00062 1 1
FTH1 1.0 12.0 13.0 0.00039 0.98 0.00076 1 2
FAM161A -2.4 6.8 12.0 0.00082 0.98 0.00130 1 3
CSPP1 -2.3 6.6 11.0 0.00130 0.98 0.00180 1 4
GMCL1 -2.4 6.6 11.0 0.00130 0.98 0.00180 1 5
SLC44A2 1.4 6.6 10.0 0.00160 0.98 0.00240 1 6
B4GALT5 -2.3 6.5 10.0 0.00170 0.98 0.00250 1 7
ZMYND11 -2.3 6.5 10.0 0.00210 0.98 0.00300 1 8
BCL9 -2.3 6.5 10.0 0.00210 0.98 0.00300 1 9
NCSTN -2.3 6.8 9.7 0.00220 0.98 0.00320 1 10
1e-04 NA NA NA NA NA NA NA 0
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
EXOC6 3.90 3.9
FTH1 4.80 2.4
FAM161A 8.30 2.8
CSPP1 11.00 2.8
GMCL1 11.00 2.3
SLC44A2 15.00 2.5
B4GALT5 16.00 2.3
ZMYND11 19.00 2.4
BCL9 19.00 2.1
NCSTN 20.00 2.0
1e-04 2.40 Inf
1e-05 0.97 Inf
1e-06 0.57 Inf
1e-07 0.40 Inf
1e-08 0.24 Inf
1e-09 0.17 Inf
1e-10 0.17 Inf
[1] "KMT2E_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
EZR 1.2 7.5 19 2.4e-05 0.15 0.00024 0.62 1
QPRT -2.7 6.8 17 5.0e-05 0.16 0.00030 0.62 2
TEAD1 1.4 6.6 15 1.2e-04 0.18 0.00044 0.62 3
CMTM8 -2.7 6.7 15 1.3e-04 0.18 0.00047 0.62 4
RNF168 -2.2 6.7 15 1.4e-04 0.18 0.00049 0.62 5
RGS5 1.4 6.7 14 2.3e-04 0.24 0.00070 0.72 6
PRR5 -2.1 6.5 14 2.6e-04 0.24 0.00079 0.72 7
COQ7 1.3 6.7 13 4.7e-04 0.34 0.00110 0.81 8
TADA1 -2.0 6.5 14 4.8e-04 0.34 0.00110 0.81 9
RAB8A -1.5 7.1 12 6.9e-04 0.42 0.00150 0.84 10
1e-04 NA NA NA NA NA NA NA 2
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
EZR 1.50 1.50
QPRT 1.90 0.96
TEAD1 2.80 0.94
CMTM8 3.00 0.74
RNF168 3.10 0.62
RGS5 4.40 0.74
PRR5 5.00 0.72
COQ7 7.20 0.91
TADA1 7.20 0.81
RAB8A 9.30 0.93
1e-04 2.50 1.20
1e-05 1.10 Inf
1e-06 0.74 Inf
1e-07 0.44 Inf
1e-08 0.37 Inf
1e-09 0.30 Inf
1e-10 0.20 Inf
[1] "KMT2E_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
TP53I3 1.50 7.0 19.0 1.9e-05 0.12 0.00017 1 1
COG5 -2.10 6.5 16.0 2.1e-04 0.43 0.00057 1 2
GPT2 -1.80 6.9 14.0 2.5e-04 0.43 0.00059 1 3
BCHE -2.10 6.5 14.0 2.7e-04 0.43 0.00063 1 4
FDXR 1.20 7.1 13.0 5.1e-04 0.64 0.00100 1 5
KCTD1 1.20 6.7 12.0 7.2e-04 0.76 0.00130 1 6
LIN28B 1.20 6.7 11.0 8.7e-04 0.79 0.00150 1 7
NCSTN -1.70 6.8 11.0 1.3e-03 1.00 0.00200 1 8
MYC -2.90 7.6 9.7 2.2e-03 1.00 0.00300 1 9
HSP90AA1 -0.49 10.0 9.3 2.7e-03 1.00 0.00350 1 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
TP53I3 1.10 1.1
COG5 3.60 1.8
GPT2 3.80 1.3
BCHE 4.00 1.0
FDXR 6.40 1.3
KCTD1 8.20 1.4
LIN28B 9.40 1.3
NCSTN 13.00 1.6
MYC 19.00 2.1
HSP90AA1 22.00 2.2
1e-04 2.50 2.5
1e-05 0.87 Inf
1e-06 0.50 Inf
1e-07 0.30 Inf
1e-08 0.20 Inf
1e-09 0.17 Inf
1e-10 0.13 Inf
[1] "LINC00637_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR
HSP90AA1 0.93 11.0 34 2.3e-08 0.00015 1.1e-05 0.067
MYC -3.20 7.5 25 1.2e-06 0.00380 6.3e-05 0.200
MALAT1 0.65 14.0 20 1.2e-05 0.02600 1.4e-04 0.300
PKMYT1 -1.50 6.7 19 2.2e-05 0.03500 1.9e-04 0.300
FKBP1B -1.30 6.7 15 1.3e-04 0.16000 4.2e-04 0.530
SPIN2B -1.20 6.5 13 7.0e-04 0.71000 1.2e-03 0.940
DERL1 -0.93 6.8 12 8.0e-04 0.71000 1.3e-03 0.940
DBNDD1 -1.20 6.5 12 9.0e-04 0.71000 1.4e-03 0.940
HSPH1 0.81 7.5 11 1.1e-03 0.78000 1.6e-03 0.940
JAG1 1.00 6.9 10 1.6e-03 0.92000 2.1e-03 0.940
1e-04 NA NA NA NA NA NA NA
1e-05 NA NA NA NA NA NA NA
1e-06 NA NA NA NA NA NA NA
1e-07 NA NA NA NA NA NA NA
1e-08 NA NA NA NA NA NA NA
1e-09 NA NA NA NA NA NA NA
1e-10 NA NA NA NA NA NA NA
#in_real #in_perm EmpiricalFDR
HSP90AA1 1 0.067 0.067
MYC 2 0.400 0.200
MALAT1 3 0.900 0.300
PKMYT1 4 1.200 0.300
FKBP1B 5 2.600 0.530
SPIN2B 6 7.500 1.200
DERL1 7 8.100 1.200
DBNDD1 8 8.700 1.100
HSPH1 9 10.000 1.100
JAG1 10 13.000 1.300
1e-04 4 2.300 0.570
1e-05 2 0.800 0.400
1e-06 1 0.400 0.400
1e-07 1 0.170 0.170
1e-08 0 0.067 Inf
1e-09 0 0.000 NaN
1e-10 0 0.000 NaN
[1] "LINC00637_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -3.4 7.5 20 1.3e-05 0.081 0.00018 0.82 1
TP53I3 1.2 7.0 18 3.0e-05 0.096 0.00026 0.82 2
TUBA1C -2.0 6.8 16 8.8e-05 0.190 0.00044 0.93 3
SRD5A1 -1.4 6.7 14 2.8e-04 0.440 0.00082 1.00 4
KCTD9 -1.5 6.6 13 3.9e-04 0.460 0.00099 1.00 5
MAFB -1.8 6.6 13 4.3e-04 0.460 0.00110 1.00 6
SRFBP1 -1.3 6.6 13 6.8e-04 0.620 0.00150 1.00 7
SPOCK1 1.0 6.7 11 8.9e-04 0.710 0.00180 1.00 8
SLC20A2 -1.3 6.6 11 1.1e-03 0.740 0.00200 1.00 9
COASY -1.2 6.7 11 1.3e-03 0.800 0.00240 1.00 10
1e-04 NA NA NA NA NA NA NA 3
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 1.200 1.20
TP53I3 1.600 0.82
TUBA1C 2.800 0.93
SRD5A1 5.200 1.30
KCTD9 6.300 1.30
MAFB 6.800 1.10
SRFBP1 9.500 1.40
SPOCK1 12.000 1.40
SLC20A2 13.000 1.40
COASY 15.000 1.50
1e-04 2.900 0.98
1e-05 1.000 Inf
1e-06 0.400 Inf
1e-07 0.270 Inf
1e-08 0.100 Inf
1e-09 0.067 Inf
1e-10 0.000 NaN
[1] "LINC00637_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR
GADD45G -3.10 7.3 30 1.3e-07 0.0008 5.3e-05 0.33
CDC25A -1.50 6.5 21 8.4e-06 0.0270 1.9e-04 0.33
DLL3 -2.00 6.9 19 2.4e-05 0.0380 2.6e-04 0.33
CDKN1C -1.80 6.7 19 2.4e-05 0.0380 2.6e-04 0.33
MIAT -1.70 6.9 18 3.3e-05 0.0420 2.7e-04 0.33
RGS5 1.20 6.7 17 4.5e-05 0.0480 3.1e-04 0.33
TPM2 1.40 7.4 17 6.7e-05 0.0610 3.7e-04 0.33
TNFRSF12A 1.10 7.9 15 1.8e-04 0.1400 5.6e-04 0.45
TPM1 0.76 8.4 14 2.8e-04 0.2000 7.4e-04 0.49
DIO3 -1.20 7.0 13 3.1e-04 0.2000 7.7e-04 0.49
1e-04 NA NA NA NA NA NA NA
1e-05 NA NA NA NA NA NA NA
1e-06 NA NA NA NA NA NA NA
1e-07 NA NA NA NA NA NA NA
1e-08 NA NA NA NA NA NA NA
1e-09 NA NA NA NA NA NA NA
1e-10 NA NA NA NA NA NA NA
#in_real #in_perm EmpiricalFDR
GADD45G 1 0.34 0.34
CDC25A 2 1.20 0.59
DLL3 3 1.60 0.54
CDKN1C 4 1.60 0.40
MIAT 5 1.70 0.34
RGS5 6 2.00 0.33
TPM2 7 2.30 0.33
TNFRSF12A 8 3.60 0.45
TPM1 9 4.70 0.52
DIO3 10 4.90 0.49
1e-04 7 2.70 0.38
1e-05 2 1.20 0.62
1e-06 1 0.57 0.57
1e-07 0 0.34 Inf
1e-08 0 0.10 Inf
1e-09 0 0.10 Inf
1e-10 0 0.10 Inf
[1] "LOC100507431_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
S100A16 2.0 6.8 27 5.8e-07 0.0037 6.8e-05 0.26 1
TPM2 2.0 7.3 22 6.8e-06 0.0190 1.2e-04 0.26 2
CDKN1C 2.2 7.1 21 9.0e-06 0.0190 1.4e-04 0.26 3
GADD45G 2.4 8.0 20 1.5e-05 0.0240 1.6e-04 0.26 4
CCND2 1.6 7.2 17 5.1e-05 0.0650 3.4e-04 0.43 5
ANAPC10 -2.3 6.5 15 1.7e-04 0.1800 6.2e-04 0.66 6
NOC3L -2.0 6.6 12 7.1e-04 0.6400 1.6e-03 1.00 7
IRS1 1.3 6.6 11 9.7e-04 0.7700 2.1e-03 1.00 8
SIGIRR -2.0 6.5 12 1.2e-03 0.7800 2.4e-03 1.00 9
MYC -3.9 7.6 11 1.2e-03 0.7800 2.4e-03 1.00 10
1e-04 NA NA NA NA NA NA NA 5
1e-05 NA NA NA NA NA NA NA 3
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
S100A16 0.43 0.43
TPM2 0.77 0.38
CDKN1C 0.90 0.30
GADD45G 1.00 0.26
CCND2 2.10 0.43
ANAPC10 3.90 0.66
NOC3L 10.00 1.50
