Last updated: 2019-02-28
Checks: 6 0
Knit directory: cropseq/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| 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 |
source("code/empiricalFDR.R")
pbins <- 10** (-4:-10)
for (gRNAfile in list.files("data/", "*edgeR-qlf_Neg1.Rd")){
print(gRNAfile)
load(paste0("data/", gRNAfile))
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)))
outm <- cbind(outm,fdrmetric)
print(signif(outm,2))
}[1] "BAG5_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 3.00 7.5 18 2.7e-05 0.22 0 3.0 Inf
LGALS3 2.00 6.6 15 1.1e-04 0.46 1 5.3 5.3
FGF19 2.00 6.6 14 1.9e-04 0.47 2 6.7 3.4
CWF19L2 -1.10 6.5 15 2.3e-04 0.47 3 7.5 2.5
FIZ1 1.30 6.6 12 6.9e-04 0.73 4 14.0 3.4
LIX1 -1.10 6.7 12 7.4e-04 0.73 5 14.0 2.8
CEP250 -1.20 6.4 14 8.3e-04 0.73 6 15.0 2.5
BTG2 1.30 7.1 11 8.7e-04 0.73 7 16.0 2.2
NSUN2 -1.00 6.5 11 8.8e-04 0.73 8 16.0 2.0
CCND1 0.77 8.0 11 9.1e-04 0.73 9 16.0 1.8
1e-04 NA NA NA NA NA 1 5.0 5.0
1e-05 NA NA NA NA NA 0 2.4 Inf
1e-06 NA NA NA NA NA 0 0.9 Inf
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.2 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "BAG5_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 3.00 7.5 19 1.8e-05 0.15 0 2.5 Inf
MLLT6 1.70 6.4 21 9.1e-05 0.37 1 5.5 5.5
NIN -1.10 6.9 15 1.7e-04 0.42 2 7.2 3.6
EPS15 1.60 6.4 17 3.0e-04 0.42 3 10.0 3.5
MALAT1 -0.61 14.0 13 3.2e-04 0.42 4 11.0 2.8
RP11-16E18.4 1.50 6.4 18 3.5e-04 0.42 5 11.0 2.3
RAB32 1.60 6.7 13 3.6e-04 0.42 6 12.0 2.0
ARFGAP1 -1.00 6.6 12 7.2e-04 0.59 7 17.0 2.5
NEDD4L 1.50 6.4 16 7.9e-04 0.59 8 18.0 2.3
PIGM -1.10 6.5 14 8.0e-04 0.59 9 18.0 2.0
1e-04 NA NA NA NA NA 2 6.0 3.0
1e-05 NA NA NA NA NA 0 1.8 Inf
1e-06 NA NA NA NA NA 0 0.7 Inf
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.3 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "BAG5_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CDKN3 -1.2 7.0 16 9.6e-05 0.39 0 4.3 Inf
NRIP1 -1.4 6.4 23 9.6e-05 0.39 1 4.3 4.3
CWF19L2 -1.2 6.5 16 2.2e-04 0.45 2 6.9 3.4
RACGAP1 -1.2 6.6 13 3.1e-04 0.45 3 8.5 2.8
MYC 2.4 7.5 13 3.7e-04 0.45 4 10.0 2.5
ASCL1 1.7 6.9 13 4.8e-04 0.45 5 11.0 2.3
BIN3 1.3 6.8 13 5.0e-04 0.45 6 12.0 1.9
RASSF7 1.6 6.4 16 5.1e-04 0.45 7 12.0 1.7
CDKN1A 1.5 7.9 12 5.6e-04 0.45 8 13.0 1.6
KIF2C -1.2 6.7 12 5.8e-04 0.45 9 13.0 1.4
1e-04 NA NA NA NA NA 2 4.5 2.2
1e-05 NA NA NA NA NA 0 1.1 Inf
1e-06 NA NA NA NA NA 0 0.1 Inf
1e-07 NA NA NA NA NA 0 0.0 NaN
1e-08 NA NA NA NA NA 0 0.0 NaN
1e-09 NA NA NA NA NA 0 0.0 NaN
1e-10 NA NA NA NA NA 0 0.0 NaN
[1] "BCL11B_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
FNDC4 -1.6 6.5 14 0.00020 0.52 0 6.7 Inf
TMEM88 -1.5 6.5 14 0.00028 0.52 1 8.3 8.3
ERMARD -1.7 6.4 18 0.00034 0.52 2 9.7 4.9
PRR11 -1.4 6.7 13 0.00036 0.52 3 9.9 3.3
TSPAN31 -1.5 6.5 13 0.00052 0.52 4 12.0 3.0
MOK -1.5 6.4 14 0.00062 0.52 5 14.0 2.7
MLXIP 2.3 6.5 14 0.00063 0.52 6 14.0 2.3
ARL6IP1 -1.1 7.9 12 0.00069 0.52 7 15.0 2.1
POMGNT2 2.2 6.5 12 0.00080 0.52 8 16.0 2.0
PTPN18 2.2 6.5 12 0.00080 0.52 9 16.0 1.8
1e-04 NA NA NA NA NA 0 4.1 Inf
1e-05 NA NA NA NA NA 0 2.0 Inf
1e-06 NA NA NA NA NA 0 1.2 Inf
1e-07 NA NA NA NA NA 0 0.7 Inf
1e-08 NA NA NA NA NA 0 0.6 Inf
1e-09 NA NA NA NA NA 0 0.5 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "BCL11B_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
S100A10 -2.2 7.1 37 5.4e-09 4.4e-05 0 0.3 Inf
SPP1 -1.9 7.0 24 1.6e-06 4.6e-03 1 0.7 0.70
RGS5 -1.5 6.7 24 1.7e-06 4.6e-03 2 0.7 0.35
PHLDA1 -1.5 7.1 23 2.6e-06 5.4e-03 3 0.7 0.23
TMEM88 -1.5 6.5 22 5.1e-06 8.2e-03 4 0.9 0.22
AXL -1.5 6.6 19 1.7e-05 2.3e-02 5 1.6 0.32
CEBPD -1.4 6.8 18 3.8e-05 4.4e-02 6 2.1 0.35
CDKN2A -1.5 6.7 17 5.0e-05 4.6e-02 7 2.4 0.34
JAG1 -1.3 6.9 17 5.1e-05 4.6e-02 8 2.4 0.30
NT5M 1.7 6.4 21 8.8e-05 7.2e-02 9 3.4 0.38
1e-04 NA NA NA NA NA 10 3.7 0.37
1e-05 NA NA NA NA NA 5 1.1 0.22
1e-06 NA NA NA NA NA 1 0.7 0.70
1e-07 NA NA NA NA NA 1 0.3 0.30
1e-08 NA NA NA NA NA 1 0.3 0.30
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "BCL11B_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SPP1 -2.5 7.0 31 1.1e-07 0.00087 0 1.1 Inf
GGA3 -1.6 6.4 17 2.8e-04 0.81000 1 6.1 6.1
PDE1B -1.5 6.5 13 3.4e-04 0.81000 2 6.8 3.4
NOP2 2.3 6.5 13 5.0e-04 0.81000 3 8.6 2.9
SPEN 2.3 6.5 13 5.2e-04 0.81000 4 8.8 2.2
DUSP1 2.6 6.8 12 6.0e-04 0.81000 5 9.8 2.0
MFSD3 2.2 6.5 12 9.1e-04 0.82000 6 14.0 2.3
TP53I11 2.2 6.5 11 9.1e-04 0.82000 7 14.0 2.0
MGRN1 2.1 6.5 12 1.2e-03 0.82000 8 16.0 2.1
DTNA 2.1 6.5 11 1.3e-03 0.82000 9 18.0 2.0
1e-04 NA NA NA NA NA 1 4.1 4.1
1e-05 NA NA NA NA NA 1 1.9 1.9
1e-06 NA NA NA NA NA 1 1.5 1.5
1e-07 NA NA NA NA NA 0 1.1 Inf
1e-08 NA NA NA NA NA 0 0.6 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.4 Inf
[1] "CHRNA3_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
AC084018.1 -2.8 6.5 23 2.8e-06 0.022 0 1.9 Inf
MT-ND4 -1.4 11.0 12 5.6e-04 0.810 1 7.6 7.6
SEPN1 -2.2 6.5 12 7.5e-04 0.810 2 8.3 4.2
ERBB2 -2.1 6.4 12 1.0e-03 0.810 3 11.0 3.6
FBXW11 -2.1 6.5 11 1.1e-03 0.810 4 11.0 2.8
ARPIN -2.1 6.4 11 1.2e-03 0.810 5 11.0 2.3
NR6A1 -2.0 6.5 10 1.4e-03 0.810 6 13.0 2.2
ABHD17A -2.0 6.7 10 1.4e-03 0.810 7 13.0 1.8
FST -2.3 6.6 10 1.5e-03 0.810 8 13.0 1.6
MTUS1 -2.1 6.4 10 1.6e-03 0.810 9 13.0 1.5
1e-04 NA NA NA NA NA 1 4.4 4.4
1e-05 NA NA NA NA NA 1 2.5 2.5
1e-06 NA NA NA NA NA 0 1.7 Inf
1e-07 NA NA NA NA NA 0 1.4 Inf
1e-08 NA NA NA NA NA 0 1.1 Inf
1e-09 NA NA NA NA NA 0 0.8 Inf
1e-10 NA NA NA NA NA 0 0.7 Inf
[1] "CHRNA3_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TOP3A 2.1 6.5 19 2.4e-05 0.14 0 3.6 Inf
DDB2 -1.5 6.5 18 3.5e-05 0.14 1 4.3 4.3
RP11-46C20.1 -1.4 6.6 17 6.4e-05 0.17 2 5.1 2.6
FIZ1 1.8 6.5 15 1.6e-04 0.25 3 7.1 2.4
PKMYT1 1.8 6.7 14 2.1e-04 0.25 4 8.0 2.0
RCAN1 -1.3 6.7 14 2.8e-04 0.25 5 9.1 1.8
FMR1 -1.3 6.4 16 3.0e-04 0.25 6 9.5 1.6
HOXB3 -1.4 6.4 16 3.0e-04 0.25 7 9.5 1.4
PLPP1 -1.4 6.4 17 3.0e-04 0.25 8 9.5 1.2
KLHL5 -1.2 6.5 13 3.1e-04 0.25 9 9.6 1.1
1e-04 NA NA NA NA NA 3 6.4 2.1
1e-05 NA NA NA NA NA 0 2.6 Inf
1e-06 NA NA NA NA NA 0 1.3 Inf
1e-07 NA NA NA NA NA 0 1.1 Inf
1e-08 NA NA NA NA NA 0 0.7 Inf
1e-09 NA NA NA NA NA 0 0.6 Inf
1e-10 NA NA NA NA NA 0 0.5 Inf
[1] "CHRNA3_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CDC42EP3 -1.8 6.8 23 3.5e-06 0.029 0 0.4 Inf
VGF -1.9 6.9 19 1.8e-05 0.075 1 1.0 1.00
RRP9 -1.3 7.0 18 4.0e-05 0.110 2 1.6 0.80
NUP98 -1.6 6.4 18 6.4e-05 0.110 3 2.5 0.83
OXR1 2.4 6.5 16 7.9e-05 0.110 4 3.0 0.75
GDF15 -1.9 6.8 16 9.0e-05 0.110 5 3.1 0.62
AKAP12 -1.3 7.4 16 9.6e-05 0.110 6 3.2 0.53
GLIPR1 -1.5 6.7 15 1.3e-04 0.130 7 3.7 0.53
BTBD1 -1.6 6.3 20 2.1e-04 0.180 8 5.4 0.68
TTC28 2.3 6.5 14 2.3e-04 0.180 9 5.7 0.63
1e-04 NA NA NA NA NA 7 3.2 0.46
1e-05 NA NA NA NA NA 1 0.6 0.60
1e-06 NA NA NA NA NA 0 0.4 Inf
1e-07 NA NA NA NA NA 0 0.3 Inf
1e-08 NA NA NA NA NA 0 0.3 Inf
1e-09 NA NA NA NA NA 0 0.2 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "DPYD_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
CTD-2006C1.2 -1.9 7.2 48 4.8e-11 3.9e-07 0 0.5
S100A10 -2.1 7.1 38 3.9e-09 1.6e-05 1 0.5
LGALS3 -1.7 6.8 25 1.3e-06 3.4e-03 2 1.6
SPP1 -1.8 7.0 24 2.5e-06 4.9e-03 3 1.7
HIST1H2AC -1.5 6.6 23 3.0e-06 4.9e-03 4 1.8
DUSP4 -1.2 6.8 21 7.8e-06 1.1e-02 5 2.7
CTSD -1.0 7.4 19 1.9e-05 2.2e-02 6 3.8
NQO1 -1.3 7.5 19 2.3e-05 2.3e-02 7 4.2
MYC 2.4 7.4 18 3.8e-05 3.4e-02 8 4.4
TAGLN2 -1.3 6.6 17 4.4e-05 3.6e-02 9 4.7
1e-04 NA NA NA NA NA 11 6.5
1e-05 NA NA NA NA NA 6 2.8
1e-06 NA NA NA NA NA 2 1.2
1e-07 NA NA NA NA NA 2 0.5
1e-08 NA NA NA NA NA 2 0.5
1e-09 NA NA NA NA NA 1 0.5
1e-10 NA NA NA NA NA 1 0.5
EmpiricalFDR
CTD-2006C1.2 Inf
S100A10 0.50
LGALS3 0.80
SPP1 0.57
HIST1H2AC 0.45
DUSP4 0.54
CTSD 0.63
NQO1 0.60
MYC 0.55
TAGLN2 0.52
1e-04 0.59
1e-05 0.47
1e-06 0.60
1e-07 0.25
1e-08 0.25
1e-09 0.50
1e-10 0.50
[1] "DPYD_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 2.70 7.3 37 5.4e-09 4.4e-05 0 1.0 Inf
RGS5 -1.40 6.7 25 1.0e-06 4.2e-03 1 1.8 1.8