IRS1 13.00 1.70
SIGIRR 15.00 1.70
MYC 15.00 1.50
1e-04 3.00 0.60
1e-05 0.93 0.31
1e-06 0.57 0.57
1e-07 0.37 Inf
1e-08 0.13 Inf
1e-09 0.10 Inf
1e-10 0.10 Inf
[1] "LOC100507431_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
S100A16 1.80 6.8 30 1.7e-07 0.0011 5.2e-05 0.33 1
S100A13 1.40 7.2 20 1.4e-05 0.0440 1.5e-04 0.34 2
DHRS7 1.30 6.7 19 2.1e-05 0.0440 1.6e-04 0.34 3
SPOCK1 1.30 6.7 17 7.0e-05 0.1100 3.1e-04 0.44 4
LAPTM4A 0.96 7.1 16 9.9e-05 0.1300 4.0e-04 0.44 5
GAP43 1.20 8.1 15 1.2e-04 0.1300 4.5e-04 0.44 6
GPM6B 0.67 8.5 15 1.5e-04 0.1400 5.0e-04 0.44 7
MYC -2.80 7.5 15 1.8e-04 0.1400 5.6e-04 0.44 8
STMN2 -2.60 7.2 14 2.9e-04 0.2000 7.6e-04 0.47 9
CRABP1 -1.80 9.9 13 3.2e-04 0.2000 8.2e-04 0.47 10
1e-04 NA NA NA NA NA NA NA 5
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
S100A16 0.33 0.33
S100A13 0.96 0.48
DHRS7 1.00 0.34
SPOCK1 2.00 0.50
LAPTM4A 2.50 0.50
GAP43 2.80 0.47
GPM6B 3.20 0.45
MYC 3.50 0.44
STMN2 4.80 0.54
CRABP1 5.20 0.52
1e-04 2.50 0.50
1e-05 0.70 0.70
1e-06 0.43 0.43
1e-07 0.30 Inf
1e-08 0.17 Inf
1e-09 0.17 Inf
1e-10 0.17 Inf
[1] "LOC100507431_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -3.20 7.4 30 1.3e-07 0.00085 3.1e-05 0.20 1
DDIT4 1.30 8.1 24 1.8e-06 0.00570 7.3e-05 0.23 2
IGFBP5 -2.00 6.5 21 9.1e-06 0.01900 1.5e-04 0.31 3
EEF2 0.40 11.0 13 3.5e-04 0.56000 8.1e-04 0.84 4
HUS1 0.94 6.5 12 5.7e-04 0.59000 1.1e-03 0.84 5
TRIB3 1.10 7.4 12 6.0e-04 0.59000 1.2e-03 0.84 6
SHMT2 0.72 7.6 12 7.6e-04 0.59000 1.4e-03 0.84 7
TAF6 0.65 7.2 11 8.5e-04 0.59000 1.5e-03 0.84 8
DBNDD1 -1.10 6.4 11 9.1e-04 0.59000 1.6e-03 0.84 9
WARS 0.79 7.4 11 9.5e-04 0.59000 1.7e-03 0.84 10
1e-04 NA NA NA NA NA NA NA 3
1e-05 NA NA NA NA NA NA NA 3
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 0.200 0.20
DDIT4 0.460 0.23
IGFBP5 0.920 0.31
EEF2 5.100 1.30
HUS1 7.100 1.40
TRIB3 7.400 1.20
SHMT2 8.800 1.30
TAF6 9.600 1.20
DBNDD1 10.000 1.10
WARS 11.000 1.10
1e-04 2.300 0.78
1e-05 0.990 0.33
1e-06 0.360 0.36
1e-07 0.160 Inf
1e-08 0.130 Inf
1e-09 0.033 Inf
1e-10 0.000 NaN
[1] "LOC105376975_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
NEFM 1.6 7.9 17 5.9e-05 0.38 0.00039 0.92 1
MYC -2.6 7.5 15 1.2e-04 0.38 0.00052 0.92 2
STMN2 1.7 7.7 13 3.9e-04 0.59 0.00110 0.92 3
TPM2 1.3 7.3 13 3.9e-04 0.59 0.00110 0.92 4
FNDC3A -1.2 6.7 13 5.1e-04 0.59 0.00120 0.92 5
CSPP1 -1.3 6.5 13 5.6e-04 0.59 0.00130 0.92 6
HS6ST1 -1.3 6.7 11 1.2e-03 0.84 0.00220 0.92 7
DIO3 -1.2 7.1 10 1.5e-03 0.84 0.00260 0.92 8
HMG20A -1.3 6.5 13 1.7e-03 0.84 0.00280 0.92 9
CCDC127 -1.1 6.6 10 1.7e-03 0.84 0.00280 0.92 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
NEFM 2.50 2.5
MYC 3.30 1.6
STMN2 6.70 2.2
TPM2 6.80 1.7
FNDC3A 7.70 1.5
CSPP1 8.40 1.4
HS6ST1 14.00 2.0
DIO3 16.00 2.0
HMG20A 17.00 1.9
CCDC127 18.00 1.8
1e-04 3.00 3.0
1e-05 1.00 Inf
1e-06 0.43 Inf
1e-07 0.30 Inf
1e-08 0.23 Inf
1e-09 0.20 Inf
1e-10 0.20 Inf
[1] "LOC105376975_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
ATF5 -1.50 6.9 15 0.00016 0.44 0.00056 0.75 1
SLC7A11 -1.40 6.6 14 0.00029 0.44 0.00079 0.75 2
PSAT1 -0.75 8.3 13 0.00040 0.44 0.00097 0.75 3
MCM5 -0.97 7.1 13 0.00041 0.44 0.00097 0.75 4
PHGDH -0.73 8.6 12 0.00051 0.44 0.00110 0.75 5
MTHFD2 -0.89 7.4 12 0.00059 0.44 0.00120 0.75 6
PLP1 1.10 6.7 12 0.00061 0.44 0.00120 0.75 7
NAT9 -0.90 6.8 12 0.00071 0.44 0.00140 0.75 8
TRIP12 0.89 6.6 12 0.00080 0.44 0.00160 0.75 9
CEBPB -1.30 6.8 12 0.00082 0.44 0.00160 0.75 10
1e-04 NA NA NA NA NA NA NA 0
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
ATF5 3.600 3.6
SLC7A11 5.000 2.5
PSAT1 6.100 2.0
MCM5 6.100 1.5
PHGDH 6.900 1.4
MTHFD2 7.700 1.3
PLP1 7.900 1.1
NAT9 8.800 1.1
TRIP12 9.900 1.1
CEBPB 10.000 1.0
1e-04 2.700 Inf
1e-05 0.770 Inf
1e-06 0.400 Inf
1e-07 0.170 Inf
1e-08 0.100 Inf
1e-09 0.067 Inf
1e-10 0.067 Inf
[1] "LOC105376975_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR
RP11-46C20.1 2.6 6.6 28 3.5e-07 0.0022 3.1e-05 0.20
ACBD3 1.7 6.8 14 2.4e-04 0.5300 5.5e-04 0.94
SPOCK1 1.9 6.6 14 3.1e-04 0.5300 6.2e-04 0.94
SDC2 1.4 7.7 13 3.3e-04 0.5300 6.3e-04 0.94
KIF5C -2.4 7.3 11 1.1e-03 0.7900 1.3e-03 0.94
A2M 1.8 6.6 11 1.2e-03 0.7900 1.4e-03 0.94
HES4 -2.3 7.7 11 1.4e-03 0.7900 1.6e-03 0.94
FNBP4 -3.1 6.8 10 1.6e-03 0.7900 1.8e-03 0.94
TOP2A -4.4 7.4 10 1.7e-03 0.7900 1.9e-03 0.94
OSBPL1A -3.0 6.8 10 1.8e-03 0.7900 2.0e-03 0.94
1e-04 NA NA NA NA NA NA NA
1e-05 NA NA NA NA NA NA NA
1e-06 NA NA NA NA NA NA NA
1e-07 NA NA NA NA NA NA NA
1e-08 NA NA NA NA NA NA NA
1e-09 NA NA NA NA NA NA NA
1e-10 NA NA NA NA NA NA NA
#in_real #in_perm EmpiricalFDR
RP11-46C20.1 1 0.200 0.20
ACBD3 2 3.500 1.80
SPOCK1 3 3.900 1.30
SDC2 4 4.000 1.00
KIF5C 5 8.300 1.70
A2M 6 8.800 1.50
HES4 7 10.000 1.50
FNBP4 8 11.000 1.40
TOP2A 9 12.000 1.30
OSBPL1A 10 13.000 1.30
1e-04 1 1.900 1.90
1e-05 1 0.960 0.96
1e-06 1 0.500 0.50
1e-07 0 0.100 Inf
1e-08 0 0.100 Inf
1e-09 0 0.033 Inf
1e-10 0 0.033 Inf
[1] "miR137_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -3.10 7.5 25 1.0e-06 0.0065 0.0001 0.66 1
PKMYT1 -1.40 6.7 16 8.9e-05 0.2800 0.0005 0.98 2
CDC6 -1.30 6.9 13 4.8e-04 0.6200 0.0012 0.98 3
APMAP -0.68 7.4 12 5.8e-04 0.6200 0.0013 0.98 4
NCAM1 -1.30 6.6 12 6.3e-04 0.6200 0.0014 0.98 5
GADD45G -1.90 7.4 12 7.1e-04 0.6200 0.0015 0.98 6
ARMCX6 0.80 7.0 11 8.9e-04 0.6200 0.0017 0.98 7
EIF4A3 -0.65 7.7 11 9.0e-04 0.6200 0.0017 0.98 8
NDC80 0.99 6.8 11 9.9e-04 0.6200 0.0019 0.98 9
LRRC28 0.92 6.7 11 1.1e-03 0.6200 0.0020 0.98 10
1e-04 NA NA NA NA NA NA NA 2
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 0.66 0.66
PKMYT1 3.20 1.60
CDC6 7.70 2.60
APMAP 8.50 2.10
NCAM1 9.00 1.80
GADD45G 9.60 1.60
ARMCX6 11.00 1.60
EIF4A3 11.00 1.40
NDC80 12.00 1.30
LRRC28 13.00 1.30
1e-04 3.40 1.70
1e-05 1.30 1.30
1e-06 0.66 Inf
1e-07 0.30 Inf
1e-08 0.17 Inf
1e-09 0.13 Inf
1e-10 0.10 Inf
[1] "miR137_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
DBNDD1 -1.8 6.4 19 3.1e-05 0.20 0.00025 0.76 1
STMN2 -2.6 7.2 15 1.3e-04 0.27 0.00046 0.76 2
SLC4A1AP -1.6 6.6 15 1.5e-04 0.27 0.00048 0.76 3
MYC -2.6 7.5 14 2.0e-04 0.27 0.00058 0.76 4
IRS1 1.1 6.6 14 2.1e-04 0.27 0.00060 0.76 5
FRZB -1.7 6.9 12 5.4e-04 0.50 0.00110 0.76 6
TRIM69 1.1 6.7 12 5.5e-04 0.50 0.00110 0.76 7
STX2 1.0 6.5 12 8.2e-04 0.53 0.00140 0.76 8
HAUS6 -1.3 6.6 12 8.4e-04 0.53 0.00140 0.76 9
MTX2 -1.0 6.9 11 9.1e-04 0.53 0.00160 0.76 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
DBNDD1 1.600 1.60
STMN2 2.900 1.50