AXL -1.10 6.6 15 1.7e-04 3.0e-01 2 7.8 3.9
MEG3 -0.95 7.7 15 1.8e-04 3.0e-01 3 7.8 2.6
PGGT1B -0.98 6.5 16 1.9e-04 3.0e-01 4 7.9 2.0
CLN8 0.97 6.6 13 3.6e-04 4.4e-01 5 11.0 2.2
ABL1 -0.93 6.4 14 4.7e-04 4.4e-01 6 12.0 2.0
CASD1 1.10 6.3 19 5.4e-04 4.4e-01 7 13.0 1.8
CSRP1 -0.97 7.3 12 5.4e-04 4.4e-01 8 13.0 1.6
KCTD10 -0.86 6.6 12 5.9e-04 4.4e-01 9 14.0 1.5
1e-04 NA NA NA NA NA 2 5.6 2.8
1e-05 NA NA NA NA NA 2 2.5 1.2
1e-06 NA NA NA NA NA 1 1.7 1.7
1e-07 NA NA NA NA NA 1 1.5 1.5
1e-08 NA NA NA NA NA 1 1.1 1.1
1e-09 NA NA NA NA NA 0 0.7 Inf
1e-10 NA NA NA NA NA 0 0.5 Inf
[1] "DPYD_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 3.5 7.5 20 1.4e-05 0.042 0 3.2 Inf
LGALS3 2.6 6.5 20 1.5e-05 0.042 1 3.2 3.2
ITGA6 -1.6 6.4 26 1.6e-05 0.042 2 3.2 1.6
NEAT1 1.7 8.1 18 4.2e-05 0.085 3 4.2 1.4
ZBTB8A 1.7 6.4 17 2.8e-04 0.360 4 11.0 2.8
AFF3 1.6 6.4 18 3.6e-04 0.360 5 12.0 2.4
TMEM88 -1.2 6.5 13 3.6e-04 0.360 6 12.0 2.0
PRR11 -1.1 6.7 13 3.7e-04 0.360 7 12.0 1.8
PITRM1 -1.3 6.4 15 4.6e-04 0.360 8 14.0 1.7
RAB32 1.7 6.7 13 4.7e-04 0.360 9 14.0 1.5
1e-04 NA NA NA NA NA 4 6.9 1.7
1e-05 NA NA NA NA NA 0 3.0 Inf
1e-06 NA NA NA NA NA 0 1.6 Inf
1e-07 NA NA NA NA NA 0 1.1 Inf
1e-08 NA NA NA NA NA 0 0.6 Inf
1e-09 NA NA NA NA NA 0 0.5 Inf
1e-10 NA NA NA NA NA 0 0.5 Inf
[1] "GALNT10_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 2.8 7.5 21 8.2e-06 0.049 0 2.4 Inf
SPP1 -1.7 7.0 20 1.2e-05 0.049 1 2.4 2.4
CDKN1C -1.6 7.1 19 1.8e-05 0.049 2 2.9 1.4
RP11-395G23.3 1.8 6.5 18 3.9e-05 0.079 3 3.8 1.3
RPRD2 1.5 6.5 17 2.5e-04 0.330 4 9.0 2.2
PDK2 1.5 6.4 17 2.8e-04 0.330 5 9.6 1.9
SEMA3A -1.2 6.4 15 2.9e-04 0.330 6 9.8 1.6
FAM104B 1.1 6.9 13 3.4e-04 0.350 7 10.0 1.5
DECR1 1.2 6.9 13 5.0e-04 0.450 8 12.0 1.6
AKAP13 1.2 6.6 12 6.4e-04 0.520 9 15.0 1.6
1e-04 NA NA NA NA NA 4 6.2 1.6
1e-05 NA NA NA NA NA 1 2.4 2.4
1e-06 NA NA NA NA NA 0 0.8 Inf
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.5 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "GALNT10_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 2.90 7.5 21 8.1e-06 0.033 0 1.9 Inf
RGS5 -1.40 6.7 21 8.2e-06 0.033 1 1.9 1.9
ROBO3 -1.40 6.5 20 1.2e-05 0.033 2 2.2 1.1
RACGAP1 -1.20 6.6 16 8.8e-05 0.180 3 5.4 1.8
SAMD4A -1.30 6.4 23 1.2e-04 0.200 4 5.9 1.5
ST7L -0.98 6.6 13 5.0e-04 0.680 5 14.0 2.7
TMEM88 -1.10 6.5 12 6.5e-04 0.750 6 16.0 2.6
SYPL1 0.91 7.1 11 1.0e-03 0.820 7 21.0 2.9
AKT3 -1.00 6.4 13 1.1e-03 0.820 8 22.0 2.8
PUS3 1.10 6.7 11 1.3e-03 0.820 9 26.0 2.8
1e-04 NA NA NA NA NA 4 5.6 1.4
1e-05 NA NA NA NA NA 2 2.0 1.0
1e-06 NA NA NA NA NA 0 0.8 Inf
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.3 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "GALNT10_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
STMN2 2.8 7.1 28 3.0e-07 0.0018 0 0.9 Inf
MYC 2.8 7.4 27 4.5e-07 0.0018 1 0.9 0.90
NEAT1 -1.3 8.8 22 4.3e-06 0.0120 2 2.1 1.00
RGS5 -1.3 6.7 21 9.4e-06 0.0190 3 2.9 0.97
GRIA1 -1.3 6.5 21 1.2e-05 0.0200 4 3.1 0.78
EML1 1.4 6.5 20 4.2e-05 0.0570 5 4.8 0.96
SLAIN2 1.3 6.4 20 1.2e-04 0.1300 6 7.4 1.20
ARMCX1 -1.1 6.5 15 1.5e-04 0.1300 7 8.1 1.20
PVT1 -1.0 6.5 15 1.6e-04 0.1300 8 8.2 1.00
TADA1 1.3 6.4 18 1.6e-04 0.1300 9 8.2 0.91
1e-04 NA NA NA NA NA 6 6.5 1.10
1e-05 NA NA NA NA NA 4 3.0 0.75
1e-06 NA NA NA NA NA 2 1.2 0.60
1e-07 NA NA NA NA NA 0 0.7 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.0 NaN
[1] "KCTD13_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TUBA1C 2.9 6.8 27 4.5e-07 0.0036 0 1.4 Inf
MYC 3.5 7.5 20 1.3e-05 0.0420 1 2.8 2.8
LGALS3 2.6 6.6 20 1.5e-05 0.0420 2 2.8 1.4
SHPRH 1.7 6.6 17 6.9e-05 0.1200 3 4.9 1.6
S100A10 2.4 6.7 16 7.3e-05 0.1200 4 5.0 1.2
AP5Z1 -1.2 6.5 16 1.1e-04 0.1400 5 6.1 1.2
CTTNBP2NL 1.6 6.5 15 1.6e-04 0.1700 6 7.5 1.2
SLC20A2 1.6 6.6 15 1.7e-04 0.1700 7 7.6 1.1
BEX2 1.8 6.7 14 2.4e-04 0.2200 8 9.4 1.2
PSTPIP2 1.6 6.4 19 2.7e-04 0.2200 9 10.0 1.1
1e-04 NA NA NA NA NA 5 5.9 1.2
1e-05 NA NA NA NA NA 1 2.8 2.8
1e-06 NA NA NA NA NA 1 1.5 1.5
1e-07 NA NA NA NA NA 0 1.1 Inf
1e-08 NA NA NA NA NA 0 1.0 Inf
1e-09 NA NA NA NA NA 0 0.9 Inf
1e-10 NA NA NA NA NA 0 0.9 Inf
[1] "KCTD13_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
KRT18 3.7 7.2 29 2.1e-07 0.0017 0 0.4 Inf
S100A10 2.6 6.7 22 5.1e-06 0.0170 1 1.2 1.20
RCAN1 2.1 6.6 22 6.2e-06 0.0170 2 1.2 0.60
OPTN 1.9 6.5 19 2.0e-05 0.0340 3 2.0 0.67
MYC 3.0 7.5 19 2.1e-05 0.0340 4 2.1 0.52
KRT8 2.4 7.0 17 4.8e-05 0.0650 5 2.9 0.58
CMTM8 1.9 6.6 17 6.1e-05 0.0710 6 3.4 0.57
LGALS3 2.0 6.6 15 1.2e-04 0.1200 7 5.4 0.77
NINJ1 1.3 6.9 14 2.0e-04 0.1800 8 6.5 0.81
SLC20A2 1.5 6.6 14 2.9e-04 0.2400 9 8.7 0.97
1e-04 NA NA NA NA NA 7 4.7 0.67
1e-05 NA NA NA NA NA 3 1.5 0.50
1e-06 NA NA NA NA NA 1 0.5 0.50
1e-07 NA NA NA NA NA 0 0.4 Inf
1e-08 NA NA NA NA NA 0 0.3 Inf
1e-09 NA NA NA NA NA 0 0.2 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "KCTD13_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MAP3K4 -1.7 6.4 20 1.6e-05 0.13 0 1.9 Inf
TLE4 -1.4 6.9 16 8.4e-05 0.34 1 4.3 4.3
GEMIN2 -1.3 6.9 14 2.0e-04 0.48 2 6.6 3.3
GDF15 -1.8 6.8 14 2.4e-04 0.48 3 7.4 2.5
GRIA1 -1.5 6.4 15 4.0e-04 0.52 4 10.0 2.6
DBT -1.4 6.4 14 5.5e-04 0.52 5 12.0 2.4
PYCRL 2.1 6.5 14 7.4e-04 0.52 6 14.0 2.3
PPIL2 2.1 6.5 14 7.4e-04 0.52 7 14.0 2.0
YJEFN3 -1.4 6.4 13 7.5e-04 0.52 8 14.0 1.8
IPO9 -1.0 7.1 12 7.7e-04 0.52 9 14.0 1.6
1e-04 NA NA NA NA NA 2 4.8 2.4
1e-05 NA NA NA NA NA 0 1.5 Inf
1e-06 NA NA NA NA NA 0 1.1 Inf
1e-07 NA NA NA NA NA 0 0.6 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "KMT2E_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
FTH1 -0.98 12.0 14 0.00027 0.77 0 9.1 Inf
EXOC6 -1.50 6.6 13 0.00039 0.77 1 11.0 11.0
PCDH19 -1.60 6.4 13 0.00055 0.77 2 13.0 6.4
FAM161A 2.40 6.8 12 0.00075 0.77 3 16.0 5.4
CSPP1 2.30 6.5 11 0.00110 0.77 4 22.0 5.4
GMCL1 2.40 6.5 11 0.00110 0.77 5 22.0 4.4
NR6A1 -1.50 6.5 11 0.00130 0.77 6 25.0 4.1
B4GALT5 2.30 6.5 10 0.00150 0.77 7 28.0 4.0
CHAC1 -1.50 6.6 10 0.00160 0.77 8 28.0 3.5
NCSTN 2.30 6.8 10 0.00180 0.77 9 32.0 3.5
1e-04 NA NA NA NA NA 0 5.1 Inf
1e-05 NA NA NA NA NA 0 2.0 Inf
1e-06 NA NA NA NA NA 0 1.0 Inf
1e-07 NA NA NA NA NA 0 0.8 Inf
1e-08 NA NA NA NA NA 0 0.6 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "KMT2E_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
EZR -1.2 7.5 19 2.6e-05 0.16 0 3.3 Inf
QPRT 2.7 6.8 18 4.0e-05 0.16 1 4.3 4.3
CMTM8 2.7 6.6 16 9.9e-05 0.20 2 5.9 2.9
SPP1 -1.8 6.9 16 1.1e-04 0.20 3 6.1 2.0
TEAD1 -1.4 6.6 15 1.5e-04 0.20 4 7.3 1.8
RNF168 2.2 6.7 15 1.5e-04 0.20 5 7.4 1.5
OSGIN1 -1.7 6.9 15 1.8e-04 0.20 6 8.2 1.4
RGS5 -1.4 6.7 14 2.2e-04 0.20 7 9.5 1.4
PRR5 2.1 6.5 14 2.2e-04 0.20 8 9.6 1.2
SEMA3A -1.5 6.5 16 2.6e-04 0.21 9 11.0 1.2
1e-04 NA NA NA NA NA 3 5.9 2.0
1e-05 NA NA NA NA NA 0 2.0 Inf
1e-06 NA NA NA NA NA 0 1.1 Inf
1e-07 NA NA NA NA NA 0 0.7 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.4 Inf
[1] "KMT2E_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TP53I3 -1.5 7.0 20 1.2e-05 0.052 0 1.2 Inf
C1orf56 -1.9 6.4 29 1.3e-05 0.052 1 1.2 1.20
ANKRD1 -1.8 6.7 19 2.6e-05 0.070 2 2.3 1.20
PALMD -1.6 6.5 18 3.6e-05 0.073 3 2.5 0.83
BCHE 2.1 6.5 14 2.3e-04 0.320 4 8.8 2.20
COG5 2.1 6.5 16 2.4e-04 0.320 5 8.9 1.80
FDXR -1.3 7.1 14 3.0e-04 0.320 6 11.0 1.80
GPT2 1.8 6.9 13 3.2e-04 0.320 7 11.0 1.60
MARCH9 2.0 6.4 14 4.6e-04 0.420 8 14.0 1.70
KCTD1 -1.2 6.7 12 5.7e-04 0.460 9 16.0 1.80
1e-04 NA NA NA NA NA 4 5.7 1.40
1e-05 NA NA NA NA NA 0 1.1 Inf
1e-06 NA NA NA NA NA 0 0.6 Inf
1e-07 NA NA NA NA NA 0 0.4 Inf
1e-08 NA NA NA NA NA 0 0.1 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "LINC00637_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
HSP90AA1 -0.86 11.0 32 5.5e-08 0.00045 0 0.8 Inf
MYC 3.20 7.4 27 5.3e-07 0.00220 1 1.2 1.20
MALAT1 -0.63 14.0 20 1.4e-05 0.03700 2 2.5 1.20
PKMYT1 1.50 6.7 19 2.2e-05 0.04500 3 3.2 1.10
SPP1 2.00 6.6 17 4.3e-05 0.06900 4 4.1 1.00