SLC4A1AP 3.100 1.00
MYC 3.600 0.91
IRS1 3.800 0.76
FRZB 6.800 1.10
TRIM69 6.800 0.98
STX2 8.900 1.10
HAUS6 9.100 1.00
MTX2 9.900 0.99
1e-04 2.500 2.50
1e-05 0.990 Inf
1e-06 0.330 Inf
1e-07 0.099 Inf
1e-08 0.066 Inf
1e-09 0.033 Inf
1e-10 0.033 Inf
[1] "miR137_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -2.40 7.4 24 2.0e-06 0.013 0.00020 0.56 1
RGS5 1.30 6.7 20 1.2e-05 0.031 0.00028 0.56 2
DST 1.10 6.7 20 1.5e-05 0.031 0.00028 0.56 3
NQO1 1.20 7.5 16 7.1e-05 0.095 0.00046 0.56 4
SLC2A3 1.00 6.6 16 7.5e-05 0.095 0.00047 0.56 5
S100A16 1.10 6.7 16 1.0e-04 0.110 0.00053 0.56 6
PDLIM7 0.58 8.5 14 2.4e-04 0.210 0.00073 0.61 7
GPN1 0.68 7.3 14 3.0e-04 0.240 0.00083 0.61 8
ACTG1 0.25 13.0 13 3.5e-04 0.240 0.00090 0.61 9
ARMCX6 0.80 7.0 13 3.8e-04 0.240 0.00096 0.61 10
1e-04 NA NA NA NA NA NA NA 5
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 1.30 1.30
RGS5 1.80 0.88
DST 1.80 0.59
NQO1 2.90 0.73
SLC2A3 3.00 0.59
S100A16 3.30 0.56
PDLIM7 4.70 0.67
GPN1 5.20 0.65
ACTG1 5.70 0.63
ARMCX6 6.10 0.61
1e-04 3.30 0.65
1e-05 1.70 1.70
1e-06 1.10 Inf
1e-07 0.78 Inf
1e-08 0.47 Inf
1e-09 0.34 Inf
1e-10 0.30 Inf
[1] "NAB2_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
DDX10 1.50 6.7 23 3.6e-06 0.019 0.00015 0.53 1
MYC -3.20 7.5 22 6.0e-06 0.019 0.00017 0.53 2
WNT7B -1.80 6.6 16 9.0e-05 0.190 0.00043 0.79 3
DTNA -1.60 6.5 17 1.4e-04 0.220 0.00050 0.79 4
CUEDC1 -1.30 6.6 13 4.3e-04 0.510 0.00090 0.92 5
CMTM8 -1.50 6.6 12 5.8e-04 0.510 0.00110 0.92 6
XPO6 0.98 6.6 12 6.3e-04 0.510 0.00110 0.92 7
ISY1 0.94 6.7 12 6.4e-04 0.510 0.00120 0.92 8
PSMA5 -0.58 7.9 11 9.9e-04 0.700 0.00150 0.98 9
HIST1H1C 1.20 6.6 11 1.1e-03 0.700 0.00170 0.98 10
1e-04 NA NA NA NA NA NA NA 3
1e-05 NA NA NA NA NA NA NA 2
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
DDX10 0.93 0.93
MYC 1.10 0.53
WNT7B 2.70 0.91
DTNA 3.20 0.79
CUEDC1 5.70 1.10
CMTM8 6.90 1.20
XPO6 7.20 1.00
ISY1 7.30 0.92
PSMA5 9.80 1.10
HIST1H1C 11.00 1.10
1e-04 2.80 0.93
1e-05 1.20 0.60
1e-06 0.60 Inf
1e-07 0.27 Inf
1e-08 0.20 Inf
1e-09 0.20 Inf
1e-10 0.17 Inf
[1] "NAB2_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR
CLU 1.90 7.7 45 2.2e-10 1.4e-06 6.4e-05 0.19
NQO1 1.90 7.6 34 3.1e-08 9.7e-05 9.0e-05 0.19
GAP43 1.70 8.2 29 2.4e-07 5.1e-04 1.1e-04 0.19
FTH1 1.10 12.0 26 1.0e-06 1.6e-03 1.2e-04 0.19
CTD-2006C1.2 1.20 7.0 19 1.9e-05 2.4e-02 2.5e-04 0.32
IFI27L1 1.20 6.7 18 3.1e-05 3.3e-02 3.2e-04 0.34
SQSTM1 1.30 8.2 15 1.6e-04 1.3e-01 6.8e-04 0.49
FOXJ1 -1.80 6.5 15 1.6e-04 1.3e-01 6.8e-04 0.49
EIF4A2 0.73 8.1 14 2.0e-04 1.4e-01 7.9e-04 0.49
NKD1 -1.70 6.4 15 2.6e-04 1.6e-01 8.8e-04 0.49
1e-04 NA NA NA NA NA NA NA
1e-05 NA NA NA NA NA NA NA
1e-06 NA NA NA NA NA NA NA
1e-07 NA NA NA NA NA NA NA
1e-08 NA NA NA NA NA NA NA
1e-09 NA NA NA NA NA NA NA
1e-10 NA NA NA NA NA NA NA
#in_real #in_perm EmpiricalFDR
CLU 1 0.40 0.40
NQO1 2 0.57 0.29
GAP43 3 0.67 0.22
FTH1 4 0.77 0.19
CTD-2006C1.2 5 1.60 0.32
IFI27L1 6 2.00 0.34
SQSTM1 7 4.30 0.61
FOXJ1 8 4.30 0.54
EIF4A2 9 5.00 0.56
NKD1 10 5.60 0.56
1e-04 6 3.30 0.55
1e-05 4 1.20 0.31
1e-06 3 0.77 0.26
1e-07 2 0.57 0.29
1e-08 1 0.50 0.50
1e-09 1 0.47 0.47
1e-10 0 0.40 Inf
[1] "NAB2_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
SLC19A1 -2.00 6.5 19 5.3e-05 0.32 0.00027 0.98 1
EVA1B 1.30 6.6 16 1.0e-04 0.32 0.00038 0.98 2
MT-ATP6 0.63 11.0 14 3.1e-04 0.66 0.00077 0.98 3
PKMYT1 -1.60 6.7 13 4.7e-04 0.70 0.00100 0.98 4
AP5S1 -1.60 6.5 15 7.5e-04 0.70 0.00140 0.98 5
ARHGAP21 -1.50 6.6 12 7.6e-04 0.70 0.00140 0.98 6
ASCL1 1.30 7.1 11 8.7e-04 0.70 0.00160 0.98 7
TP53 -1.10 7.1 11 9.9e-04 0.70 0.00180 0.98 8
DLGAP5 1.20 6.7 11 1.1e-03 0.70 0.00200 0.98 9
TMCO3 -1.50 6.6 12 1.1e-03 0.70 0.00200 0.98 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
SLC19A1 1.70 1.7
EVA1B 2.40 1.2
MT-ATP6 4.90 1.6
PKMYT1 6.40 1.6
AP5S1 9.00 1.8
ARHGAP21 9.00 1.5
ASCL1 10.00 1.5
TP53 11.00 1.4
DLGAP5 12.00 1.4
TMCO3 12.00 1.2
1e-04 2.40 2.4
1e-05 0.70 Inf
1e-06 0.33 Inf
1e-07 0.27 Inf
1e-08 0.23 Inf
1e-09 0.13 Inf
1e-10 0.10 Inf
[1] "NGEF_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
NQO1 1.70 7.4 15 0.00013 0.64 0.00045 0.96 1
CTTN 1.40 7.0 13 0.00033 0.64 0.00076 0.96 2
SKP1 -0.73 8.9 13 0.00040 0.64 0.00086 0.96 3
CMBL -2.40 6.8 12 0.00056 0.64 0.00110 0.96 4
AKAP8L -2.70 6.7 12 0.00059 0.64 0.00110 0.96 5
TPX2 1.40 7.1 11 0.00089 0.64 0.00160 0.96 6
PHLDA3 -1.90 7.8 11 0.00097 0.64 0.00170 0.96 7
APRT -0.99 8.3 11 0.00100 0.64 0.00180 0.96 8
TTC39C 1.40 6.5 11 0.00110 0.64 0.00180 0.96 9
DEF8 -1.30 7.4 11 0.00110 0.64 0.00190 0.96 10
1e-04 NA NA NA NA NA NA NA 0
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
NQO1 2.90 2.9
CTTN 4.80 2.4
SKP1 5.50 1.8
CMBL 6.90 1.7
AKAP8L 7.30 1.5
TPX2 10.00 1.7
PHLDA3 11.00 1.6
APRT 11.00 1.4
TTC39C 12.00 1.3
DEF8 12.00 1.2
1e-04 2.60 Inf
1e-05 1.20 Inf
1e-06 0.86 Inf
1e-07 0.63 Inf
1e-08 0.43 Inf
1e-09 0.30 Inf
1e-10 0.23 Inf
[1] "NGEF_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
C2orf69 2.7 6.6 16 9.8e-05 0.62 0.00042 0.85 1
MSANTD2 2.4 6.5 13 5.1e-04 0.84 0.00081 0.85 2
EMG1 1.8 7.7 12 7.1e-04 0.84 0.00094 0.85 3
SKA3 2.4 6.6 12 7.3e-04 0.84 0.00097 0.85 4
SGO2 2.4 6.8 12 7.8e-04 0.84 0.00098 0.85 5
NDC80 2.4 6.7 12 8.5e-04 0.84 0.00100 0.85 6
TROAP 2.4 6.7 11 9.6e-04 0.84 0.00110 0.85 7
CDCA3 2.4 6.9 11 1.3e-03 0.84 0.00120 0.85 8
FAM83D 2.5 6.6 10 1.7e-03 0.84 0.00140 0.85 9
SRD5A3 2.2 6.6 10 1.9e-03 0.84 0.00150 0.85 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
C2orf69 2.60 2.60
MSANTD2 5.20 2.60
EMG1 5.90 2.00
SKA3 6.10 1.50
SGO2 6.20 1.20
NDC80 6.40 1.10
TROAP 6.90 0.99
CDCA3 7.70 0.97
FAM83D 9.00 1.00
SRD5A3 9.80 0.98
1e-04 2.60 2.60
1e-05 1.60 Inf
1e-06 1.10 Inf
1e-07 0.64 Inf
1e-08 0.44 Inf
1e-09 0.30 Inf
1e-10 0.13 Inf
[1] "PBRM1_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR
NDC80 2.6 6.7 23 3.5e-06 0.021 7.4e-05 0.24
PLK1 2.7 7.5 22 6.5e-06 0.021 9.0e-05 0.24
CDC25B 2.5 7.2 16 7.6e-05 0.120 1.7e-04 0.24
RP11-339B21.12 2.3 7.0 16 7.7e-05 0.120 1.7e-04 0.24
DLL1 2.7 7.0 16 1.1e-04 0.140 2.1e-04 0.24
JUN 1.8 7.9 15 1.3e-04 0.140 2.3e-04 0.24
TPX2 2.1 7.0 14 2.7e-04 0.230 3.4e-04 0.24
DLGAP5 2.3 6.7 14 2.9e-04 0.230 3.5e-04 0.24
PTTG1 2.0 8.5 13 3.8e-04 0.250 4.1e-04 0.24
ECT2 2.2 6.5 13 4.1e-04 0.250 4.1e-04 0.24
1e-04 NA NA NA NA NA NA NA
1e-05 NA NA NA NA NA NA NA
1e-06 NA NA NA NA NA NA NA
1e-07 NA NA NA NA NA NA NA
1e-08 NA NA NA NA NA NA NA