FKBP1B 1.30 6.7 15 1.3e-04 0.17000 5 6.7 1.30
CTB-31O20.2 1.40 6.4 18 3.1e-04 0.36000 6 11.0 1.80
CAMKK2 1.40 6.3 20 3.5e-04 0.36000 7 12.0 1.70
SMAD1 -0.98 6.5 13 5.8e-04 0.53000 8 16.0 2.00
SPIN2B 1.20 6.4 13 6.9e-04 0.56000 9 18.0 2.00
1e-04 NA NA NA NA NA 5 6.3 1.30
1e-05 NA NA NA NA NA 2 2.4 1.20
1e-06 NA NA NA NA NA 2 1.5 0.75
1e-07 NA NA NA NA NA 1 0.9 0.90
1e-08 NA NA NA NA NA 0 0.7 Inf
1e-09 NA NA NA NA NA 0 0.5 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "LINC00637_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 3.4 7.5 22 6.3e-06 0.051 0 1.1 Inf
TP53I3 -1.2 7.0 19 2.3e-05 0.075 1 2.2 2.20
GDF15 -1.6 6.8 18 3.3e-05 0.075 2 2.2 1.10
TRIO -1.4 6.4 22 3.7e-05 0.075 3 2.3 0.77
TUBA1C 2.0 6.7 17 6.9e-05 0.110 4 3.6 0.90
TMEM200C 1.7 6.4 22 9.5e-05 0.130 5 4.0 0.80
SRD5A1 1.4 6.6 14 2.9e-04 0.340 6 8.4 1.40
MAFB 1.8 6.6 13 3.6e-04 0.350 7 9.6 1.40
KCTD9 1.5 6.5 13 3.9e-04 0.350 8 9.9 1.20
SRFBP1 1.3 6.5 12 6.9e-04 0.560 9 15.0 1.60
1e-04 NA NA NA NA NA 6 4.0 0.67
1e-05 NA NA NA NA NA 1 1.3 1.30
1e-06 NA NA NA NA NA 0 0.9 Inf
1e-07 NA NA NA NA NA 0 0.6 Inf
1e-08 NA NA NA NA NA 0 0.5 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.4 Inf
[1] "LINC00637_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
GADD45G 3.1 7.3 32 5.7e-08 0.00046 0 0.8 Inf
CDC25A 1.5 6.5 21 7.0e-06 0.02800 1 2.4 2.40
DLL3 2.0 6.9 20 1.4e-05 0.02900 2 3.0 1.50
CDKN1C 1.8 6.7 19 1.7e-05 0.02900 3 3.1 1.00
MIAT 1.8 6.9 19 2.2e-05 0.02900 4 3.1 0.78
SEMA3A -1.2 6.4 19 2.2e-05 0.02900 5 3.1 0.62
RGS5 -1.2 6.7 17 4.4e-05 0.04800 6 3.8 0.63
SPP1 -1.5 7.0 17 4.7e-05 0.04800 7 4.0 0.57
TPM2 -1.4 7.4 17 5.3e-05 0.04800 8 4.5 0.56
TNFRSF12A -1.1 7.9 15 1.4e-04 0.11000 9 6.4 0.71
1e-04 NA NA NA NA NA 9 5.0 0.56
1e-05 NA NA NA NA NA 2 2.5 1.20
1e-06 NA NA NA NA NA 1 1.7 1.70
1e-07 NA NA NA NA NA 1 0.8 0.80
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.4 Inf
[1] "LOC100507431_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
S100A16 -2.0 6.7 28 3.0e-07 0.0024 0 0.9 Inf
TPM2 -2.1 7.3 24 2.1e-06 0.0085 1 1.1 1.10
S100A10 -2.1 6.9 23 3.7e-06 0.0100 2 1.1 0.55
CDKN1C -2.1 7.0 22 6.5e-06 0.0130 3 1.4 0.47
GADD45G -2.3 7.9 21 9.1e-06 0.0150 4 1.5 0.38
CCND2 -1.6 7.1 19 2.5e-05 0.0340 5 2.1 0.42
THAP5 -1.6 6.5 18 2.9e-05 0.0340 6 2.3 0.38
ANAPC10 2.3 6.5 15 1.6e-04 0.1700 7 4.3 0.61
DPY19L3 -1.5 6.4 18 2.8e-04 0.2500 8 6.0 0.75
LAMC1 -1.4 6.4 13 4.3e-04 0.3500 9 8.4 0.93
1e-04 NA NA NA NA NA 7 3.6 0.51
1e-05 NA NA NA NA NA 5 1.5 0.30
1e-06 NA NA NA NA NA 1 1.0 1.00
1e-07 NA NA NA NA NA 0 0.7 Inf
1e-08 NA NA NA NA NA 0 0.5 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "LOC100507431_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
LGALS3 -2.6 7.0 50 2.4e-11 2.0e-07 0 0.3 Inf
TIMP2 -1.9 6.5 31 7.4e-08 3.0e-04 1 0.3 0.30
S100A16 -1.8 6.8 29 1.9e-07 5.1e-04 2 0.5 0.25
S100A10 -1.9 7.0 23 2.6e-06 5.2e-03 3 1.3 0.43
SEMA3A -1.5 6.4 22 7.8e-06 1.3e-02 4 1.9 0.48
S100A13 -1.3 7.1 20 1.4e-05 1.9e-02 5 2.3 0.46
AXL -1.5 6.6 19 2.7e-05 2.7e-02 6 2.5 0.42
DHRS7 -1.3 6.7 18 2.7e-05 2.7e-02 7 2.5 0.36
ANKRD1 -1.6 6.8 17 5.5e-05 5.0e-02 8 3.7 0.46
SPOCK1 -1.3 6.7 16 7.7e-05 6.2e-02 9 4.0 0.44
1e-04 NA NA NA NA NA 11 4.6 0.42
1e-05 NA NA NA NA NA 5 2.2 0.44
1e-06 NA NA NA NA NA 3 1.0 0.33
1e-07 NA NA NA NA NA 2 0.3 0.15
1e-08 NA NA NA NA NA 1 0.3 0.30
1e-09 NA NA NA NA NA 1 0.3 0.30
1e-10 NA NA NA NA NA 1 0.3 0.30
[1] "LOC100507431_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 3.10 7.4 31 6.4e-08 0.00052 0 0.3 Inf
DDIT4 -1.40 8.1 26 7.8e-07 0.00320 1 0.8 0.80
SPP1 -1.80 7.1 23 3.8e-06 0.01000 2 1.4 0.70
EEF2 -0.41 11.0 14 2.4e-04 0.49000 3 6.8 2.30
TRIB3 -1.10 7.3 13 4.0e-04 0.55000 4 10.0 2.50
HUS1 -0.94 6.5 12 5.5e-04 0.55000 5 12.0 2.40
CYP2R1 -1.10 6.4 15 6.4e-04 0.55000 6 14.0 2.30
SHMT2 -0.72 7.6 12 6.4e-04 0.55000 7 14.0 2.00
WARS -0.79 7.4 12 7.3e-04 0.55000 8 14.0 1.80
TAF6 -0.66 7.2 12 7.5e-04 0.55000 9 15.0 1.70
1e-04 NA NA NA NA NA 3 4.6 1.50
1e-05 NA NA NA NA NA 3 1.7 0.57
1e-06 NA NA NA NA NA 2 0.8 0.40
1e-07 NA NA NA NA NA 1 0.4 0.40
1e-08 NA NA NA NA NA 0 0.1 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "LOC105376975_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SPP1 -2.1 7.1 29 2.2e-07 0.0018 0 0.9 Inf
NEFM -1.6 7.9 18 3.0e-05 0.1200 1 3.5 3.5
MYC 2.6 7.5 17 6.9e-05 0.1900 2 4.6 2.3
DHX8 1.5 6.4 20 2.1e-04 0.3700 3 9.0 3.0
TPM2 -1.3 7.3 14 2.7e-04 0.3700 4 10.0 2.5
STMN2 -1.6 7.7 14 2.7e-04 0.3700 5 10.0 2.0
CSPP1 1.3 6.5 12 6.0e-04 0.6400 6 15.0 2.4
FNDC3A 1.2 6.6 12 6.3e-04 0.6400 7 15.0 2.1
CDK20 1.4 6.5 13 7.1e-04 0.6400 8 16.0 2.0
PLCD1 -1.1 6.5 11 1.1e-03 0.8400 9 22.0 2.4
1e-04 NA NA NA NA NA 3 6.1 2.0
1e-05 NA NA NA NA NA 1 2.3 2.3
1e-06 NA NA NA NA NA 1 1.0 1.0
1e-07 NA NA NA NA NA 0 0.9 Inf
1e-08 NA NA NA NA NA 0 0.7 Inf
1e-09 NA NA NA NA NA 0 0.5 Inf
1e-10 NA NA NA NA NA 0 0.4 Inf
[1] "LOC105376975_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ATF5 1.50 6.9 16 9.4e-05 0.38 0 5.5 Inf
CHAC1 1.40 6.4 15 1.7e-04 0.38 1 6.2 6.2
SLC7A11 1.40 6.6 14 2.0e-04 0.38 2 6.7 3.4
PSAT1 0.77 8.3 14 2.5e-04 0.38 3 7.1 2.4
MCM5 0.99 7.1 14 2.7e-04 0.38 4 7.4 1.8
PHGDH 0.75 8.6 14 2.8e-04 0.38 5 7.7 1.5
MTHFD2 0.91 7.3 13 4.3e-04 0.41 6 9.5 1.6
TRMO -0.99 6.5 13 4.3e-04 0.41 7 9.6 1.4
CEBPB 1.30 6.8 12 5.7e-04 0.41 8 11.0 1.4
EIF5AL1 -1.10 6.4 16 5.8e-04 0.41 9 11.0 1.3
1e-04 NA NA NA NA NA 1 5.6 5.6
1e-05 NA NA NA NA NA 0 2.8 Inf
1e-06 NA NA NA NA NA 0 1.9 Inf
1e-07 NA NA NA NA NA 0 1.2 Inf
1e-08 NA NA NA NA NA 0 0.8 Inf
1e-09 NA NA NA NA NA 0 0.7 Inf
1e-10 NA NA NA NA NA 0 0.6 Inf
[1] "LOC105376975_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
RP11-46C20.1 -2.6 6.6 27 5.3e-07 0.0043 0 0.5 Inf
ACBD3 -1.7 6.8 13 3.5e-04 0.8400 1 5.0 5.0
SPOCK1 -1.9 6.6 13 3.6e-04 0.8400 2 5.0 2.5
SDC2 -1.4 7.7 13 4.2e-04 0.8400 3 5.9 2.0
METTL15 -1.9 6.4 14 8.9e-04 0.8400 4 9.0 2.2
KIF5C 2.4 7.3 11 1.1e-03 0.8400 5 11.0 2.2
TOP2A 4.4 7.4 11 1.2e-03 0.8400 6 11.0 1.9
HES4 2.3 7.7 11 1.2e-03 0.8400 7 12.0 1.6
A2M -1.8 6.6 10 1.5e-03 0.8400 8 14.0 1.8
FNBP4 3.1 6.8 10 1.5e-03 0.8400 9 14.0 1.6
1e-04 NA NA NA NA NA 1 2.4 2.4
1e-05 NA NA NA NA NA 1 1.0 1.0
1e-06 NA NA NA NA NA 1 0.6 0.6
1e-07 NA NA NA NA NA 0 0.3 Inf
1e-08 NA NA NA NA NA 0 0.1 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "miR137_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 3.2 7.5 27 4.2e-07 0.0034 0 0.7 Inf
FAM228B -1.3 6.5 23 2.7e-05 0.1100 1 2.6 2.6
PKMYT1 1.4 6.7 16 7.6e-05 0.1700 2 3.5 1.8
KRT18 1.9 7.2 16 8.2e-05 0.1700 3 3.5 1.2
CDC6 1.3 6.9 13 3.6e-04 0.3500 4 7.7 1.9
EXTL3 1.4 6.4 18 4.0e-04 0.3500 5 7.9 1.6
APMAP 0.7 7.4 13 4.2e-04 0.3500 6 8.3 1.4
HERPUD2 -1.0 6.5 13 4.6e-04 0.3500 7 8.9 1.3
GADD45G 1.9 7.4 13 4.6e-04 0.3500 8 8.9 1.1
LGALS3 1.5 6.6 13 4.7e-04 0.3500 9 9.1 1.0
1e-04 NA NA NA NA NA 4 3.6 0.9
1e-05 NA NA NA NA NA 1 1.9 1.9
1e-06 NA NA NA NA NA 1 0.9 0.9
1e-07 NA NA NA NA NA 0 0.6 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "miR137_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
STMN2 2.6 7.2 16 7.7e-05 0.28 0 5.1 Inf
MYC 2.6 7.5 15 1.2e-04 0.28 1 6.0 6.0
SLC4A1AP 1.6 6.6 15 1.4e-04 0.28 2 6.6 3.3
FAM105A 1.6 6.4 19 2.0e-04 0.28 3 8.2 2.7
SEMA3A -1.3 6.4 16 2.1e-04 0.28 4 8.2 2.0
TUBD1 -1.2 6.5 14 2.1e-04 0.28 5 8.2 1.6
IRS1 -1.1 6.6 14 2.6e-04 0.30 6 8.6 1.4
GAS2L3 -1.2 6.4 14 3.2e-04 0.33 7 9.4 1.3
FRZB 1.7 6.9 13 3.8e-04 0.34 8 10.0 1.3
SLC30A6 1.5 6.3 18 4.9e-04 0.40 9 12.0 1.3
1e-04 NA NA NA NA NA 1 5.7 5.7
1e-05 NA NA NA NA NA 0 1.9 Inf
1e-06 NA NA NA NA NA 0 0.9 Inf
1e-07 NA NA NA NA NA 0 0.6 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "miR137_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 2.4 7.4 25 1.3e-06 0.010 0 1.4 Inf
SPP1 -1.7 7.1 23 2.9e-06 0.012 1 1.6 1.60
RGS5 -1.3 6.7 21 8.4e-06 0.023 2 1.8 0.90
DST -1.1 6.7 20 1.2e-05 0.024 3 2.1 0.70
ZNF660 1.5 6.4 25 1.8e-05 0.029 4 2.2 0.55