1e-09 NA NA NA NA NA NA NA
1e-10 NA NA NA NA NA NA NA
#in_real #in_perm EmpiricalFDR
NDC80 1 0.470 0.47
PLK1 2 0.570 0.28
CDC25B 3 1.100 0.36
RP11-339B21.12 4 1.100 0.27
DLL1 5 1.300 0.27
JUN 6 1.500 0.24
TPX2 7 2.200 0.31
DLGAP5 8 2.200 0.28
PTTG1 9 2.600 0.29
ECT2 10 2.600 0.26
1e-04 4 1.300 0.33
1e-05 2 0.570 0.28
1e-06 0 0.300 Inf
1e-07 0 0.170 Inf
1e-08 0 0.067 Inf
1e-09 0 0.000 NaN
1e-10 0 0.000 NaN
[1] "PBRM1_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
A2M 1.9 6.7 19 2.3e-05 0.14 0.00017 0.55 1
INTU 1.5 6.8 16 7.7e-05 0.18 0.00027 0.55 2
IFITM3 1.6 8.7 16 1.1e-04 0.18 0.00032 0.55 3
TPM2 1.9 7.3 16 1.1e-04 0.18 0.00035 0.55 4
PRC1 1.5 6.7 14 2.8e-04 0.35 0.00062 0.79 5
RGS5 1.5 6.6 13 3.7e-04 0.39 0.00075 0.79 6
CD9 1.5 6.7 12 7.2e-04 0.65 0.00120 0.98 7
MKI67 1.3 7.3 11 9.9e-04 0.66 0.00160 0.98 8
TFPT -2.0 6.8 11 1.0e-03 0.66 0.00160 0.98 9
PDCD2L -2.2 6.5 12 1.0e-03 0.66 0.00170 0.98 10
1e-04 NA NA NA NA NA NA NA 2
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
A2M 1.10 1.10
INTU 1.70 0.87
IFITM3 2.00 0.68
TPM2 2.20 0.55
PRC1 4.00 0.79
RGS5 4.70 0.79
CD9 7.90 1.10
MKI67 10.00 1.30
TFPT 10.00 1.20
PDCD2L 11.00 1.10
1e-04 2.00 1.00
1e-05 0.90 Inf
1e-06 0.50 Inf
1e-07 0.33 Inf
1e-08 0.20 Inf
1e-09 0.17 Inf
1e-10 0.17 Inf
[1] "PBRM1_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
TPM2 3.9 7.4 47 1.3e-10 8.2e-07 3.2e-05 0.10 1
RGS5 3.1 6.7 35 2.1e-08 6.6e-05 4.7e-05 0.10 2
TPPP3 3.1 6.6 28 3.3e-07 5.3e-04 6.3e-05 0.10 3
IGFBP5 3.3 6.8 28 3.3e-07 5.3e-04 6.3e-05 0.10 4
SPARC 1.6 8.6 20 1.5e-05 1.6e-02 1.3e-04 0.14 5
SESN3 2.6 6.6 20 1.5e-05 1.6e-02 1.3e-04 0.14 6
HDAC2 -2.0 8.5 16 1.1e-04 9.9e-02 2.5e-04 0.19 7
CCND2 2.3 7.1 15 1.5e-04 1.1e-01 2.8e-04 0.19 8
HEBP1 1.9 6.9 15 1.6e-04 1.1e-01 2.8e-04 0.19 9
CEBPD 2.3 6.7 14 2.4e-04 1.5e-01 3.5e-04 0.19 10
1e-04 NA NA NA NA NA NA NA 6
1e-05 NA NA NA NA NA NA NA 4
1e-06 NA NA NA NA NA NA NA 4
1e-07 NA NA NA NA NA NA NA 2
1e-08 NA NA NA NA NA NA NA 1
1e-09 NA NA NA NA NA NA NA 1
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
TPM2 0.20 0.20
RGS5 0.30 0.15
TPPP3 0.40 0.13
IGFBP5 0.40 0.10
SPARC 0.83 0.17
SESN3 0.83 0.14
HDAC2 1.60 0.22
CCND2 1.80 0.22
HEBP1 1.80 0.20
CEBPD 2.20 0.22
1e-04 1.60 0.26
1e-05 0.77 0.19
1e-06 0.50 0.12
1e-07 0.37 0.18
1e-08 0.30 0.30
1e-09 0.27 0.27
1e-10 0.20 Inf
[1] "PCDHA123_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
RGS5 1.40 6.7 27 5.4e-07 0.0034 0.00011 0.53 1
ARMCX6 0.90 7.0 17 5.7e-05 0.1800 0.00031 0.53 2
NUP58 -1.20 6.6 16 9.5e-05 0.2000 0.00041 0.53 3
GAP43 0.92 8.1 14 2.8e-04 0.2500 0.00070 0.53 4
PHLDA1 1.10 7.1 14 3.0e-04 0.2500 0.00072 0.53 5
PDLIM2 0.79 7.4 13 3.2e-04 0.2500 0.00075 0.53 6
DST 0.96 6.7 13 3.3e-04 0.2500 0.00075 0.53 7
FAM111B -1.20 6.5 13 3.6e-04 0.2500 0.00079 0.53 8
MYC -1.70 7.5 13 3.6e-04 0.2500 0.00080 0.53 9
SSR3 0.52 8.0 13 4.0e-04 0.2500 0.00083 0.53 10
1e-04 NA NA NA NA NA NA NA 3
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
RGS5 0.700 0.70
ARMCX6 2.000 0.99
NUP58 2.600 0.87
GAP43 4.400 1.10
PHLDA1 4.600 0.92
PDLIM2 4.800 0.80
DST 4.800 0.68
FAM111B 5.000 0.63
MYC 5.100 0.56
SSR3 5.300 0.53
1e-04 2.700 0.90
1e-05 1.300 1.30
1e-06 0.770 0.77
1e-07 0.200 Inf
1e-08 0.067 Inf
1e-09 0.033 Inf
1e-10 0.033 Inf
[1] "PCDHA123_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -3.40 7.3 43 3.8e-10 2.4e-06 0.00000 0.00 1
SNAPC1 1.20 6.7 17 5.9e-05 1.7e-01 0.00025 0.57 2
KCTD10 0.95 6.6 16 8.2e-05 1.7e-01 0.00031 0.57 3
CDCA7 -1.00 6.6 14 2.1e-04 3.3e-01 0.00057 0.57 4
CTGF 0.85 8.5 14 2.6e-04 3.3e-01 0.00064 0.57 5
MARCH7 0.85 6.6 13 5.6e-04 3.8e-01 0.00100 0.57 6
LASP1 0.83 6.8 12 5.7e-04 3.8e-01 0.00100 0.57 7
MSRA 0.87 6.6 12 5.9e-04 3.8e-01 0.00100 0.57 8
SPIN2B -1.00 6.4 14 6.1e-04 3.8e-01 0.00110 0.57 9
RACGAP1 0.88 6.6 12 6.3e-04 3.8e-01 0.00110 0.57 10
1e-04 NA NA NA NA NA NA NA 3
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 1
1e-08 NA NA NA NA NA NA NA 1
1e-09 NA NA NA NA NA NA NA 1
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 0.000 0.000
SNAPC1 1.600 0.790
KCTD10 2.000 0.660
CDCA7 3.600 0.900
CTGF 4.100 0.820
MARCH7 6.300 1.100
LASP1 6.500 0.920
MSRA 6.500 0.820
SPIN2B 6.700 0.740
RACGAP1 6.800 0.680
1e-04 2.200 0.750
1e-05 0.640 0.640
1e-06 0.370 0.370
1e-07 0.230 0.230
1e-08 0.067 0.067
1e-09 0.033 0.033
1e-10 0.000 NaN
[1] "PCDHA123_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -3.40 7.3 42 5.4e-10 3.4e-06 0.00001 0.065 1
SMG1 1.00 6.6 17 5.6e-05 1.8e-01 0.00027 0.610 2
STMN2 -1.80 7.1 16 9.9e-05 2.1e-01 0.00035 0.610 3
GPM6B 0.46 8.5 14 2.2e-04 2.7e-01 0.00054 0.610 4
NRDC -0.82 7.0 14 2.5e-04 2.7e-01 0.00057 0.610 5
PTPN11 0.84 6.6 14 2.6e-04 2.7e-01 0.00058 0.610 6
NUP214 -0.94 6.5 12 8.0e-04 7.0e-01 0.00130 1.000 7
HPCAL1 0.82 6.6 11 8.9e-04 7.0e-01 0.00130 1.000 8
MSRA 0.84 6.6 11 1.2e-03 8.6e-01 0.00180 1.000 9
EVA1B 0.82 6.6 10 1.5e-03 9.2e-01 0.00210 1.000 10
1e-04 NA NA NA NA NA NA NA 3
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 1
1e-08 NA NA NA NA NA NA NA 1
1e-09 NA NA NA NA NA NA NA 1
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 0.065 0.065
SMG1 1.700 0.850
STMN2 2.200 0.740
GPM6B 3.400 0.850
NRDC 3.600 0.720
PTPN11 3.700 0.610
NUP214 8.000 1.100
HPCAL1 8.500 1.100
MSRA 11.000 1.200
EVA1B 13.000 1.300
1e-04 2.200 0.740
1e-05 0.750 0.750
1e-06 0.390 0.390
1e-07 0.160 0.160
1e-08 0.130 0.130
1e-09 0.065 0.065
1e-10 0.000 NaN
[1] "pos_SNAP91_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR
EDC3 2.2 6.6 10.0 0.0018 0.83 0.0014 1
GUF1 2.1 6.6 9.6 0.0023 0.83 0.0017 1
NHLRC3 2.1 6.7 9.5 0.0024 0.83 0.0017 1
DTX3 2.1 6.6 9.3 0.0027 0.83 0.0019 1
TDG -4.1 7.3 8.8 0.0035 0.83 0.0025 1
EFCC1 2.1 6.6 8.6 0.0039 0.83 0.0028 1
RP11-357C3.3 1.9 6.6 8.2 0.0048 0.83 0.0034 1
USP16 -4.0 7.2 7.9 0.0055 0.83 0.0039 1
RP11-329L6.2 -4.3 7.3 7.9 0.0056 0.83 0.0039 1
LLPH -4.0 7.2 7.7 0.0062 0.83 0.0043 1
1e-04 NA NA NA NA NA NA NA
1e-05 NA NA NA NA NA NA NA
1e-06 NA NA NA NA NA NA NA
1e-07 NA NA NA NA NA NA NA
1e-08 NA NA NA NA NA NA NA
1e-09 NA NA NA NA NA NA NA
1e-10 NA NA NA NA NA NA NA
#in_real #in_perm EmpiricalFDR
EDC3 1 8.90 8.9
GUF1 2 11.00 5.3
NHLRC3 3 11.00 3.6
DTX3 4 12.00 3.0
TDG 5 16.00 3.2
EFCC1 6 18.00 3.0
RP11-357C3.3 7 22.00 3.1
USP16 8 25.00 3.1
RP11-329L6.2 9 25.00 2.8
LLPH 10 27.00 2.7
1e-04 0 1.50 Inf
1e-05 0 0.70 Inf
1e-06 0 0.30 Inf
1e-07 0 0.17 Inf
1e-08 0 0.17 Inf
1e-09 0 0.17 Inf
1e-10 0 0.13 Inf