NQO1 -1.2 7.5 18 4.0e-05 0.054 5 3.4 0.68
SLC2A3 -1.0 6.6 16 7.3e-05 0.085 6 4.3 0.72
S100A16 -1.1 6.7 16 9.2e-05 0.093 7 4.6 0.66
SAMD4A -1.2 6.3 21 1.2e-04 0.110 8 5.1 0.64
PDLIM7 -0.6 8.4 15 1.5e-04 0.120 9 5.5 0.61
1e-04 NA NA NA NA NA 8 4.8 0.60
1e-05 NA NA NA NA NA 3 2.1 0.70
1e-06 NA NA NA NA NA 0 1.3 Inf
1e-07 NA NA NA NA NA 0 0.6 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "NAB2_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 3.3 7.5 23 2.8e-06 0.013 0 0.8 Inf
DDX10 -1.5 6.7 23 3.3e-06 0.013 1 0.8 0.80
ZBTB20 -1.3 6.6 19 2.6e-05 0.070 2 2.6 1.30
WNT7B 1.8 6.6 16 7.0e-05 0.140 3 4.6 1.50
DTNA 1.6 6.5 18 1.3e-04 0.210 4 6.8 1.70
TBKBP1 1.6 6.4 19 2.1e-04 0.280 5 8.4 1.70
SEMA3A -1.2 6.4 15 2.5e-04 0.290 6 9.2 1.50
SMIM14 -1.1 6.5 14 3.1e-04 0.320 7 9.9 1.40
CUEDC1 1.3 6.5 13 4.3e-04 0.390 8 12.0 1.40
CMTM8 1.5 6.6 13 4.8e-04 0.390 9 12.0 1.40
1e-04 NA NA NA NA NA 4 5.9 1.50
1e-05 NA NA NA NA NA 2 1.3 0.65
1e-06 NA NA NA NA NA 0 0.4 Inf
1e-07 NA NA NA NA NA 0 0.2 Inf
1e-08 NA NA NA NA NA 0 0.1 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "NAB2_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
CLU -1.9 7.7 47 8.3e-11 5.8e-07 0 0.2
S100A10 -2.5 7.1 46 1.4e-10 5.8e-07 1 0.2
NQO1 -1.9 7.5 36 8.9e-09 2.4e-05 2 0.5
LGALS3 -2.1 6.8 32 4.8e-08 9.7e-05 3 0.6
GAP43 -1.7 8.2 31 1.0e-07 1.7e-04 4 0.7
FTH1 -1.1 12.0 28 2.9e-07 4.0e-04 5 1.0
ETV1 -1.6 6.4 26 1.0e-05 1.2e-02 6 1.7
GNG3 -1.7 6.5 20 1.3e-05 1.3e-02 7 1.8
CTD-2006C1.2 -1.2 7.0 19 2.0e-05 1.8e-02 8 2.4
IFI27L1 -1.2 6.7 18 3.4e-05 2.7e-02 9 3.3
1e-04 NA NA NA NA NA 15 4.8
1e-05 NA NA NA NA NA 6 1.7
1e-06 NA NA NA NA NA 6 1.1
1e-07 NA NA NA NA NA 4 0.7
1e-08 NA NA NA NA NA 3 0.5
1e-09 NA NA NA NA NA 2 0.3
1e-10 NA NA NA NA NA 1 0.2
EmpiricalFDR
CLU Inf
S100A10 0.20
NQO1 0.25
LGALS3 0.20
GAP43 0.18
FTH1 0.20
ETV1 0.28
GNG3 0.26
CTD-2006C1.2 0.30
IFI27L1 0.37
1e-04 0.32
1e-05 0.28
1e-06 0.18
1e-07 0.18
1e-08 0.17
1e-09 0.15
1e-10 0.20
[1] "NAB2_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
PAK3 -1.70 6.5 24 1.8e-06 0.015 0 0.7 Inf
SLC19A1 2.00 6.4 20 4.2e-05 0.170 1 2.5 2.5
CWF19L2 -1.30 6.5 18 6.6e-05 0.180 2 3.4 1.7
EVA1B -1.20 6.6 14 1.9e-04 0.390 3 5.9 2.0
MT-ATP6 -0.63 11.0 14 3.0e-04 0.430 4 7.3 1.8
PKMYT1 1.70 6.7 13 3.3e-04 0.430 5 8.1 1.6
APPL2 1.70 6.4 17 3.7e-04 0.430 6 8.4 1.4
ARHGAP21 1.60 6.6 12 5.7e-04 0.470 7 12.0 1.8
RANBP9 1.60 6.4 17 5.7e-04 0.470 8 12.0 1.6
AP5S1 1.70 6.4 16 5.9e-04 0.470 9 13.0 1.4
1e-04 NA NA NA NA NA 3 3.9 1.3
1e-05 NA NA NA NA NA 1 1.1 1.1
1e-06 NA NA NA NA NA 0 0.7 Inf
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.5 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.4 Inf
[1] "NGEF_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NQO1 -1.7 7.4 16 7.9e-05 0.53 0 4.5 Inf
KMT5A -1.7 6.5 15 1.3e-04 0.53 1 5.6 5.6
PLPP3 -1.5 6.5 14 2.6e-04 0.61 2 7.1 3.6
CTTN -1.4 6.9 13 3.3e-04 0.61 3 7.7 2.6
SPP1 -1.8 6.9 13 4.6e-04 0.61 4 9.2 2.3
CNTROB -1.6 6.4 16 5.8e-04 0.61 5 11.0 2.1
AKAP8L 2.7 6.6 12 6.0e-04 0.61 6 11.0 1.8
CMBL 2.4 6.8 12 6.5e-04 0.61 7 12.0 1.7
TPX2 -1.4 7.0 12 6.7e-04 0.61 8 12.0 1.5
CCNF -1.5 6.5 12 8.4e-04 0.65 9 14.0 1.6
1e-04 NA NA NA NA NA 1 4.9 4.9
1e-05 NA NA NA NA NA 0 2.4 Inf
1e-06 NA NA NA NA NA 0 1.0 Inf
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.2 Inf
1e-09 NA NA NA NA NA 0 0.2 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "NGEF_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
PIF1 -3.3 6.5 21 8.1e-06 0.066 0 1.6 Inf
CDCA2 -2.9 6.5 20 1.7e-05 0.069 1 1.9 1.90
BORA -2.9 6.4 18 2.9e-05 0.079 2 2.1 1.00
C2orf69 -2.7 6.6 16 1.1e-04 0.190 3 3.1 1.00
TTK -2.7 6.5 16 1.1e-04 0.190 4 3.1 0.78
CCNF -2.5 6.5 13 3.4e-04 0.460 5 6.2 1.20
RP11-343C2.12 -2.6 6.4 14 4.3e-04 0.500 6 7.1 1.20
MSANTD2 -2.5 6.5 12 5.5e-04 0.550 7 8.0 1.10
SGO2 -2.4 6.8 12 6.7e-04 0.550 8 8.8 1.10
EMG1 -1.8 7.7 12 6.8e-04 0.550 9 8.8 0.98
1e-04 NA NA NA NA NA 3 2.9 0.97
1e-05 NA NA NA NA NA 1 1.8 1.80
1e-06 NA NA NA NA NA 0 1.2 Inf
1e-07 NA NA NA NA NA 0 1.0 Inf
1e-08 NA NA NA NA NA 0 0.7 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "PBRM1_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
PLK1 -2.6 7.5 23 4.2e-06 0.019 0 2.5
NDC80 -2.6 6.7 22 4.6e-06 0.019 1 2.6
CDC25B -2.4 7.2 17 6.0e-05 0.140 2 5.5
RP11-339B21.12 -2.2 7.0 16 7.7e-05 0.140 3 5.7
DLL1 -2.7 7.0 16 8.6e-05 0.140 4 5.8
JUN -1.8 7.8 15 1.4e-04 0.180 5 7.0
TPX2 -2.1 7.0 14 2.5e-04 0.280 6 9.0
PTTG1 -1.9 8.5 13 3.2e-04 0.280 7 9.9
NEK2 -2.2 6.5 13 3.4e-04 0.280 8 9.9
DLGAP5 -2.2 6.7 13 3.5e-04 0.280 9 9.9
1e-04 NA NA NA NA NA 5 6.2
1e-05 NA NA NA NA NA 2 3.0
1e-06 NA NA NA NA NA 0 1.9
1e-07 NA NA NA NA NA 0 1.3
1e-08 NA NA NA NA NA 0 0.8
1e-09 NA NA NA NA NA 0 0.2
1e-10 NA NA NA NA NA 0 0.1
EmpiricalFDR
PLK1 Inf
NDC80 2.6
CDC25B 2.8
RP11-339B21.12 1.9
DLL1 1.4
JUN 1.4
TPX2 1.5
PTTG1 1.4
NEK2 1.2
DLGAP5 1.1
1e-04 1.2
1e-05 1.5
1e-06 Inf
1e-07 Inf
1e-08 Inf
1e-09 Inf
1e-10 Inf
[1] "PBRM1_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
A2M -1.9 6.6 20 1.7e-05 0.14 0 1.7 Inf
IFITM3 -1.6 8.7 18 4.4e-05 0.14 1 2.3 2.30
TPM2 -1.9 7.2 17 5.4e-05 0.14 2 2.4 1.20
INTU -1.5 6.8 16 7.7e-05 0.14 3 2.5 0.83
EFCAB11 -1.7 6.4 19 8.9e-05 0.14 4 2.5 0.62
MED13 -1.6 6.4 16 2.2e-04 0.28 5 4.3 0.86
PRC1 -1.5 6.7 14 2.9e-04 0.28 6 4.9 0.82
RGS5 -1.5 6.6 14 3.1e-04 0.28 7 5.1 0.73
ZNF134 -1.6 6.4 16 3.2e-04 0.28 8 5.4 0.68
ITGA6 -1.7 6.4 19 3.9e-04 0.32 9 6.1 0.68
1e-04 NA NA NA NA NA 5 2.7 0.54
1e-05 NA NA NA NA NA 0 1.5 Inf
1e-06 NA NA NA NA NA 0 1.1 Inf
1e-07 NA NA NA NA NA 0 0.9 Inf
1e-08 NA NA NA NA NA 0 0.7 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.4 Inf
[1] "PBRM1_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TPM2 -3.7 7.3 45 2.1e-10 1.7e-06 0 0.1 Inf
RGS5 -3.0 6.7 33 4.1e-08 1.6e-04 1 0.3 0.30
TPPP3 -3.1 6.6 29 2.5e-07 6.9e-04 2 0.5 0.25
SPARC -1.6 8.5 20 1.4e-05 2.6e-02 3 0.8 0.27
SESN3 -2.6 6.5 20 1.6e-05 2.6e-02 4 0.8 0.20
CCND2 -2.3 7.1 16 9.1e-05 1.2e-01 5 1.6 0.32
HDAC2 2.0 8.5 15 1.2e-04 1.4e-01 6 1.6 0.27
HEBP1 -1.9 6.9 14 2.1e-04 1.8e-01 7 2.1 0.30
CEBPD -2.4 6.7 14 2.1e-04 1.8e-01 8 2.1 0.26
SCD -1.7 7.6 14 2.3e-04 1.8e-01 9 2.1 0.23
1e-04 NA NA NA NA NA 6 1.6 0.27
1e-05 NA NA NA NA NA 3 0.7 0.23
1e-06 NA NA NA NA NA 3 0.5 0.17
1e-07 NA NA NA NA NA 2 0.4 0.20
1e-08 NA NA NA NA NA 1 0.3 0.30
1e-09 NA NA NA NA NA 1 0.1 0.10
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "PCDHA123_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
RGS5 -1.40 6.7 27 4.9e-07 0.0028 0 0.9 Inf
SEMA3A -1.40 6.4 26 6.9e-07 0.0028 1 1.0 1.00
GRIA1 -1.30 6.4 23 2.6e-06 0.0070 2 1.3 0.65
SPP1 2.00 6.6 22 5.4e-06 0.0110 3 1.5 0.50
ARMCX6 -0.90 7.0 17 5.1e-05 0.0820 4 3.8 0.95
C2orf49 -1.00 6.5 17 9.7e-05 0.1100 5 4.7 0.94
C1orf56 -1.20 6.4 21 9.8e-05 0.1100 6 4.7 0.78
NUP58 1.20 6.6 16 1.1e-04 0.1100 7 5.1 0.73
GAP43 -0.92 8.1 14 2.3e-04 0.1700 8 6.9 0.86
PHLDA1 -1.10 7.0 14 2.5e-04 0.1700 9 7.5 0.83
1e-04 NA NA NA NA NA 7 4.7 0.67
1e-05 NA NA NA NA NA 4 1.9 0.48
1e-06 NA NA NA NA NA 2 1.2 0.60
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "PCDHA123_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 3.40 7.3 45 1.5e-10 1.2e-06 0 0.1 Inf
LGALS3 -1.60 6.9 22 4.9e-06 2.0e-02 1 1.8 1.8
SAMD4A -1.20 6.4 24 2.7e-05 7.2e-02 2 3.2 1.6
SNAPC1 -1.20 6.7 17 4.8e-05 9.7e-02 3 3.9 1.3
KCTD10 -0.96 6.6 16 8.6e-05 1.4e-01 4 5.4 1.4
KMT5A -1.00 6.5 15 1.3e-04 1.7e-01 5 6.2 1.2
CTGF -0.85 8.5 14 1.9e-04 2.2e-01 6 7.0 1.2
CDCA7 1.00 6.6 14 2.2e-04 2.2e-01 7 7.7 1.1
CITED1 1.10 6.4 16 3.4e-04 3.1e-01 8 9.9 1.2
ZNF660 1.10 6.4 16 4.9e-04 3.2e-01 9 11.0 1.3
1e-04 NA NA NA NA NA 5 5.7 1.1
1e-05 NA NA NA NA NA 2 2.0 1.0
1e-06 NA NA NA NA NA 1 1.4 1.4
1e-07 NA NA NA NA NA 1 1.2 1.2
1e-08 NA NA NA NA NA 1 0.8 0.8
1e-09 NA NA NA NA NA 1 0.3 0.3
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "PCDHA123_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 3.40 7.3 44 2.1e-10 1.7e-06 0 0.2 Inf
SMG1 -1.00 6.6 17 5.2e-05 1.8e-01 1 3.3 3.3
STMN2 1.80 7.1 16 6.7e-05 1.8e-01 2 3.5 1.8
CNPY4 -1.10 6.4 19 9.3e-05 1.9e-01 3 4.3 1.4
GPM6B -0.49 8.5 15 1.2e-04 2.0e-01 4 5.0 1.2
NCAPG -1.00 6.6 14 1.8e-04 2.5e-01 5 5.7 1.1
PTPN11 -0.86 6.6 14 2.3e-04 2.7e-01 6 6.5 1.1
CYP2R1 -1.00 6.4 16 2.9e-04 3.0e-01 7 7.4 1.1
NRDC 0.80 6.9 13 3.8e-04 3.5e-01 8 9.1 1.1
HIST1H2AC 1.10 6.4 13 4.6e-04 3.7e-01 9 10.0 1.2
1e-04 NA NA NA NA NA 4 4.5 1.1
1e-05 NA NA NA NA NA 1 1.6 1.6
1e-06 NA NA NA NA NA 1 1.2 1.2
1e-07 NA NA NA NA NA 1 0.6 0.6
1e-08 NA NA NA NA NA 1 0.6 0.6
1e-09 NA NA NA NA NA 1 0.3 0.3
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "pos_SNAP91_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
HYOU1 -2.5 6.5 15.0 0.00025 0.83 0 4.9 Inf
TRMO -2.2 6.4 10.0 0.00140 0.83 1 12.0 12.0
EDC3 -2.2 6.5 9.9 0.00200 0.83 2 15.0 7.5
UPRT -2.5 6.4 14.0 0.00220 0.83 3 16.0 5.4
TCF19 -2.2 6.5 10.0 0.00260 0.83 4 19.0 4.7
NHLRC3 -2.1 6.6 9.2 0.00280 0.83 5 20.0 4.0
GUF1 -2.1 6.5 9.1 0.00290 0.83 6 20.0 3.4
DTX3 -2.1 6.6 8.9 0.00320 0.83 7 23.0 3.2
TDG 4.1 7.2 8.8 0.00350 0.83 8 24.0 3.0
EFCC1 -2.1 6.5 8.4 0.00430 0.83 9 29.0 3.2
1e-04 NA NA NA NA NA 0 3.4 Inf
1e-05 NA NA NA NA NA 0 1.8 Inf
1e-06 NA NA NA NA NA 0 1.3 Inf
1e-07 NA NA NA NA NA 0 0.8 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "PPP1R16B_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 2.50 7.4 22 6.0e-06 0.049 0 3.2 Inf
ELMO1 1.50 6.4 21 2.4e-05 0.085 1 5.0 5.0
FGF19 1.80 6.5 18 3.1e-05 0.085 2 5.3 2.6
CAV1 -1.30 7.4 16 8.6e-05 0.170 3 6.7 2.2
ZNF273 1.30 6.4 17 1.7e-04 0.270 4 9.4 2.3
CEP250 -1.10 6.4 15 3.1e-04 0.390 5 13.0 2.6
POLR3A 1.20 6.5 13 3.4e-04 0.390 6 13.0 2.2
PLS3 1.20 6.4 15 5.7e-04 0.570 7 17.0 2.4
ATF2 -0.98 6.4 12 8.3e-04 0.570 8 21.0 2.7
LAMP5 1.20 6.4 12 8.6e-04 0.570 9 21.0 2.4
1e-04 NA NA NA NA NA 4 6.9 1.7
1e-05 NA NA NA NA NA 1 3.5 3.5
1e-06 NA NA NA NA NA 0 1.9 Inf
1e-07 NA NA NA NA NA 0 1.1 Inf
1e-08 NA NA NA NA NA 0 0.8 Inf
1e-09 NA NA NA NA NA 0 0.6 Inf
1e-10 NA NA NA NA NA 0 0.5 Inf
[1] "PPP1R16B_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
DDX10 -1.50 6.7 21 1.0e-05 0.082 0 2.3 Inf
MYC 2.90 7.5 18 3.7e-05 0.095 1 3.4 3.4
TMEM88 -1.40 6.5 18 4.0e-05 0.095 2 3.4 1.7
HIST1H1C -1.50 6.6 17 4.7e-05 0.095 3 3.7 1.2
GDF15 -1.60 6.8 15 1.2e-04 0.190 4 5.9 1.5
ATF2 -1.20 6.5 16 2.8e-04 0.370 5 8.7 1.7
GADD45G -1.60 7.9 13 4.4e-04 0.440 6 10.0 1.7
PMP22 1.50 6.5 13 4.6e-04 0.440 7 11.0 1.5
EZR -0.83 7.5 12 5.5e-04 0.440 8 12.0 1.4
NKAIN3 -1.10 6.4 13 5.8e-04 0.440 9 12.0 1.3
1e-04 NA NA NA NA NA 4 5.4 1.4
1e-05 NA NA NA NA NA 0 2.3 Inf
1e-06 NA NA NA NA NA 0 0.8 Inf
1e-07 NA NA NA NA NA 0 0.4 Inf
1e-08 NA NA NA NA NA 0 0.2 Inf
1e-09 NA NA NA NA NA 0 0.2 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "PPP1R16B_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 3.3 7.5 23 3.7e-06 0.03 0 1.3 Inf
EIF4ENIF1 1.6 6.5 19 7.3e-05 0.23 1 3.4 3.4
LGALS3 1.8 6.5 15 1.6e-04 0.23 2 6.2 3.1
FAM83D 1.6 6.5 15 1.7e-04 0.23 3 6.5 2.2
FGF19 1.8 6.6 15 1.7e-04 0.23 4 6.6 1.6
PROM1 1.6 6.5 16 1.9e-04 0.23 5 7.0 1.4
ASCL1 -1.3 7.2 14 2.0e-04 0.23 6 7.2 1.2
VGF 1.8 6.7 14 2.3e-04 0.24 7 7.8 1.1
CASP9 1.5 6.4 19 3.0e-04 0.27 8 8.8 1.1
PTRF 1.7 6.9 12 5.0e-04 0.39 9 12.0 1.3
1e-04 NA NA NA NA NA 2 4.0 2.0
1e-05 NA NA NA NA NA 1 2.2 2.2
1e-06 NA NA NA NA NA 0 0.7 Inf
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.3 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "RERE_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
C1orf56 -1.50 6.4 26 4.1e-06 0.030 0 1.6 Inf
TSC22D4 1.60 6.5 22 7.5e-06 0.030 1 2.0 2.0
MYC 2.40 7.5 19 1.9e-05 0.051 2 2.9 1.4
STMN2 2.00 7.2 15 1.7e-04 0.350 3 6.1 2.0
EIF1AD 1.30 6.5 13 3.1e-04 0.510 4 9.4 2.3
TPX2 -0.96 7.1 13 4.3e-04 0.530 5 12.0 2.4
S100A10 1.50 6.7 12 5.2e-04 0.530 6 14.0 2.3
ASGR1 1.20 6.7 12 6.2e-04 0.530 7 16.0 2.2
NDC80 -0.97 6.8 12 7.2e-04 0.530 8 17.0 2.1
SNX27 -0.85 6.7 12 7.5e-04 0.530 9 17.0 1.9
1e-04 NA NA NA NA NA 3 5.0 1.7
1e-05 NA NA NA NA NA 2 2.4 1.2
1e-06 NA NA NA NA NA 0 1.2 Inf
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "RERE_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SPP1 -2.30 7.2 40 1.4e-09 1.1e-05 0 0.7 Inf
MYC 3.20 7.5 28 3.1e-07 1.2e-03 1 1.0 1.00
SH3KBP1 1.40 6.4 16 2.4e-04 5.5e-01 2 8.5 4.20
USMG5 0.46 8.7 14 2.7e-04 5.5e-01 3 9.2 3.10
KDELR2 0.60 8.0 13 4.6e-04 6.3e-01 4 12.0 3.00
FBXO5 1.20 6.9 12 5.1e-04 6.3e-01 5 13.0 2.60
KCTD10 -0.99 6.6 12 5.9e-04 6.3e-01 6 13.0 2.20
TAGLN3 -1.20 7.4 12 6.3e-04 6.3e-01 7 13.0 1.90
HIST1H1C -1.10 6.6 12 7.2e-04 6.4e-01 8 15.0 1.80
GCHFR -1.10 6.5 12 8.0e-04 6.4e-01 9 16.0 1.80
1e-04 NA NA NA NA NA 2 5.5 2.80
1e-05 NA NA NA NA NA 2 2.5 1.20
1e-06 NA NA NA NA NA 2 1.3 0.65
1e-07 NA NA NA NA NA 1 0.8 0.80
1e-08 NA NA NA NA NA 1 0.7 0.70
1e-09 NA NA NA NA NA 0 0.7 Inf
1e-10 NA NA NA NA NA 0 0.6 Inf
[1] "RERE_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
S100A10 -2.10 7.0 28 3.7e-07 0.003 0 1.0 Inf
MAFF 2.50 6.5 20 1.7e-05 0.069 1 1.7 1.7
HIST1H2AC 2.10 6.4 16 8.1e-05 0.200 2 3.8 1.9
GLIPR1 -1.40 6.7 15 1.2e-04 0.200 3 4.7 1.6
AC093323.3 1.70 6.6 16 1.2e-04 0.200 4 4.7 1.2
GNG10 1.70 6.4 18 4.6e-04 0.520 5 11.0 2.3
BRCA1 -1.20 6.7 13 4.7e-04 0.520 6 12.0 2.0
FGF19 2.00 6.6 12 7.5e-04 0.520 7 16.0 2.3
HIPK2 -0.94 7.0 12 8.3e-04 0.520 8 17.0 2.1
SLC2A3 -1.10 6.6 11 9.2e-04 0.520 9 19.0 2.1
1e-04 NA NA NA NA NA 3 4.0 1.3
1e-05 NA NA NA NA NA 1 1.7 1.7
1e-06 NA NA NA NA NA 1 1.1 1.1
1e-07 NA NA NA NA NA 0 0.7 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.2 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "SETD1A_1st_exon_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
EMP3 2.6 6.7 19 1.7e-05 0.14 0 2.2 Inf
CNN1 -1.6 6.6 18 4.3e-05 0.17 1 3.5 3.5
ZNF33A 2.0 6.5 17 6.4e-05 0.17 2 3.9 2.0
DLL3 3.1 7.0 16 1.1e-04 0.19 3 4.9 1.6
QSER1 2.0 6.4 18 1.2e-04 0.19 4 5.0 1.2
KLHL8 1.9 6.4 17 2.1e-04 0.25 5 6.8 1.4
AGPAT2 1.9 6.6 14 2.4e-04 0.25 6 7.0 1.2
PLXNB1 -1.4 6.4 18 2.5e-04 0.25 7 7.0 1.0
ANKRD1 2.1 6.6 13 5.0e-04 0.40 8 11.0 1.3
JAKMIP2 1.7 6.5 13 5.0e-04 0.40 9 11.0 1.2
1e-04 NA NA NA NA NA 3 4.5 1.5
1e-05 NA NA NA NA NA 0 1.9 Inf
1e-06 NA NA NA NA NA 0 1.0 Inf
1e-07 NA NA NA NA NA 0 0.8 Inf
1e-08 NA NA NA NA NA 0 0.5 Inf
1e-09 NA NA NA NA NA 0 0.5 Inf
1e-10 NA NA NA NA NA 0 0.5 Inf
[1] "SETD1A_1st_exon_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SPP1 -2.80 7.2 56 2.9e-12 2.4e-08 0 0.7 Inf
S100A10 -2.10 7.0 32 4.9e-08 2.0e-04 1 1.3 1.30
TAGLN2 -1.70 6.7 25 1.3e-06 3.5e-03 2 2.6 1.30
RGS5 -1.60 6.7 24 1.9e-06 3.7e-03 3 2.7 0.90
SERPINE2 -1.60 6.7 24 2.3e-06 3.7e-03 4 2.8 0.70
RAB13 -0.83 7.9 20 1.3e-05 1.3e-02 5 4.3 0.86
KCTD10 -1.30 6.5 20 1.3e-05 1.3e-02 6 4.3 0.72
CALD1 -1.10 8.1 20 1.3e-05 1.3e-02 7 4.3 0.61
TPM2 -1.60 7.3 19 2.4e-05 2.2e-02 8 4.8 0.60
MMP2 -1.30 6.5 18 3.0e-05 2.4e-02 9 5.2 0.58
1e-04 NA NA NA NA NA 16 7.9 0.49
1e-05 NA NA NA NA NA 5 4.1 0.82
1e-06 NA NA NA NA NA 2 2.4 1.20
1e-07 NA NA NA NA NA 2 1.3 0.65
1e-08 NA NA NA NA NA 1 1.1 1.10
1e-09 NA NA NA NA NA 1 0.8 0.80
1e-10 NA NA NA NA NA 1 0.7 0.70
[1] "SETD1A_1st_exon_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
UBB 4.1 9.5 19 1.9e-05 0.15 0 1.9 Inf
FXYD6 3.6 8.0 15 1.2e-04 0.50 1 2.7 2.7
BEX2 -2.2 6.9 12 5.7e-04 0.77 2 5.5 2.8
CST3 2.3 8.2 12 7.1e-04 0.77 3 6.2 2.1
COX11 4.1 7.2 12 8.1e-04 0.77 4 6.8 1.7
MSTO1 -2.1 6.5 11 8.7e-04 0.77 5 6.8 1.4
PTN -1.8 8.0 11 1.1e-03 0.77 6 8.1 1.4
ARHGEF2 -2.2 6.5 11 1.1e-03 0.77 7 8.3 1.2
NOL11 4.1 7.2 11 1.1e-03 0.77 8 8.6 1.1
CREB3 4.0 7.2 11 1.3e-03 0.77 9 9.4 1.0
1e-04 NA NA NA NA NA 1 2.7 2.7
1e-05 NA NA NA NA NA 0 1.7 Inf
1e-06 NA NA NA NA NA 0 1.0 Inf
1e-07 NA NA NA NA NA 0 0.7 Inf
1e-08 NA NA NA NA NA 0 0.5 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "STAT6_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