[1] "pos_SNAP91_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
RGS5 1.80 6.7 29 2.3e-07 0.0014 3.1e-05 0.20 1
WDFY1 1.60 6.6 21 1.1e-05 0.0340 1.1e-04 0.35 2
THG1L 1.10 6.9 16 1.0e-04 0.2100 3.5e-04 0.70 3
MYC -3.10 7.5 15 1.6e-04 0.2100 5.1e-04 0.70 4
SLC25A17 -1.60 6.6 15 1.7e-04 0.2100 5.5e-04 0.70 5
LIN28B 1.00 6.7 12 7.0e-04 0.7400 1.4e-03 1.00 6
RSRP1 1.10 6.6 11 9.5e-04 0.8300 1.7e-03 1.00 7
PRSS23 0.77 8.2 11 1.1e-03 0.8300 1.8e-03 1.00 8
ARMC9 -1.50 6.5 11 1.2e-03 0.8400 2.0e-03 1.00 9
CAV1 1.20 7.3 11 1.3e-03 0.8400 2.2e-03 1.00 10
1e-04 NA NA NA NA NA NA NA 2
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
RGS5 0.200 0.20
WDFY1 0.700 0.35
THG1L 2.200 0.73
MYC 3.300 0.81
SLC25A17 3.500 0.70
LIN28B 9.000 1.50
RSRP1 11.000 1.60
PRSS23 12.000 1.50
ARMC9 13.000 1.40
CAV1 14.000 1.40
1e-04 2.200 1.10
1e-05 0.700 0.70
1e-06 0.230 0.23
1e-07 0.130 Inf
1e-08 0.100 Inf
1e-09 0.100 Inf
1e-10 0.033 Inf
[1] "PPP1R16B_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -2.50 7.4 20 1.6e-05 0.097 0.00027 0.74 1
ELMO1 -1.50 6.4 20 3.1e-05 0.097 0.00031 0.74 2
CAV1 1.30 7.4 16 1.0e-04 0.210 0.00049 0.74 3
ZNF273 -1.30 6.4 16 2.1e-04 0.330 0.00064 0.74 4
IGFBP5 -1.60 6.6 14 2.8e-04 0.360 0.00081 0.74 5
POLR3A -1.20 6.5 13 4.1e-04 0.430 0.00098 0.74 6
SRPK2 0.65 7.4 12 7.1e-04 0.600 0.00140 0.74 7
KCTD10 0.92 6.6 12 7.6e-04 0.600 0.00140 0.74 8
NEFM 1.30 7.8 11 1.1e-03 0.620 0.00190 0.74 9
RAD54L -1.10 6.5 11 1.1e-03 0.620 0.00200 0.74 10
1e-04 NA NA NA NA NA NA NA 2
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 1.70 1.70
ELMO1 2.00 0.99
CAV1 3.10 1.00
ZNF273 4.10 1.00
IGFBP5 5.20 1.00
POLR3A 6.20 1.00
SRPK2 8.70 1.20
KCTD10 9.00 1.10
NEFM 12.00 1.40
RAD54L 12.00 1.20
1e-04 3.10 1.60
1e-05 1.60 Inf
1e-06 0.74 Inf
1e-07 0.37 Inf
1e-08 0.27 Inf
1e-09 0.17 Inf
1e-10 0.10 Inf
[1] "PPP1R16B_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
DDX10 1.50 6.7 20 1.1e-05 0.072 0.00012 0.77 1
HIST1H1C 1.60 6.6 17 5.0e-05 0.150 0.00032 0.79 2
MYC -2.90 7.5 17 7.0e-05 0.150 0.00037 0.79 3
CCNE2 -1.60 6.5 13 3.6e-04 0.500 0.00096 1.00 4
PMP22 -1.50 6.5 13 5.1e-04 0.500 0.00130 1.00 5
EZR 0.83 7.5 12 5.4e-04 0.500 0.00130 1.00 6
GADD45G 1.60 7.9 12 5.6e-04 0.500 0.00140 1.00 7
TMX3 -1.30 6.5 12 6.4e-04 0.500 0.00150 1.00 8
ZNF512 0.95 6.7 11 9.4e-04 0.670 0.00190 1.00 9
DBNDD1 -1.30 6.5 11 1.1e-03 0.720 0.00220 1.00 10
1e-04 NA NA NA NA NA NA NA 3
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
DDX10 0.77 0.77
HIST1H1C 2.00 1.00
MYC 2.40 0.79
CCNE2 6.10 1.50
PMP22 8.10 1.60
EZR 8.40 1.40
GADD45G 8.60 1.20
TMX3 9.60 1.20
ZNF512 12.00 1.30
DBNDD1 14.00 1.40
1e-04 2.80 0.92
1e-05 0.77 Inf
1e-06 0.43 Inf
1e-07 0.27 Inf
1e-08 0.23 Inf
1e-09 0.17 Inf
1e-10 0.17 Inf
[1] "PPP1R16B_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -3.20 7.5 21 7.5e-06 0.047 8.9e-05 0.56 1
EIF4ENIF1 -1.60 6.5 19 7.0e-05 0.220 2.6e-04 0.62 2
PROM1 -1.60 6.5 16 1.9e-04 0.300 4.8e-04 0.62 3
FAM83D -1.60 6.5 15 1.9e-04 0.300 4.8e-04 0.62 4
VGF -1.80 6.7 14 2.7e-04 0.320 5.6e-04 0.62 5
ASCL1 1.30 7.2 14 3.0e-04 0.320 5.9e-04 0.62 6
LIX1 -1.40 6.5 13 5.4e-04 0.440 9.2e-04 0.73 7
PTRF -1.70 7.0 12 6.1e-04 0.440 1.0e-03 0.73 8
SMG1 0.99 6.6 12 6.3e-04 0.440 1.0e-03 0.73 9
SNAPC2 0.83 7.1 11 1.0e-03 0.520 1.5e-03 0.75 10
1e-04 NA NA NA NA NA NA NA 2
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 0.560 0.56
EIF4ENIF1 1.700 0.83
PROM1 3.000 1.00
FAM83D 3.000 0.75
VGF 3.600 0.71
ASCL1 3.700 0.62
LIX1 5.800 0.83
PTRF 6.400 0.80
SMG1 6.600 0.73
SNAPC2 9.800 0.98
1e-04 2.000 1.00
1e-05 0.630 0.63
1e-06 0.230 Inf
1e-07 0.130 Inf
1e-08 0.066 Inf
1e-09 0.066 Inf
1e-10 0.033 Inf
[1] "RERE_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
TSC22D4 -1.60 6.6 23 7.4e-06 0.047 0.00017 0.90 1
MYC -2.40 7.5 18 3.2e-05 0.100 0.00031 0.90 2
DBNDD1 -1.50 6.5 18 6.9e-05 0.150 0.00043 0.90 3
STMN2 -2.00 7.2 14 2.4e-04 0.390 0.00076 0.98 4
EIF1AD -1.30 6.5 14 3.1e-04 0.390 0.00085 0.98 5
TPX2 0.96 7.1 12 5.3e-04 0.490 0.00110 0.98 6
ASGR1 -1.20 6.7 12 6.2e-04 0.490 0.00130 0.98 7
SNX27 0.85 6.8 12 6.2e-04 0.490 0.00130 0.98 8
NDC80 0.97 6.8 12 7.4e-04 0.520 0.00140 0.98 9
ISG20L2 -0.92 6.9 11 9.2e-04 0.560 0.00170 0.98 10
1e-04 NA NA NA NA NA NA NA 3
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
TSC22D4 1.10 1.10
MYC 2.00 0.99
DBNDD1 2.70 0.90
STMN2 4.80 1.20
EIF1AD 5.40 1.10
TPX2 7.20 1.20
ASGR1 8.00 1.10
SNX27 8.10 1.00
NDC80 9.10 1.00
ISG20L2 11.00 1.10
1e-04 3.10 1.00
1e-05 1.20 1.20
1e-06 0.64 Inf
1e-07 0.47 Inf
1e-08 0.37 Inf
1e-09 0.23 Inf
1e-10 0.10 Inf
[1] "RERE_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -3.20 7.5 26 6.9e-07 0.0044 5.3e-05 0.33 1
USMG5 -0.46 8.7 15 1.8e-04 0.5600 5.2e-04 1.00 2
KDELR2 -0.61 8.0 13 3.2e-04 0.6500 7.5e-04 1.00 3
FBXO5 -1.20 6.9 12 5.2e-04 0.6500 1.1e-03 1.00 4
KCTD10 0.98 6.6 12 5.6e-04 0.6500 1.1e-03 1.00 5
MRPL23 -0.69 7.5 12 7.3e-04 0.6500 1.3e-03 1.00 6
TAGLN3 1.20 7.5 12 7.6e-04 0.6500 1.3e-03 1.00 7
HIST1H1C 1.10 6.6 12 8.2e-04 0.6500 1.4e-03 1.00 8
ZNF48 0.84 6.7 11 1.1e-03 0.7500 1.7e-03 1.00 9
N4BP2 0.86 6.7 10 1.4e-03 0.7700 2.2e-03 1.00 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 0.330 0.33
USMG5 3.300 1.70
KDELR2 4.700 1.60
FBXO5 6.700 1.70
KCTD10 7.200 1.40
MRPL23 8.300 1.40
TAGLN3 8.500 1.20
HIST1H1C 8.900 1.10
ZNF48 11.000 1.20
N4BP2 14.000 1.40
1e-04 2.200 2.20
1e-05 0.800 0.80
1e-06 0.430 0.43
1e-07 0.130 Inf
1e-08 0.067 Inf
1e-09 0.067 Inf
1e-10 0.067 Inf
[1] "RERE_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MAFF -2.50 6.6 19 2.3e-05 0.14 0.00027 1 1
AC093323.3 -1.70 6.6 16 1.1e-04 0.32 0.00061 1 2
GLIPR1 1.40 6.7 15 1.5e-04 0.32 0.00076 1 3
BRCA1 1.10 6.7 12 6.0e-04 0.93 0.00170 1 4
SLC2A3 1.10 6.6 11 9.5e-04 0.93 0.00230 1 5
HIPK2 0.92 7.0 11 1.1e-03 0.93 0.00270 1 6
TADA1 -1.60 6.5 13 1.1e-03 0.93 0.00270 1 7
METTL8 -1.50 6.6 10 1.4e-03 0.93 0.00310 1 8
CADM1 1.00 7.0 10 1.4e-03 0.93 0.00310 1 9
STMN2 -2.40 7.3 10 1.5e-03 0.93 0.00310 1 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MAFF 1.70 1.7
AC093323.3 3.90 1.9
GLIPR1 4.80 1.6
BRCA1 11.00 2.7
SLC2A3 15.00 2.9
HIPK2 17.00 2.8
TADA1 17.00 2.4
METTL8 20.00 2.4
CADM1 20.00 2.2
STMN2 20.00 2.0
1e-04 3.80 3.8
1e-05 1.20 Inf
1e-06 0.50 Inf
1e-07 0.37 Inf
1e-08 0.27 Inf
1e-09 0.20 Inf
1e-10 0.17 Inf
[1] "SETD1A_1st_exon_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
EMP3 -2.6 6.7 19 1.9e-05 0.12 0.00031 1 1