S100A10 3.0 6.6 19 1.9e-05 0.12 0 1.8 Inf
MYC 3.5 7.5 18 3.0e-05 0.12 1 2.4 2.4
TOR1AIP1 1.7 6.4 18 2.7e-04 0.72 2 8.5 4.2
NUP98 -1.2 6.4 15 3.6e-04 0.73 3 10.0 3.4
DHODH -1.2 6.6 13 5.0e-04 0.81 4 13.0 3.2
EMP3 1.7 6.7 12 6.8e-04 0.90 5 17.0 3.3
DCAF6 1.5 6.3 16 1.0e-03 0.90 6 22.0 3.6
KCTD2 -1.2 6.4 15 1.1e-03 0.90 7 23.0 3.2
RAB11FIP2 1.6 6.4 13 1.2e-03 0.90 8 24.0 3.0
SERGEF 1.6 6.4 14 1.2e-03 0.90 9 24.0 2.7
1e-04 NA NA NA NA NA 2 4.8 2.4
1e-05 NA NA NA NA NA 0 1.4 Inf
1e-06 NA NA NA NA NA 0 0.7 Inf
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.5 Inf
1e-09 NA NA NA NA NA 0 0.5 Inf
1e-10 NA NA NA NA NA 0 0.5 Inf
[1] "STAT6_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SPP1 -2.50 7.3 44 2.8e-10 2.3e-06 0 0.5 Inf
LGALS3 -1.70 6.8 23 2.5e-06 1.0e-02 1 1.9 1.90
IMPA2 1.50 6.8 17 6.2e-05 1.5e-01 2 4.2 2.10
TP53I3 -1.20 7.0 16 7.2e-05 1.5e-01 3 4.4 1.50
DHFR 0.98 7.7 16 1.1e-04 1.7e-01 4 5.1 1.30
ZNF561 1.40 6.5 15 1.3e-04 1.7e-01 5 5.2 1.00
STMN2 2.10 7.2 14 1.9e-04 2.2e-01 6 6.3 1.00
LTBP1 1.50 6.4 18 2.1e-04 2.2e-01 7 6.7 0.96
CYFIP2 -0.92 6.8 13 4.1e-04 3.6e-01 8 9.9 1.20
ENHO 1.20 6.7 13 4.5e-04 3.6e-01 9 11.0 1.20
1e-04 NA NA NA NA NA 4 4.9 1.20
1e-05 NA NA NA NA NA 2 2.4 1.20
1e-06 NA NA NA NA NA 1 1.9 1.90
1e-07 NA NA NA NA NA 1 0.8 0.80
1e-08 NA NA NA NA NA 1 0.6 0.60
1e-09 NA NA NA NA NA 1 0.5 0.50
1e-10 NA NA NA NA NA 0 0.5 Inf
[1] "STAT6_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 2.40 7.4 23 2.5e-06 0.02 0 1.7 Inf
SEMA3A -1.20 6.4 18 5.7e-05 0.19 1 4.0 4.0
PIF1 1.40 6.4 16 7.1e-05 0.19 2 4.1 2.0
GADD45G -1.60 8.0 15 1.3e-04 0.25 3 4.9 1.6
TACC3 1.10 6.8 14 2.8e-04 0.43 4 6.9 1.7
SPTY2D1 1.20 6.4 13 4.1e-04 0.43 5 8.9 1.8
MPZL1 -0.79 6.8 13 4.3e-04 0.43 6 9.2 1.5
RILPL2 1.30 6.4 21 4.4e-04 0.43 7 9.5 1.4
LTN1 -1.00 6.4 15 5.3e-04 0.43 8 11.0 1.3
LIX1 -0.99 6.7 12 5.5e-04 0.43 9 11.0 1.2
1e-04 NA NA NA NA NA 3 4.7 1.6
1e-05 NA NA NA NA NA 1 2.3 2.3
1e-06 NA NA NA NA NA 0 1.4 Inf
1e-07 NA NA NA NA NA 0 1.0 Inf
1e-08 NA NA NA NA NA 0 0.6 Inf
1e-09 NA NA NA NA NA 0 0.2 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "TCF4-ITF2_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MT1X -1.90 6.7 30 1.0e-07 0.00083 0 1.0 Inf
TSPAN15 1.50 6.7 19 1.7e-05 0.07000 1 2.2 2.2
SPP1 2.00 6.7 18 2.7e-05 0.07400 2 2.9 1.4
GOLGA8B 1.40 6.4 24 8.9e-05 0.16000 3 5.0 1.7
ANKRD1 1.50 6.6 15 1.1e-04 0.16000 4 5.6 1.4
IDI1 0.67 8.2 15 1.2e-04 0.16000 5 5.8 1.2
SLC20A2 1.20 6.6 15 1.6e-04 0.19000 6 7.2 1.2
TRIO -1.10 6.5 15 2.8e-04 0.25000 7 10.0 1.4
SCD5 1.20 6.5 15 2.8e-04 0.25000 8 10.0 1.3
FAM111B 1.20 6.5 13 3.5e-04 0.28000 9 11.0 1.3
1e-04 NA NA NA NA NA 4 5.4 1.4
1e-05 NA NA NA NA NA 1 2.1 2.1
1e-06 NA NA NA NA NA 1 1.5 1.5
1e-07 NA NA NA NA NA 0 1.0 Inf
1e-08 NA NA NA NA NA 0 0.7 Inf
1e-09 NA NA NA NA NA 0 0.5 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "TCF4-ITF2_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 3.10 7.5 27 5.0e-07 0.0041 0 0.9 Inf
RGS5 -1.30 6.7 19 1.7e-05 0.0480 1 1.8 1.8
STMN2 2.40 7.2 19 1.8e-05 0.0480 2 1.8 0.9
NFXL1 1.40 6.4 19 2.3e-04 0.3100 3 5.6 1.9
NNAT 1.40 6.5 14 2.7e-04 0.3100 4 6.5 1.6
CMTR2 1.30 6.4 16 3.0e-04 0.3100 5 6.9 1.4
GADD45G 1.90 7.4 14 3.0e-04 0.3100 6 6.9 1.2
ATPIF1 -0.51 8.3 13 3.1e-04 0.3100 7 7.1 1.0
JAKMIP2 1.20 6.5 14 4.2e-04 0.3800 8 8.2 1.0
FAT3 -0.98 6.5 12 5.0e-04 0.4100 9 9.1 1.0
1e-04 NA NA NA NA NA 3 3.0 1.0
1e-05 NA NA NA NA NA 1 1.7 1.7
1e-06 NA NA NA NA NA 1 1.0 1.0
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.5 Inf
1e-09 NA NA NA NA NA 0 0.5 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "TCF4-ITF2_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SNAPC1 -3.0 6.8 58 1.4e-12 1.2e-08 0 0.2 Inf
BORA -1.7 6.5 14 2.6e-04 6.1e-01 1 4.3 4.3
CLN8 2.8 6.7 14 3.0e-04 6.1e-01 2 5.0 2.5
CCDC84 -1.6 6.5 13 4.1e-04 6.1e-01 3 6.0 2.0
SLC7A11 -1.7 6.8 13 5.1e-04 6.1e-01 4 6.6 1.6
RNF25 2.7 6.6 13 5.2e-04 6.1e-01 5 6.6 1.3
MRPS28 2.4 6.8 12 6.1e-04 6.1e-01 6 7.5 1.2
CHMP4A 2.6 6.6 12 6.6e-04 6.1e-01 7 8.2 1.2
DIO3 -1.5 7.3 12 6.8e-04 6.1e-01 8 8.5 1.1
PTRH1 2.5 6.6 12 7.9e-04 6.2e-01 9 9.5 1.1
1e-04 NA NA NA NA NA 1 2.6 2.6
1e-05 NA NA NA NA NA 1 0.5 0.5
1e-06 NA NA NA NA NA 1 0.3 0.3
1e-07 NA NA NA NA NA 1 0.2 0.2
1e-08 NA NA NA NA NA 1 0.2 0.2
1e-09 NA NA NA NA NA 1 0.2 0.2
1e-10 NA NA NA NA NA 1 0.2 0.2
[1] "TRANK1_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NRIP1 -2.8 6.4 23.0 7.3e-05 0.59 0 1.9 Inf
KRT18 -2.7 7.5 13.0 4.6e-04 0.85 1 4.3 4.3
METTL18 -2.5 6.5 14.0 4.8e-04 0.85 2 4.5 2.2
HMGCS1 -1.6 8.1 11.0 9.2e-04 0.85 3 6.3 2.1
SDF2L1 -1.9 7.3 11.0 1.3e-03 0.85 4 8.6 2.2
CKAP2L -2.2 6.6 10.0 1.7e-03 0.85 5 10.0 2.0
ACVR2A -2.2 6.5 10.0 1.8e-03 0.85 6 11.0 1.8
MRPS34 1.9 8.4 9.7 2.2e-03 0.85 7 12.0 1.7
INIP -1.8 6.9 9.6 2.3e-03 0.85 8 13.0 1.6
PYCR1 -2.2 6.9 9.5 2.3e-03 0.85 9 14.0 1.5
1e-04 NA NA NA NA NA 1 2.3 2.3
1e-05 NA NA NA NA NA 0 1.0 Inf
1e-06 NA NA NA NA NA 0 0.6 Inf
1e-07 NA NA NA NA NA 0 0.4 Inf
1e-08 NA NA NA NA NA 0 0.3 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "TRANK1_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
FZD7 -1.5 6.5 17 0.00007 0.53 0 3.7 Inf
CDKN1C -1.7 7.0 15 0.00014 0.53 1 5.0 5.0
MYC 3.8 7.6 14 0.00020 0.53 2 6.1 3.0
AC084018.1 -1.3 6.5 14 0.00026 0.53 3 7.4 2.5
WWP2 -1.3 6.4 15 0.00066 0.83 4 14.0 3.6
EXD2 1.8 6.4 14 0.00075 0.83 5 16.0 3.1
LOXL1 1.9 6.6 11 0.00085 0.83 6 17.0 2.8
APC2 -1.3 6.5 12 0.00089 0.83 7 17.0 2.4
IGF1R -1.2 6.6 11 0.00110 0.83 8 19.0 2.4
MANEAL -1.3 6.4 15 0.00130 0.83 9 22.0 2.5
1e-04 NA NA NA NA NA 1 4.5 4.5
1e-05 NA NA NA NA NA 0 1.4 Inf
1e-06 NA NA NA NA NA 0 0.7 Inf
1e-07 NA NA NA NA NA 0 0.6 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "TRANK1_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC 3.20 7.3 42 6.9e-10 5.6e-06 0 0.2 Inf
ATF7IP2 1.20 6.4 18 3.1e-05 1.2e-01 1 2.7 2.7
TAMM41 -1.10 6.4 20 4.3e-05 1.2e-01 2 2.9 1.4
IER3 1.20 6.4 16 9.8e-05 2.0e-01 3 4.3 1.4
NUP155 1.10 6.4 16 1.6e-04 2.6e-01 4 5.1 1.3
DOLK -0.85 6.5 13 4.3e-04 5.8e-01 5 8.4 1.7
KCTD10 -0.85 6.5 12 6.6e-04 6.9e-01 6 12.0 2.0
CLK3 -0.76 6.7 12 6.8e-04 6.9e-01 7 12.0 1.7
RPUSD1 0.78 6.7 11 9.1e-04 7.2e-01 8 14.0 1.8
ATOH8 -0.97 6.4 13 1.0e-03 7.2e-01 9 16.0 1.7
1e-04 NA NA NA NA NA 4 4.3 1.1
1e-05 NA NA NA NA NA 1 2.1 2.1
1e-06 NA NA NA NA NA 1 1.1 1.1
1e-07 NA NA NA NA NA 1 1.0 1.0
1e-08 NA NA NA NA NA 1 0.5 0.5
1e-09 NA NA NA NA NA 1 0.2 0.2
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "UBE2Q2P1_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
JAG1 -2.1 6.9 28 3.5e-07 0.0028 0 0.3 Inf
SPP1 -2.4 6.9 26 7.4e-07 0.0030 1 0.3 0.30
S100A10 -2.1 6.9 20 1.3e-05 0.0340 2 1.2 0.60
NQO1 -1.7 7.3 17 6.9e-05 0.1400 3 3.0 1.00
TPM2 -1.9 7.2 16 1.2e-04 0.1800 4 4.3 1.10
SERPINH1 -1.1 7.8 15 1.3e-04 0.1800 5 4.7 0.94
SHPRH 2.6 6.6 15 1.6e-04 0.1900 6 5.5 0.92
SGO1 2.6 6.8 15 1.9e-04 0.1900 7 6.0 0.86
NRSN2 2.5 6.5 14 2.5e-04 0.2100 8 6.7 0.84
RP11-75C9.1 -1.7 6.4 17 2.6e-04 0.2100 9 6.8 0.76
1e-04 NA NA NA NA NA 4 3.8 0.95
1e-05 NA NA NA NA NA 2 1.1 0.55
1e-06 NA NA NA NA NA 2 0.3 0.15
1e-07 NA NA NA NA NA 0 0.2 Inf
1e-08 NA NA NA NA NA 0 0.1 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "UBE2Q2P1_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
LGALS3 -3.90 6.9 71 1.1e-14 9.0e-11 0 0.0 NaN
PCDH9 -2.30 6.4 23 6.0e-06 2.4e-02 1 1.7 1.70
TERF2IP -1.50 7.4 16 9.2e-05 2.4e-01 2 3.6 1.80
AFF4 -1.80 6.6 16 1.2e-04 2.4e-01 3 3.8 1.30
SPOCK1 -1.80 6.6 15 1.6e-04 2.6e-01 4 4.4 1.10
MALAT1 -0.91 14.0 13 3.4e-04 4.6e-01 5 6.7 1.30
KCTD2 -1.90 6.4 17 4.0e-04 4.7e-01 6 7.9 1.30
UFSP2 2.50 6.9 12 6.9e-04 6.2e-01 7 10.0 1.50
SFRP1 3.80 7.0 12 7.1e-04 6.2e-01 8 11.0 1.30
ATP5B -0.75 9.6 12 8.3e-04 6.2e-01 9 12.0 1.30
1e-04 NA NA NA NA NA 3 3.6 1.20
1e-05 NA NA NA NA NA 2 1.9 0.95
1e-06 NA NA NA NA NA 1 0.8 0.80
1e-07 NA NA NA NA NA 1 0.6 0.60
1e-08 NA NA NA NA NA 1 0.4 0.40
1e-09 NA NA NA NA NA 1 0.1 0.10
1e-10 NA NA NA NA NA 1 0.1 0.10
[1] "UBE2Q2P1_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TAF1A -2.0 6.5 22 5.2e-06 0.042 0 2.5 Inf
NAV1 -1.5 6.8 16 9.0e-05 0.250 1 5.3 5.3
RHBDL3 -1.8 6.4 17 9.1e-05 0.250 2 5.3 2.6
RALGAPA1 -1.6 6.4 15 2.5e-04 0.510 3 8.5 2.8
MAP3K4 -1.6 6.4 15 3.3e-04 0.540 4 9.6 2.4
HERC1 -1.6 6.4 14 5.2e-04 0.680 5 12.0 2.5
GNG12 2.7 6.6 12 8.0e-04 0.680 6 17.0 2.8
A2M -1.5 6.6 12 8.5e-04 0.680 7 17.0 2.4
ZNF496 -1.5 6.4 13 9.0e-04 0.680 8 18.0 2.2
METTL8 2.5 6.6 11 9.4e-04 0.680 9 18.0 2.0
1e-04 NA NA NA NA NA 3 5.7 1.9
1e-05 NA NA NA NA NA 1 3.1 3.1
1e-06 NA NA NA NA NA 0 1.5 Inf
1e-07 NA NA NA NA NA 0 1.0 Inf
1e-08 NA NA NA NA NA 0 0.7 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.4 Inf
[1] "VPS45_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
A2M -3.0 6.8 76 1.6e-15 1.3e-11 0 0.1 Inf
IFITM3 -2.1 8.9 40 1.9e-09 7.9e-06 1 0.1 0.100
PTN -1.9 8.1 31 9.1e-08 2.5e-04 2 0.2 0.100
CLU -1.8 7.6 28 3.2e-07 6.1e-04 3 0.4 0.130
GPM6B -1.2 8.5 28 3.7e-07 6.1e-04 4 0.4 0.100
LGALS3 -2.3 6.8 25 1.2e-06 1.6e-03 5 0.6 0.120
S100A10 -2.0 6.9 19 2.6e-05 3.0e-02 6 1.5 0.250
SULF2 -1.7 6.7 18 3.3e-05 3.2e-02 7 1.5 0.210
TIMP2 -1.7 6.4 18 4.1e-05 3.2e-02 8 1.6 0.200
WLS -1.4 7.1 17 4.5e-05 3.2e-02 9 1.6 0.180
1e-04 NA NA NA NA NA 17 2.1 0.120
1e-05 NA NA NA NA NA 6 1.1 0.180
1e-06 NA NA NA NA NA 5 0.6 0.120
1e-07 NA NA NA NA NA 3 0.2 0.067
1e-08 NA NA NA NA NA 2 0.1 0.050
1e-09 NA NA NA NA NA 1 0.1 0.100
1e-10 NA NA NA NA NA 1 0.1 0.100
[1] "VPS45_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
LAMP5 -2.8 6.6 33 4.1e-08 0.00034 0 0.5 Inf
SPP1 -2.7 6.9 25 1.4e-06 0.00580 1 0.7 0.70
NKAIN4 -2.1 7.0 18 2.9e-05 0.07800 2 1.5 0.75
WDR26 -1.9 6.5 18 8.0e-05 0.16000 3 2.2 0.73
PCGF2 3.5 6.9 16 9.6e-05 0.16000 4 2.6 0.65
TXNRD1 -1.6 7.2 14 2.8e-04 0.38000 5 4.1 0.82
JUNB -1.8 6.7 13 4.1e-04 0.43000 6 4.9 0.82
GNPDA1 -1.7 6.9 13 4.3e-04 0.43000 7 5.1 0.73
UCK2 2.9 6.7 13 5.0e-04 0.45000 8 5.4 0.68
TSC1 -1.7 6.5 13 6.7e-04 0.50000 9 7.0 0.78
1e-04 NA NA NA NA NA 5 2.6 0.52
1e-05 NA NA NA NA NA 2 0.9 0.45
1e-06 NA NA NA NA NA 1 0.7 0.70
1e-07 NA NA NA NA NA 1 0.5 0.50
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.3 Infsource("code/empiricalFDR.R")
pbins <- 10** (-4:-10)
for (gRNAfile in list.files("data/", "*edgeR-qlf_Neg2.Rd")){
print(gRNAfile)
load(paste0("data/", gRNAfile))
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)))
outm <- cbind(outm,fdrmetric)
print(signif(outm,2))
}[1] "BAG5_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CCND1 0.93 8.1 13 0.00026 0.54 0 7.5 Inf
LARP1 0.85 7.2 13 0.00028 0.54 1 7.5 7.5
FAXC 1.50 6.3 14 0.00028 0.54 2 7.5 3.8
ARPC3 0.45 8.4 13 0.00032 0.54 3 8.1 2.7
LGALS3 2.50 6.6 13 0.00034 0.54 4 8.2 2.0
SIN3A 1.50 6.3 15 0.00044 0.60 5 9.3 1.9
CNOT11 1.10 6.7 12 0.00055 0.63 6 11.0 1.8
PCF11 1.20 6.5 12 0.00064 0.65 7 12.0 1.7
USP36 1.30 6.3 12 0.00080 0.68 8 14.0 1.8
SBK1 1.30 6.5 11 0.00086 0.68 9 15.0 1.6
1e-04 NA NA NA NA NA 0 4.4 Inf
1e-05 NA NA NA NA NA 0 1.4 Inf
1e-06 NA NA NA NA NA 0 0.7 Inf
1e-07 NA NA NA NA NA 0 0.3 Inf
1e-08 NA NA NA NA NA 0 0.2 Inf
1e-09 NA NA NA NA NA 0 0.2 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "BAG5_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
RP11-16E18.4 1.60 6.2 21 7.1e-05 0.42 0 4.0 Inf
MLLT6 1.60 6.2 21 1.0e-04 0.42 1 5.0 5.0
SLC39A9 1.50 6.3 15 2.5e-04 0.47 2 7.8 3.9
ZDHHC2 1.50 6.3 16 3.4e-04 0.47 3 8.3 2.8
MIAT -1.20 7.0 13 3.7e-04 0.47 4 9.0 2.2
RAB32 1.60 6.6 13 3.8e-04 0.47 5 9.0 1.8
EPS15 1.50 6.3 15 4.8e-04 0.47 6 10.0 1.7
NIN -0.87 6.7 12 5.0e-04 0.47 7 11.0 1.5
FKBP5 1.40 6.4 12 5.2e-04 0.47 8 11.0 1.3
ADAT1 -0.90 6.3 12 6.1e-04 0.49 9 12.0 1.3
1e-04 NA NA NA NA NA 1 4.8 4.8
1e-05 NA NA NA NA NA 0 1.6 Inf
1e-06 NA NA NA NA NA 0 0.8 Inf
1e-07 NA NA NA NA NA 0 0.6 Inf
1e-08 NA NA NA NA NA 0 0.5 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "BAG5_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
DFFA -0.81 7.0 16 5.5e-05 0.45 0 3.1 Inf
ASCL1 2.20 7.0 14 2.1e-04 0.60 1 5.7 5.7
KRT8 -1.40 7.0 14 2.4e-04 0.60 2 6.1 3.0
RASSF7 1.60 6.3 15 3.7e-04 0.60 3 9.0 3.0
ZYG11B 1.40 6.4 13 3.7e-04 0.60 4 9.0 2.2
CDKN1A 1.60 8.1 12 6.5e-04 0.72 5 12.0 2.4
MED4 0.68 7.3 11 7.8e-04 0.72 6 13.0 2.2
DLL1 2.10 6.8 11 8.5e-04 0.72 7 14.0 2.0
LAMTOR5 0.50 8.2 11 8.6e-04 0.72 8 14.0 1.8
RP11-220I1.1 1.30 6.4 11 9.9e-04 0.72 9 16.0 1.7
1e-04 NA NA NA NA NA 1 3.8 3.8
1e-05 NA NA NA NA NA 0 1.3 Inf
1e-06 NA NA NA NA NA 0 0.9 Inf
1e-07 NA NA NA NA NA 0 0.6 Inf
1e-08 NA NA NA NA NA 0 0.5 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "BCL11B_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MLXIP 2.4 6.4 13 0.00033 0.8 0 5.7 Inf
ERMARD -1.5 6.2 17 0.00046 0.8 1 7.2 7.2
ZCCHC8 2.4 6.4 13 0.00047 0.8 2 7.3 3.6
POMGNT2 2.3 6.4 13 0.00059 0.8 3 9.4 3.1
UBR7 2.3 6.4 12 0.00069 0.8 4 11.0 2.7
ATF7IP2 2.3 6.4 11 0.00082 0.8 5 13.0 2.5
ZHX1 2.2 6.3 12 0.00120 0.8 6 17.0 2.9
CADM4 -1.2 6.5 10 0.00130 0.8 7 18.0 2.6
SFT2D2 2.2 6.3 11 0.00130 0.8 8 19.0 2.3
FNDC4 -1.3 6.3 10 0.00140 0.8 9 19.0 2.2
1e-04 NA NA NA NA NA 0 1.9 Inf
1e-05 NA NA NA NA NA 0 0.4 Inf
1e-06 NA NA NA NA NA 0 0.2 Inf
1e-07 NA NA NA NA NA 0 0.1 Inf
1e-08 NA NA NA NA NA 0 0.0 NaN
1e-09 NA NA NA NA NA 0 0.0 NaN
1e-10 NA NA NA NA NA 0 0.0 NaN
[1] "BCL11B_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CEBPD -1.7 6.4 44 3.1e-11 2.5e-07 0 0.1 Inf
S100A10 -1.6 6.8 24 9.5e-07 3.8e-03 1 0.4 0.40
CDKN2A -1.4 6.5 22 3.3e-06 8.8e-03 2 0.6 0.30
SLC12A2 -1.1 6.4 20 7.9e-06 1.6e-02 3 1.2 0.40
CCP110 1.7 6.4 17 4.0e-05 5.5e-02 4 2.4 0.60
FLRT3 1.7 6.2 21 4.1e-05 5.5e-02 5 2.4 0.48
JAG1 -1.1 6.8 16 5.9e-05 6.1e-02 6 2.9 0.48
HIST1H2AC -1.2 6.3 16 6.1e-05 6.1e-02 7 2.9 0.41
DHRS12 1.6 6.2 21 8.6e-05 6.6e-02 8 3.3 0.41
PHLDA1 -1.1 6.9 15 8.6e-05 6.6e-02 9 3.3 0.37
1e-04 NA NA NA NA NA 11 3.5 0.32
1e-05 NA NA NA NA NA 4 1.3 0.32
1e-06 NA NA NA NA NA 2 0.4 0.20
1e-07 NA NA NA NA NA 1 0.3 0.30
1e-08 NA NA NA NA NA 1 0.1 0.10
1e-09 NA NA NA NA NA 1 0.1 0.10
1e-10 NA NA NA NA NA 1 0.1 0.10
[1] "BCL11B_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SPP1 -1.9 6.9 13 0.00031 0.8 0 8.0 Inf
MGRN1 2.4 6.4 13 0.00036 0.8 1 8.7 8.7
DKK3 -1.2 6.6 12 0.00055 0.8 2 11.0 5.6
SPEN 2.3 6.4 12 0.00075 0.8 3 14.0 4.5
CCP110 2.3 6.4 12 0.00083 0.8 4 14.0 3.5
EIF5 0.8 8.9 11 0.00110 0.8 5 17.0 3.4
PDE1B -1.3 6.3 11 0.00110 0.8 6 18.0 2.9
MXRA7 2.1 6.5 10 0.00130 0.8 7 20.0 2.8
FASTK 1.5 6.9 10 0.00140 0.8 8 20.0 2.4
DYRK2 2.2 6.3 12 0.00140 0.8 9 20.0 2.3
1e-04 NA NA NA NA NA 0 4.6 Inf
1e-05 NA NA NA NA NA 0 1.7 Inf
1e-06 NA NA NA NA NA 0 0.9 Inf
1e-07 NA NA NA NA NA 0 0.4 Inf
1e-08 NA NA NA NA NA 0 0.3 Inf
1e-09 NA NA NA NA NA 0 0.2 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "CHRNA3_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
AC084018.1 -2.5 6.3 17.0 3.3e-05 0.27 0 0.5 Inf
FST -2.4 6.3 13.0 3.9e-04 0.79 1 1.9 1.9
ARPIN -2.2 6.2 13.0 5.4e-04 0.79 2 2.4 1.2
ERBB2 -2.1 6.3 11.0 9.1e-04 0.79 3 3.8 1.3
ABHD17A -1.9 6.5 10.0 1.5e-03 0.79 4 6.5 1.6
ACVR2B -1.9 6.4 9.7 1.9e-03 0.79 5 7.9 1.6
BTBD7 -2.0 6.3 9.7 1.9e-03 0.79 6 7.9 1.3
FBXW11 -1.9 6.3 9.4 2.2e-03 0.79 7 8.7 1.2
PHF12 -2.1 6.2 11.0 2.8e-03 0.79 8 11.0 1.4
PHAX 2.8 7.3 8.6 3.5e-03 0.79 9 14.0 1.6
1e-04 NA NA NA NA NA 1 0.9 0.9
1e-05 NA NA NA NA NA 0 0.2 Inf
1e-06 NA NA NA NA NA 0 0.1 Inf
1e-07 NA NA NA NA NA 0 0.1 Inf
1e-08 NA NA NA NA NA 0 0.1 Inf
1e-09 NA NA NA NA NA 0 0.0 NaN
1e-10 NA NA NA NA NA 0 0.0 NaN
[1] "CHRNA3_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
RCAN1 -1.4 6.5 21 4.9e-06 0.04 0 1.1 Inf
TOP3A 1.9 6.3 18 8.5e-05 0.21 1 3.1 3.10
RP11-46C20.1 -1.2 6.4 15 9.0e-05 0.21 2 3.1 1.60
DDB2 -1.2 6.3 15 1.0e-04 0.21 3 3.4 1.10
ARFGAP3 1.8 6.4 14 1.6e-04 0.27 4 4.1 1.00
SLC25A26 1.5 6.6 14 2.0e-04 0.27 5 4.7 0.94
MKNK1 1.6 6.4 13 3.2e-04 0.33 6 6.3 1.00