ZNF33A -2.0 6.6 17 5.9e-05 0.19 0.00047 1 2
DLL3 -3.1 7.1 15 1.6e-04 0.29 0.00071 1 3
KLHL8 -1.9 6.4 16 2.0e-04 0.29 0.00083 1 4
AGPAT2 -1.9 6.6 14 2.3e-04 0.29 0.00090 1 5
JAKMIP2 -1.7 6.6 13 4.7e-04 0.50 0.00130 1 6
SCPEP1 1.2 6.6 12 5.8e-04 0.50 0.00150 1 7
SKA3 1.2 6.6 12 6.3e-04 0.50 0.00160 1 8
TRIM26 -1.7 6.5 13 9.3e-04 0.61 0.00210 1 9
SNAPC3 1.1 6.8 11 9.9e-04 0.61 0.00220 1 10
1e-04 NA NA NA NA NA NA NA 2
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
EMP3 2.00 2.0
ZNF33A 3.00 1.5
DLL3 4.50 1.5
KLHL8 5.30 1.3
AGPAT2 5.70 1.1
JAKMIP2 8.60 1.4
SCPEP1 9.80 1.4
SKA3 10.00 1.3
TRIM26 13.00 1.5
SNAPC3 14.00 1.4
1e-04 3.70 1.9
1e-05 1.70 Inf
1e-06 0.97 Inf
1e-07 0.73 Inf
1e-08 0.67 Inf
1e-09 0.63 Inf
1e-10 0.53 Inf
[1] "SETD1A_1st_exon_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
SERPINE2 1.60 6.7 25 1.3e-06 0.0046 0.00016 0.29 1
RGS5 1.60 6.7 25 1.5e-06 0.0046 0.00016 0.29 2
RAB13 0.86 8.0 22 4.9e-06 0.0100 0.00019 0.29 3
KCTD10 1.40 6.6 21 7.3e-06 0.0110 0.00022 0.29 4
CALD1 1.10 8.1 21 8.7e-06 0.0110 0.00024 0.29 5
MMP2 1.30 6.5 19 1.9e-05 0.0200 0.00030 0.29 6
TPM2 1.60 7.3 19 2.2e-05 0.0200 0.00031 0.29 7
ASRGL1 -1.50 7.0 18 4.4e-05 0.0350 0.00040 0.29 8
TAGLN 1.30 9.3 17 6.0e-05 0.0390 0.00047 0.29 9
S100A16 1.30 6.7 17 6.1e-05 0.0390 0.00048 0.29 10
1e-04 NA NA NA NA NA NA NA 12
1e-05 NA NA NA NA NA NA NA 5
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
SERPINE2 1.00 1.00
RGS5 1.00 0.51
RAB13 1.20 0.41
KCTD10 1.40 0.35
CALD1 1.50 0.30
MMP2 1.90 0.32
TPM2 2.00 0.29
ASRGL1 2.50 0.32
TAGLN 3.00 0.33
S100A16 3.00 0.30
1e-04 3.90 0.32
1e-05 1.60 0.32
1e-06 0.95 Inf
1e-07 0.47 Inf
1e-08 0.44 Inf
1e-09 0.37 Inf
1e-10 0.27 Inf
[1] "SETD1A_1st_exon_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
UBB -4.0 9.5 17 5.4e-05 0.35 0.00020 0.66 1
FXYD6 -3.5 8.0 14 2.5e-04 0.69 0.00036 0.66 2
BEX2 2.3 6.9 13 4.0e-04 0.69 0.00050 0.66 3
MSTO1 2.2 6.5 13 4.7e-04 0.69 0.00055 0.66 4
PTN 2.0 8.0 12 5.4e-04 0.69 0.00064 0.66 5
FTH1 1.3 12.0 11 1.1e-03 0.74 0.00110 0.66 6
COX11 -4.1 7.3 11 1.1e-03 0.74 0.00110 0.66 7
CST3 -2.1 8.2 11 1.2e-03 0.74 0.00110 0.66 8
TMSB10 1.0 12.0 11 1.4e-03 0.74 0.00120 0.66 9
MGRN1 2.0 6.6 11 1.4e-03 0.74 0.00130 0.66 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
UBB 1.20 1.20
FXYD6 2.30 1.10
BEX2 3.10 1.00
MSTO1 3.50 0.88
PTN 4.00 0.81
FTH1 6.70 1.10
COX11 6.90 0.98
CST3 7.20 0.90
TMSB10 7.90 0.88
MGRN1 8.10 0.81
1e-04 1.60 1.60
1e-05 0.50 Inf
1e-06 0.17 Inf
1e-07 0.10 Inf
1e-08 0.00 NaN
1e-09 0.00 NaN
1e-10 0.00 NaN
[1] "STAT6_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -3.60 7.5 17.0 5.1e-05 0.32 0.00021 1 1
IGFBP5 -2.40 6.6 15.0 1.8e-04 0.57 0.00039 1 2
DHODH 1.20 6.6 12.0 5.8e-04 1.00 0.00094 1 3
EMP3 -1.80 6.7 12.0 6.5e-04 1.00 0.00100 1 4
SOX21 1.00 6.7 10.0 1.6e-03 1.00 0.00210 1 5
CCDC138 0.98 6.6 10.0 1.8e-03 1.00 0.00240 1 6
PDCD11 -1.20 6.7 10.0 1.8e-03 1.00 0.00240 1 7
MYO6 -1.30 6.6 9.7 2.2e-03 1.00 0.00290 1 8
EIF2D -1.10 6.8 9.5 2.3e-03 1.00 0.00310 1 9
RAB28 0.89 6.9 9.4 2.5e-03 1.00 0.00330 1 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 1.400 1.4
IGFBP5 2.500 1.2
DHODH 6.000 2.0
EMP3 6.500 1.6
SOX21 13.000 2.7
CCDC138 15.000 2.5
PDCD11 16.000 2.2
MYO6 18.000 2.3
EIF2D 19.000 2.2
RAB28 21.000 2.1
1e-04 1.900 1.9
1e-05 0.660 Inf
1e-06 0.430 Inf
1e-07 0.270 Inf
1e-08 0.100 Inf
1e-09 0.033 Inf
1e-10 0.033 Inf
[1] "STAT6_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
TP53I3 1.30 7.1 18 3.6e-05 0.23 0.00030 0.82 1
IMPA2 -1.40 6.8 16 1.0e-04 0.29 0.00044 0.82 2
CYFIP2 0.97 6.9 14 2.0e-04 0.29 0.00068 0.82 3
ZNF561 -1.40 6.5 14 2.0e-04 0.29 0.00068 0.82 4
DHFR -0.94 7.7 14 2.3e-04 0.29 0.00073 0.82 5
LTBP1 -1.50 6.5 17 2.9e-04 0.31 0.00083 0.82 6
STMN2 -2.10 7.2 13 3.6e-04 0.32 0.00091 0.82 7
CDKN1C 1.40 7.1 12 6.1e-04 0.40 0.00130 0.87 8
CCNH 0.89 6.7 12 6.5e-04 0.40 0.00140 0.87 9
LAMTOR5 0.49 8.4 12 6.7e-04 0.40 0.00150 0.87 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
TP53I3 1.900 1.90
IMPA2 2.800 1.40
CYFIP2 4.300 1.40
ZNF561 4.300 1.10
DHFR 4.600 0.92
LTBP1 5.200 0.87
STMN2 5.800 0.82
CDKN1C 8.500 1.10
CCNH 9.200 1.00
LAMTOR5 9.400 0.94
1e-04 2.800 2.80
1e-05 1.200 Inf
1e-06 0.470 Inf
1e-07 0.130 Inf
1e-08 0.100 Inf
1e-09 0.100 Inf
1e-10 0.034 Inf
[1] "STAT6_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -2.40 7.4 22 5.7e-06 0.036 0.00020 1 1
GADD45G 1.60 8.1 14 2.0e-04 0.570 0.00069 1 2
MPZL1 0.80 6.8 13 3.5e-04 0.570 0.00100 1 3
TACC3 -1.10 6.9 13 3.6e-04 0.570 0.00100 1 4
LIX1 1.00 6.7 12 5.1e-04 0.640 0.00120 1 5
CCNDBP1 -0.98 6.7 11 8.7e-04 0.750 0.00170 1 6
PLK1 -1.10 7.2 11 9.1e-04 0.750 0.00180 1 7
TUBA1C -1.20 6.8 11 1.1e-03 0.750 0.00200 1 8
OLMALINC -1.10 6.5 11 1.2e-03 0.750 0.00220 1 9
NFKBIE -1.00 6.5 11 1.2e-03 0.750 0.00220 1 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 1.30 1.3
GADD45G 4.40 2.2
MPZL1 6.40 2.1
TACC3 6.40 1.6
LIX1 7.80 1.6
CCNDBP1 11.00 1.8
PLK1 11.00 1.6
TUBA1C 13.00 1.6
OLMALINC 14.00 1.5
NFKBIE 14.00 1.4
1e-04 3.00 3.0
1e-05 1.40 1.4
1e-06 0.85 Inf
1e-07 0.59 Inf
1e-08 0.26 Inf
1e-09 0.13 Inf
1e-10 0.13 Inf
[1] "TCF4-ITF2_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
TSPAN15 -1.50 6.7 18 2.8e-05 0.17 0.00019 0.97 1
SLC20A2 -1.20 6.6 14 2.5e-04 0.54 0.00060 0.97 2
IDI1 -0.62 8.2 13 3.6e-04 0.54 0.00076 0.97 3
CLK3 0.89 6.8 13 4.1e-04 0.54 0.00083 0.97 4
SCD5 -1.20 6.6 14 4.2e-04 0.54 0.00084 0.97 5
FAM111B -1.20 6.5 12 5.4e-04 0.58 0.00110 0.97 6
GPATCH11 -1.20 6.5 16 7.7e-04 0.70 0.00130 0.97 7
HMBS -0.72 7.2 11 9.1e-04 0.72 0.00150 0.97 8
GPI -0.77 7.1 11 1.0e-03 0.73 0.00160 0.97 9
SEC16A -1.10 6.6 12 1.2e-03 0.74 0.00170 0.97 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
TSPAN15 1.200 1.2
SLC20A2 3.800 1.9
IDI1 4.800 1.6
CLK3 5.300 1.3
SCD5 5.400 1.1
FAM111B 6.700 1.1
GPATCH11 8.300 1.2
HMBS 9.200 1.2
GPI 10.000 1.1
SEC16A 11.000 1.1
1e-04 2.200 2.2
1e-05 0.770 Inf
1e-06 0.340 Inf
1e-07 0.270 Inf
1e-08 0.200 Inf
1e-09 0.067 Inf
1e-10 0.000 NaN
[1] "TCF4-ITF2_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -3.00 7.5 25 1.2e-06 0.0079 0.00011 0.55 1
RGS5 1.40 6.7 20 1.4e-05 0.0440 0.00020 0.55 2
STMN2 -2.40 7.2 18 3.4e-05 0.0720 0.00026 0.55 3
ATPIF1 0.54 8.3 15 1.2e-04 0.1900 0.00040 0.63 4
CMTR2 -1.30 6.5 16 3.4e-04 0.4300 0.00079 0.86 5
GADD45G -1.90 7.4 13 4.9e-04 0.4500 0.00095 0.86 6
JAKMIP2 -1.20 6.6 13 5.0e-04 0.4500 0.00095 0.86 7
FOS 1.00 6.9 12 6.4e-04 0.5000 0.00110 0.87 8
KCTD10 0.92 6.6 11 1.2e-03 0.7200 0.00170 0.90 9
PLSCR1 -1.00 6.6 11 1.2e-03 0.7200 0.00170 0.90 10
1e-04 NA NA NA NA NA NA NA 3
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 0.67 0.67
RGS5 1.30 0.63
STMN2 1.60 0.55
ATPIF1 2.50 0.63
CMTR2 5.00 1.00
GADD45G 6.00 1.00
JAKMIP2 6.00 0.86
FOS 7.00 0.87
KCTD10 10.00 1.20
PLSCR1 11.00 1.10
1e-04 2.40 0.80
1e-05 1.10 1.10
1e-06 0.60 Inf
1e-07 0.23 Inf
1e-08 0.20 Inf
1e-09 0.13 Inf
1e-10 0.13 Inf
[1] "TCF4-ITF2_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
SNAPC1 3.1 6.8 57 2.6e-12 1.7e-08 1.6e-05 0.10 1
CLN8 -2.8 6.7 14 3.1e-04 5.8e-01 6.9e-04 0.94 2
SLC7A11 1.7 6.8 13 4.9e-04 5.8e-01 9.0e-04 0.94 3
RNF25 -2.7 6.7 12 5.6e-04 5.8e-01 1.0e-03 0.94 4
MRPS28 -2.4 6.8 12 5.9e-04 5.8e-01 1.0e-03 0.94 5
CHMP4A -2.6 6.6 12 6.6e-04 5.8e-01 1.1e-03 0.94 6
DIO3 1.5 7.3 12 7.6e-04 5.8e-01 1.2e-03 0.94 7
PTRH1 -2.5 6.6 12 8.1e-04 5.8e-01 1.3e-03 0.94 8
TWF1 1.4 6.7 12 8.2e-04 5.8e-01 1.3e-03 0.94 9
CCDC160 -2.4 6.6 11 1.1e-03 6.4e-01 1.8e-03 1.00 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 1
1e-08 NA NA NA NA NA NA NA 1
1e-09 NA NA NA NA NA NA NA 1
1e-10 NA NA NA NA NA NA NA 1
#in_perm EmpiricalFDR
SNAPC1 0.10 0.10
CLN8 4.40 2.20
SLC7A11 5.70 1.90
RNF25 6.30 1.60
MRPS28 6.60 1.30
CHMP4A 7.10 1.20
DIO3 7.90 1.10
PTRH1 8.40 1.00
TWF1 8.50 0.94
CCDC160 11.00 1.10
1e-04 2.10 2.10
1e-05 1.00 1.00
1e-06 0.67 0.67
1e-07 0.43 0.43
1e-08 0.23 0.23
1e-09 0.20 0.20
1e-10 0.20 0.20
[1] "TRANK1_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
HMGCS1 1.6 8.1 12.0 0.00068 0.86 0.00099 1 1
CKAP2L 2.3 6.6 11.0 0.00100 0.86 0.00130 1 2
SDF2L1 2.0 7.3 11.0 0.00120 0.86 0.00150 1 3
INIP 1.9 7.0 11.0 0.00140 0.86 0.00160 1 4
PYCR1 2.3 7.0 10.0 0.00170 0.86 0.00200 1 5
STX2 2.2 6.5 9.9 0.00200 0.86 0.00220 1 6
MRPS34 -1.8 8.4 8.9 0.00320 0.86 0.00310 1 7
HSPB11 -4.4 7.4 8.6 0.00380 0.86 0.00350 1 8
EEF2KMT 1.9 6.8 8.4 0.00440 0.86 0.00390 1 9
KRT8 2.4 7.2 8.3 0.00450 0.86 0.00400 1 10
1e-04 NA NA NA NA NA NA NA 0
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
HMGCS1 6.30 6.3
CKAP2L 8.50 4.3
SDF2L1 9.20 3.1
INIP 10.00 2.6
PYCR1 13.00 2.6
STX2 14.00 2.3
MRPS34 20.00 2.8
HSPB11 22.00 2.8
EEF2KMT 25.00 2.8
KRT8 26.00 2.6
1e-04 2.60 Inf
1e-05 1.50 Inf
1e-06 0.64 Inf
1e-07 0.40 Inf
1e-08 0.27 Inf
1e-09 0.17 Inf
1e-10 0.10 Inf
[1] "TRANK1_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
CDKN1C 1.70 7.0 14.0 0.00020 1 0.00059 1 1
MYC -3.80 7.6 13.0 0.00032 1 0.00074 1 2
LOXL1 -1.90 6.6 12.0 0.00081 1 0.00140 1 3
IGF1R 1.20 6.6 11.0 0.00110 1 0.00180 1 4
UGP2 -1.20 7.2 10.0 0.00150 1 0.00220 1 5
STMN2 -2.70 7.3 9.6 0.00220 1 0.00310 1 6
ALDH1B1 1.10 6.6 10.0 0.00230 1 0.00320 1 7
BTBD7 -1.60 6.5 11.0 0.00290 1 0.00370 1 8
FZD3 0.66 7.6 9.1 0.00290 1 0.00380 1 9
PIM1 -1.50 6.6 9.1 0.00300 1 0.00390 1 10
1e-04 NA NA NA NA NA NA NA 0
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
CDKN1C 3.70 3.7
MYC 4.70 2.3
LOXL1 8.90 3.0
IGF1R 11.00 2.8
UGP2 14.00 2.8
STMN2 20.00 3.3
ALDH1B1 20.00 2.9
BTBD7 24.00 3.0
FZD3 24.00 2.6
PIM1 25.00 2.5
1e-04 2.40 Inf
1e-05 1.10 Inf
1e-06 0.66 Inf
1e-07 0.49 Inf
1e-08 0.33 Inf
1e-09 0.30 Inf
1e-10 0.20 Inf
[1] "TRANK1_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
MYC -3.20 7.3 40 1.6e-09 9.9e-06 5.3e-06 0.033 1
NUP155 -1.10 6.4 16 1.5e-04 4.8e-01 5.2e-04 1.000 2
DOLK 0.84 6.6 13 4.5e-04 8.6e-01 9.9e-04 1.000 3
CLK3 0.76 6.8 12 6.9e-04 8.6e-01 1.3e-03 1.000 4
KCTD10 0.84 6.6 12 7.2e-04 8.6e-01 1.3e-03 1.000 5
RPUSD1 -0.78 6.8 12 8.1e-04 8.6e-01 1.4e-03 1.000 6
NAB2 -0.94 6.6 11 1.0e-03 9.4e-01 1.7e-03 1.000 7
NDC80 0.89 6.7 11 1.4e-03 9.9e-01 2.0e-03 1.000 8
RND3 0.77 6.9 10 1.6e-03 9.9e-01 2.3e-03 1.000 9
RPRD1A 0.64 6.9 10 1.8e-03 9.9e-01 2.5e-03 1.000 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 1
1e-08 NA NA NA NA NA NA NA 1
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
MYC 0.033 0.033
NUP155 3.300 1.600
DOLK 6.300 2.100
CLK3 8.100 2.000
KCTD10 8.300 1.700
RPUSD1 8.900 1.500
NAB2 11.000 1.500
NDC80 13.000 1.600
RND3 15.000 1.600
RPRD1A 16.000 1.600
1e-04 2.600 2.600
1e-05 0.870 0.870
1e-06 0.440 0.440
1e-07 0.270 0.270
1e-08 0.067 0.067
1e-09 0.033 Inf
1e-10 0.000 NaN
[1] "UBE2Q2P1_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
JAG1 2.20 6.9 29 2.0e-07 0.0013 4.3e-05 0.22 1
SERPINH1 1.10 7.8 17 5.5e-05 0.1500 1.8e-04 0.22 2
TPM2 1.90 7.2 16 9.5e-05 0.1500 2.5e-04 0.22 3
NQO1 1.70 7.4 16 9.7e-05 0.1500 2.5e-04 0.22 4
HSP90AA1 0.72 10.0 15 1.3e-04 0.1600 2.8e-04 0.22 5
SHPRH -2.60 6.6 15 2.0e-04 0.1600 3.4e-04 0.22 6
SGO1 -2.60 6.8 14 2.4e-04 0.1600 3.6e-04 0.22 7
PPP1CB 1.20 7.4 14 2.5e-04 0.1600 3.7e-04 0.22 8
RGS5 1.60 6.6 14 2.7e-04 0.1600 4.1e-04 0.22 9
COX7A2 0.56 9.4 14 2.8e-04 0.1600 4.1e-04 0.22 10
1e-04 NA NA NA NA NA NA NA 4
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 1
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
JAG1 0.270 0.27
SERPINH1 1.100 0.56
TPM2 1.600 0.52
NQO1 1.600 0.39
HSP90AA1 1.800 0.35
SHPRH 2.100 0.35
SGO1 2.300 0.33
PPP1CB 2.400 0.30
RGS5 2.600 0.29
COX7A2 2.600 0.26
1e-04 1.600 0.39
1e-05 0.640 0.64
1e-06 0.410 0.41
1e-07 0.270 Inf
1e-08 0.140 Inf
1e-09 0.068 Inf
1e-10 0.068 Inf
[1] "UBE2Q2P1_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
TERF2IP 1.60 7.4 16 8.5e-05 0.33 0.00032 0.87 1
AFF4 1.80 6.7 16 1.0e-04 0.33 0.00037 0.87 2
SPOCK1 1.80 6.7 15 1.9e-04 0.41 0.00049 0.87 3
MALAT1 0.93 14.0 13 3.8e-04 0.60 0.00077 0.87 4
UFSP2 -2.50 6.9 12 6.0e-04 0.64 0.00097 0.87 5
SFRP1 -3.80 7.0 12 8.6e-04 0.64 0.00130 0.87 6
PPP1R2 1.40 6.9 11 8.8e-04 0.64 0.00130 0.87 7
ATP5B 0.73 9.6 11 9.1e-04 0.64 0.00130 0.87 8
C1orf21 -2.50 6.9 11 1.1e-03 0.64 0.00150 0.87 9
IDH3A 1.50 6.7 11 1.3e-03 0.64 0.00170 0.87 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
TERF2IP 2.000 2.0
AFF4 2.400 1.2
SPOCK1 3.100 1.0
MALAT1 4.900 1.2
UFSP2 6.100 1.2
SFRP1 8.000 1.3
PPP1R2 8.200 1.2
ATP5B 8.300 1.0
C1orf21 9.300 1.0
IDH3A 11.000 1.1
1e-04 2.300 2.3
1e-05 0.930 Inf
1e-06 0.430 Inf
1e-07 0.300 Inf
1e-08 0.170 Inf
1e-09 0.100 Inf
1e-10 0.067 Inf
[1] "UBE2Q2P1_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
NAV1 1.5 6.8 16 7.5e-05 0.48 0.00041 1 1
GNG12 -2.7 6.6 12 8.4e-04 1.00 0.00190 1 2
A2M 1.5 6.6 11 8.9e-04 1.00 0.00200 1 3
METTL8 -2.5 6.6 11 9.7e-04 1.00 0.00220 1 4
ARFIP1 -2.3 6.5 11 1.1e-03 1.00 0.00240 1 5
CCNH 1.3 6.7 11 1.1e-03 1.00 0.00250 1 6
ZNHIT2 -2.3 6.5 11 1.3e-03 1.00 0.00290 1 7
CEBPD -2.5 6.6 11 1.4e-03 1.00 0.00310 1 8
REEP2 -2.2 6.9 10 1.6e-03 1.00 0.00330 1 9
CDKN1B -2.0 6.8 10 1.9e-03 1.00 0.00400 1 10
1e-04 NA NA NA NA NA NA NA 1
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
NAV1 2.600 2.6
GNG12 12.000 6.1
A2M 13.000 4.3
METTL8 14.000 3.5
ARFIP1 15.000 3.0
CCNH 16.000 2.6
ZNHIT2 18.000 2.6
CEBPD 19.000 2.4
REEP2 21.000 2.3
CDKN1B 25.000 2.5
1e-04 2.900 2.9
1e-05 0.940 Inf
1e-06 0.440 Inf
1e-07 0.370 Inf
1e-08 0.300 Inf
1e-09 0.200 Inf
1e-10 0.067 Inf
[1] "VPS45_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
A2M 3.0 6.8 77 2.0e-15 1.3e-11 5.3e-06 0.033 1
IFITM3 2.2 8.9 39 3.0e-09 9.6e-06 2.1e-05 0.067 2
PTN 2.0 8.2 31 9.6e-08 2.0e-04 4.8e-05 0.080 3
GPM6B 1.2 8.5 30 1.4e-07 2.3e-04 5.3e-05 0.080 4
CLU 1.8 7.6 29 2.8e-07 3.5e-04 6.3e-05 0.080 5
SULF2 1.7 6.7 19 2.0e-05 2.1e-02 2.3e-04 0.200 6
WLS 1.5 7.2 19 2.7e-05 2.4e-02 2.6e-04 0.200 7
TTC17 1.6 6.6 18 3.0e-05 2.4e-02 2.6e-04 0.200 8
CTSC 1.6 6.9 18 3.8e-05 2.7e-02 3.0e-04 0.200 9
GAP43 1.6 8.1 18 4.4e-05 2.8e-02 3.2e-04 0.200 10
1e-04 NA NA NA NA NA NA NA 12
1e-05 NA NA NA NA NA NA NA 5
1e-06 NA NA NA NA NA NA NA 5
1e-07 NA NA NA NA NA NA NA 3
1e-08 NA NA NA NA NA NA NA 2
1e-09 NA NA NA NA NA NA NA 1
1e-10 NA NA NA NA NA NA NA 1
#in_perm EmpiricalFDR
A2M 0.033 0.033
IFITM3 0.130 0.067
PTN 0.300 0.100
GPM6B 0.330 0.084
CLU 0.400 0.080
SULF2 1.400 0.240
WLS 1.600 0.230
TTC17 1.700 0.210
CTSC 1.900 0.210
GAP43 2.000 0.200
1e-04 2.700 0.230
1e-05 1.100 0.220
1e-06 0.600 0.120
1e-07 0.300 0.100
1e-08 0.230 0.120
1e-09 0.130 0.130
1e-10 0.067 0.067
[1] "VPS45_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
A2M 1.30 6.8 21 7.6e-06 0.048 0.00012 0.47 1
SLF2 -1.20 6.5 23 1.5e-05 0.048 0.00015 0.47 2
NINJ1 -0.97 6.9 17 4.4e-05 0.094 0.00028 0.60 3
TRMT2A -0.93 6.6 14 2.2e-04 0.350 0.00068 0.78 4
CMTM8 -1.00 6.6 13 4.0e-04 0.350 0.00098 0.78 5
GAP43 0.86 8.2 13 4.0e-04 0.350 0.00098 0.78 6
SUMO3 -0.48 7.9 13 4.0e-04 0.350 0.00099 0.78 7
QRICH1 0.84 6.6 13 4.5e-04 0.350 0.00100 0.78 8
KCTD10 0.82 6.6 12 5.4e-04 0.380 0.00110 0.78 9
RACGAP1 0.89 6.6 12 7.4e-04 0.470 0.00140 0.87 10
1e-04 NA NA NA NA NA NA NA 3
1e-05 NA NA NA NA NA NA NA 1
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
A2M 0.77 0.77
SLF2 0.93 0.47
NINJ1 1.80 0.60
TRMT2A 4.30 1.10
CMTM8 6.20 1.20
GAP43 6.20 1.00
SUMO3 6.30 0.90
QRICH1 6.40 0.80
KCTD10 7.00 0.78
RACGAP1 8.90 0.89
1e-04 2.80 0.92
1e-05 0.83 0.83
1e-06 0.43 Inf
1e-07 0.27 Inf
1e-08 0.20 Inf
1e-09 0.20 Inf
1e-10 0.13 Inf
[1] "VPS45_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR empiricalP empiricalP.FDR #in_real
NKAIN4 2.1 7.0 18 3.6e-05 0.23 0.00021 0.74 1
PCGF2 -3.5 6.9 16 9.2e-05 0.29 0.00032 0.74 2
UCK2 -2.9 6.7 13 4.2e-04 0.54 0.00074 0.74 3
JUNB 1.8 6.7 13 4.7e-04 0.54 0.00077 0.74 4
GNPDA1 1.7 6.9 13 5.2e-04 0.54 0.00083 0.74 5
TXNRD1 1.6 7.3 12 5.9e-04 0.54 0.00091 0.74 6
NADK -2.8 6.7 12 7.5e-04 0.54 0.00100 0.74 7
AKAP8 -2.9 6.7 12 8.3e-04 0.54 0.00110 0.74 8
CTDSP2 -2.9 6.7 11 9.7e-04 0.54 0.00130 0.74 9
NDUFAF6 -2.7 6.7 11 1.1e-03 0.54 0.00150 0.74 10
1e-04 NA NA NA NA NA NA NA 2
1e-05 NA NA NA NA NA NA NA 0
1e-06 NA NA NA NA NA NA NA 0
1e-07 NA NA NA NA NA NA NA 0
1e-08 NA NA NA NA NA NA NA 0
1e-09 NA NA NA NA NA NA NA 0
1e-10 NA NA NA NA NA NA NA 0
#in_perm EmpiricalFDR
NKAIN4 1.30 1.30
PCGF2 2.00 1.00
UCK2 4.70 1.60
JUNB 4.90 1.20
GNPDA1 5.20 1.00
TXNRD1 5.80 0.97
NADK 6.60 0.95
AKAP8 7.10 0.89
CTDSP2 8.10 0.90
NDUFAF6 9.80 0.98
1e-04 2.10 1.00
1e-05 0.83 Inf
1e-06 0.53 Inf
1e-07 0.43 Inf
1e-08 0.27 Inf
1e-09 0.17 Inf
1e-10 0.13 InfUsing all cells except the ones with targeted gRNA as controls
source("code/empiricalFDR.R")
pbins <- 10** (-4:-10)
for (gRNAfile in list.files("data/gRNA_edgeR-QLF/", "*edgeR-qlf_Neg2.Rd")){
print(gRNAfile)
gRNA <- strsplit(gRNAfile, "_edgeR")[[1]][1]
gRNAlocus <- strsplit(gRNA, split = "_")[[1]][1]
load(paste0("data/gRNA_edgeR-QLF/", gRNAfile))
fdrmetricall <- empiricalFDR(res2$table$PValue, res2$table$PValue, unlist(lapply(permres2, function(x) x$table$PValue)))
empiricalPall <- empiricalPvalue(res2$table$PValue, unlist(lapply(permres2, function(x) x$table$PValue)))
empiricalPfdrall <- p.adjust(empiricalPall, method="BH")
resEmpiricalp <- cbind(res2$table, fdrmetricall,empiricalPall,empiricalPfdrall)
save(resEmpiricalp, file=paste0("data/gRNA_edgeR-QLF/", gRNA,"_edgeR-qlf_Neg2_Empricialp.Rd"))
outpvalues <- c(res2$table[1:10,"PValue"], pbins)
outpbins <- matrix(NA, nrow=length(pbins), ncol=dim(res2$table)[2])
rownames(outpbins) <- pbins
colnames(outpbins) <- colnames(res2$table)
outm <- rbind(res2$table[1:10,], outpbins)
fdrmetric <- empiricalFDR(outpvalues, res2$table$PValue, unlist(lapply(permres2, function(x) x$table$PValue)))
empiricalP <- c(empiricalPall[1:10], rep(NA,length(pbins)))
empiricalP.FDR <- c(empiricalPfdrall[1:10], rep(NA,length(pbins)))
outm <- cbind(outm,empiricalP,empiricalP.FDR, fdrmetric)
outm$logFC <- -outm$logFC
print(signif(outm,2))
plotgn <- rownames(outm[1:10,][outm[1:10, "EmpiricalFDR"] <0.2,])
if (length(plotgn)!=0){
for (gn in plotgn){
gcount <- dm[gn, gRNAdm0[gRNA,] >0 & colSums(gRNAdm0[rownames(gRNAdm0) != gRNA,]) == 0]
ncount1 <- dm[gn, colnames(dm1dfagg)[dm1dfagg["neg",] >0 & nlocus==1]]
a <- rbind(cbind(gcount,1),cbind(ncount1,2))
colnames(a) <- c("count","categ")
par(mfrow=c(1,3))
boxplot(count ~categ, data = a, lwd = 2, main=paste(gRNA, gn, sep=":"), outcol="white")
stripchart(count ~categ, data=a, vertical = TRUE, method = "jitter", add = TRUE, pch = 21, cex=2, col = 'blue')
qqplot( -log10(unlist(lapply(permres2, function(x) x$table$PValue))),-log10(res2$table$PValue), xlab="permuted (-log10 pvalue)", ylab="observed (-log10 pvalue)")
abline(a=0, b=1, col="red")
grid()
qqplot(-log10(runif(length(empiricalPall))),-log10(empiricalPall))
abline(a=0, b=1, col="red")
grid()
}
}
}
sessionInfo()R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] edgeR_3.24.3 limma_3.38.2 lattice_0.20-38 Matrix_1.2-15
loaded via a namespace (and not attached):
[1] locfit_1.5-9.1 workflowr_1.2.0 Rcpp_1.0.0 digest_0.6.18
[5] rprojroot_1.3-2 grid_3.5.1 backports_1.1.2 git2r_0.23.0
[9] magrittr_1.5 evaluate_0.12 stringi_1.3.1 fs_1.2.6
[13] whisker_0.3-2 rmarkdown_1.10 tools_3.5.1 stringr_1.4.0
[17] glue_1.3.0 yaml_2.2.0 compiler_3.5.1 htmltools_0.3.6
[21] knitr_1.20