JOSD1 1.7 6.3 14 3.3e-04 0.33 7 6.5 0.93
TPD52 -1.1 6.4 13 3.9e-04 0.35 8 7.2 0.90
KRT18 -1.5 7.1 12 5.2e-04 0.37 9 8.7 0.97
1e-04 NA NA NA NA NA 3 3.3 1.10
1e-05 NA NA NA NA NA 1 1.3 1.30
1e-06 NA NA NA NA NA 0 0.9 Inf
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.4 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "CHRNA3_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
VGF -1.9 6.6 27 2.4e-07 0.0016 0 0.2 Inf
ARF4 -1.1 8.2 26 3.9e-07 0.0016 1 0.2 0.20
NANS -1.4 6.8 22 2.7e-06 0.0073 2 0.4 0.20
CDC42EP3 -1.5 6.6 21 5.1e-06 0.0100 3 0.6 0.20
TFPI2 -1.7 6.5 20 1.0e-05 0.0170 4 0.9 0.22
GDF15 -1.9 6.5 18 2.0e-05 0.0270 5 1.1 0.22
OXR1 2.6 6.4 18 2.7e-05 0.0320 6 1.6 0.27
ALG3 -1.1 7.0 15 8.8e-05 0.0880 7 2.5 0.36
TTC28 2.4 6.4 15 9.8e-05 0.0880 8 2.6 0.32
CITED4 -1.4 6.2 16 1.3e-04 0.0960 9 3.1 0.34
1e-04 NA NA NA NA NA 9 2.6 0.29
1e-05 NA NA NA NA NA 4 0.9 0.22
1e-06 NA NA NA NA NA 2 0.3 0.15
1e-07 NA NA NA NA NA 0 0.2 Inf
1e-08 NA NA NA NA NA 0 0.2 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "GALNT10_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
RPRD2 1.60 6.4 20 9.5e-06 0.071 0 0.8 Inf
CDKN1C -1.40 6.8 18 1.8e-05 0.071 1 1.1 1.10
NNAT -1.20 6.3 17 3.7e-05 0.099 2 1.5 0.75
RP11-395G23.3 1.60 6.3 16 6.2e-05 0.130 3 1.7 0.57
FAM104B 1.00 6.8 15 1.2e-04 0.190 4 2.9 0.72
FAM110A -1.00 6.3 13 3.2e-04 0.300 5 5.4 1.10
ZNF784 1.40 6.3 17 3.3e-04 0.300 6 5.5 0.92
PRAG1 1.40 6.3 13 3.3e-04 0.300 7 5.5 0.79
SRD5A1 -0.83 6.5 13 3.8e-04 0.300 8 6.0 0.75
MED7 1.20 6.4 13 4.1e-04 0.300 9 6.7 0.74
1e-04 NA NA NA NA NA 4 2.8 0.70
1e-05 NA NA NA NA NA 1 0.8 0.80
1e-06 NA NA NA NA NA 0 0.4 Inf
1e-07 NA NA NA NA NA 0 0.2 Inf
1e-08 NA NA NA NA NA 0 0.2 Inf
1e-09 NA NA NA NA NA 0 0.2 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "GALNT10_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ROBO3 -1.20 6.3 21 6.0e-06 0.048 0 1.7 Inf
STMN2 -1.60 7.1 16 6.8e-05 0.280 1 5.5 5.5
RALYL -1.00 6.3 15 1.4e-04 0.370 2 7.5 3.8
IRF7 -0.91 6.3 14 2.1e-04 0.420 3 9.6 3.2
FAAP100 1.40 6.3 16 2.9e-04 0.460 4 11.0 2.8
TFE3 -0.87 6.4 13 3.7e-04 0.460 5 12.0 2.4
ZSCAN16 1.40 6.3 15 4.0e-04 0.460 6 12.0 2.0
MAP2K6 -0.88 6.3 11 7.7e-04 0.730 7 18.0 2.5
MFSD2A 1.30 6.3 12 8.1e-04 0.730 8 18.0 2.2
ST7L -0.77 6.4 10 1.5e-03 1.000 9 27.0 3.0
1e-04 NA NA NA NA NA 2 6.5 3.2
1e-05 NA NA NA NA NA 1 2.3 2.3
1e-06 NA NA NA NA NA 0 0.9 Inf
1e-07 NA NA NA NA NA 0 0.6 Inf
1e-08 NA NA NA NA NA 0 0.5 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "GALNT10_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SLAIN2 1.30 6.3 19 3.0e-05 0.12 0 3.1 Inf
NEAT1 -0.97 8.5 17 4.2e-05 0.12 1 3.6 3.6
STMN2 2.50 7.1 17 4.8e-05 0.12 2 4.0 2.0
EML1 1.30 6.3 18 5.9e-05 0.12 3 4.1 1.4
CHAF1B -0.82 6.5 14 1.5e-04 0.24 4 5.7 1.4
CASK 1.20 6.2 18 2.4e-04 0.33 5 7.0 1.4
SCAF4 0.98 6.4 12 4.6e-04 0.53 6 8.9 1.5
ARHGEF12 1.10 6.3 14 6.2e-04 0.56 7 11.0 1.5
GADD45G -1.10 7.5 11 7.5e-04 0.56 8 12.0 1.5
CUTC -0.67 6.5 11 7.8e-04 0.56 9 12.0 1.3
1e-04 NA NA NA NA NA 4 5.3 1.3
1e-05 NA NA NA NA NA 0 1.9 Inf
1e-06 NA NA NA NA NA 0 0.7 Inf
1e-07 NA NA NA NA NA 0 0.4 Inf
1e-08 NA NA NA NA NA 0 0.3 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.0 NaN
[1] "KCTD13_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TUBA1C 3.10 6.8 21 5.6e-06 0.046 0 0.7 Inf
AP5Z1 -1.20 6.3 19 1.5e-05 0.060 1 0.8 0.80
SLC25A39 0.85 7.5 16 5.2e-05 0.089 2 1.4 0.70
LGALS3 3.10 6.6 16 5.7e-05 0.089 3 1.5 0.50
CTTNBP2NL 1.70 6.4 16 6.3e-05 0.089 4 1.7 0.42
FUOM -1.10 6.4 16 6.5e-05 0.089 5 1.7 0.34
DMTF1 1.70 6.3 16 1.8e-04 0.150 6 3.0 0.50
S100A10 3.10 6.9 14 1.9e-04 0.150 7 3.2 0.46
NDUFB2 0.50 8.7 14 2.0e-04 0.150 8 3.5 0.44
TMSB10 0.68 12.0 14 2.0e-04 0.150 9 3.6 0.40
1e-04 NA NA NA NA NA 6 2.3 0.38
1e-05 NA NA NA NA NA 1 0.7 0.70
1e-06 NA NA NA NA NA 0 0.6 Inf
1e-07 NA NA NA NA NA 0 0.4 Inf
1e-08 NA NA NA NA NA 0 0.2 Inf
1e-09 NA NA NA NA NA 0 0.0 NaN
1e-10 NA NA NA NA NA 0 0.0 NaN
[1] "KCTD13_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
RCAN1 2.2 6.5 20 6.9e-06 0.056 0 1.4 Inf
OPTN 2.1 6.4 18 2.2e-05 0.079 1 1.6 1.60
KRT18 3.6 7.1 17 3.8e-05 0.079 2 2.2 1.10
S100A10 3.4 6.9 17 3.9e-05 0.079 3 2.3 0.77
LPP 1.5 6.7 15 1.4e-04 0.220 4 4.0 1.00
TENM3 1.4 6.6 14 2.0e-04 0.240 5 4.8 0.96
EPN2 1.6 6.3 16 2.1e-04 0.240 6 4.9 0.82
RPS6KA3 1.5 6.3 16 3.4e-04 0.300 7 6.7 0.96
EFCC1 1.5 6.3 13 3.4e-04 0.300 8 6.7 0.84
LGALS3 2.5 6.6 13 3.8e-04 0.300 9 7.2 0.80
1e-04 NA NA NA NA NA 4 3.6 0.90
1e-05 NA NA NA NA NA 1 1.4 1.40
1e-06 NA NA NA NA NA 0 0.9 Inf
1e-07 NA NA NA NA NA 0 0.7 Inf
1e-08 NA NA NA NA NA 0 0.6 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "KCTD13_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
GDF15 -1.8 6.5 15 8.7e-05 0.51 0 1.4 Inf
GEMIN2 -1.1 6.7 13 3.5e-04 0.51 1 5.1 5.10
ALKBH8 -1.3 6.2 15 3.6e-04 0.51 2 5.1 2.60
MAP3K4 -1.3 6.3 13 3.9e-04 0.51 3 5.4 1.80
GINM1 2.1 6.5 12 4.1e-04 0.51 4 5.6 1.40
FAM35A -1.4 6.2 16 4.7e-04 0.51 5 5.9 1.20
YJEFN3 -1.4 6.2 14 4.9e-04 0.51 6 6.0 1.00
GRK4 -1.3 6.2 14 5.0e-04 0.51 7 6.1 0.87
JOSD2 2.1 6.3 12 7.1e-04 0.62 8 8.5 1.10
STK24 -1.1 6.5 11 8.2e-04 0.62 9 9.2 1.00
1e-04 NA NA NA NA NA 1 1.6 1.60
1e-05 NA NA NA NA NA 0 0.6 Inf
1e-06 NA NA NA NA NA 0 0.2 Inf
1e-07 NA NA NA NA NA 0 0.1 Inf
1e-08 NA NA NA NA NA 0 0.1 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.0 NaN
[1] "KMT2E_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
EXOC6 -1.4 6.4 13 0.00029 0.76 0 3.5 Inf
ZMYND11 2.6 6.4 12 0.00057 0.76 1 6.3 6.3
NCSTN 2.3 6.6 11 0.00073 0.76 2 7.7 3.8
CNRIP1 -1.3 6.6 11 0.00077 0.76 3 8.2 2.7
GMCL1 2.5 6.4 11 0.00079 0.76 4 8.4 2.1
FAM161A 2.4 6.7 11 0.00086 0.76 5 9.5 1.9
BIN1 -1.3 6.6 10 0.00130 0.76 6 14.0 2.4
B4GALT5 2.3 6.4 10 0.00150 0.76 7 16.0 2.3
BET1 1.8 6.8 10 0.00160 0.76 8 17.0 2.1
UCKL1 2.3 6.4 11 0.00160 0.76 9 17.0 1.9
1e-04 NA NA NA NA NA 0 2.0 Inf
1e-05 NA NA NA NA NA 0 1.0 Inf
1e-06 NA NA NA NA NA 0 0.8 Inf
1e-07 NA NA NA NA NA 0 0.5 Inf
1e-08 NA NA NA NA NA 0 0.3 Inf
1e-09 NA NA NA NA NA 0 0.3 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "KMT2E_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CCDC107 1.7 6.8 16 5.3e-05 0.16 0 3.3 Inf
OSGIN1 -1.6 6.6 16 5.8e-05 0.16 1 3.4 3.40
RNF168 2.3 6.5 16 5.8e-05 0.16 2 3.4 1.70
RAB8A 1.6 6.9 15 1.2e-04 0.16 3 4.4 1.50
CCDC28B 2.1 6.6 15 1.2e-04 0.16 4 4.4 1.10
DCLK1 2.2 6.3 15 1.4e-04 0.16 5 4.4 0.88
CSNK1D 1.4 7.1 14 1.5e-04 0.16 6 4.5 0.75
PRR5 2.2 6.3 15 1.6e-04 0.16 7 4.6 0.66
QPRT 2.8 6.7 13 2.5e-04 0.22 8 6.1 0.76
SLC2A3 2.0 6.5 13 3.5e-04 0.29 9 7.6 0.84
1e-04 NA NA NA NA NA 3 3.9 1.30
1e-05 NA NA NA NA NA 0 1.9 Inf
1e-06 NA NA NA NA NA 0 0.9 Inf
1e-07 NA NA NA NA NA 0 0.4 Inf
1e-08 NA NA NA NA NA 0 0.0 NaN
1e-09 NA NA NA NA NA 0 0.0 NaN
1e-10 NA NA NA NA NA 0 0.0 NaN
[1] "KMT2E_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ANKRD1 -1.6 6.5 18 2.0e-05 0.17 0 1.4 Inf
MARCH9 2.2 6.3 17 9.3e-05 0.38 1 2.8 2.8
TP53I3 -1.2 6.8 14 2.0e-04 0.53 2 4.8 2.4
GPT2 1.7 6.7 13 3.4e-04 0.53 3 6.7 2.2
RECQL 2.0 6.3 14 3.8e-04 0.53 4 7.2 1.8
NCSTN 1.7 6.6 13 3.9e-04 0.53 5 7.4 1.5
DEDD -1.1 6.4 12 4.8e-04 0.55 6 8.7 1.4
BCHE 1.9 6.3 13 5.7e-04 0.55 7 9.4 1.3
LRP3 1.9 6.3 14 6.3e-04 0.55 8 10.0 1.2
ARHGAP1 1.8 6.3 14 8.0e-04 0.55 9 13.0 1.4
1e-04 NA NA NA NA NA 2 2.9 1.4
1e-05 NA NA NA NA NA 0 1.3 Inf
1e-06 NA NA NA NA NA 0 1.0 Inf
1e-07 NA NA NA NA NA 0 0.7 Inf
1e-08 NA NA NA NA NA 0 0.5 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.4 Inf
[1] "LOC105376975_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NEFM -1.60 7.4 32 1.3e-08 0.0001 0 0.1 Inf
STMN2 -2.00 7.1 29 7.4e-08 0.0003 1 0.1 0.10
SH3KBP1 -1.20 6.3 19 1.4e-05 0.0390 2 1.1 0.55
PLCD1 -1.10 6.3 18 1.9e-05 0.0390 3 1.1 0.37
SCML1 -0.97 6.5 16 5.6e-05 0.0910 4 1.5 0.38
FNDC3A 1.30 6.6 15 1.0e-04 0.1400 5 2.3 0.46
SPP1 -1.40 6.9 15 1.2e-04 0.1400 6 2.5 0.42
PSMB7 0.45 9.1 14 1.5e-04 0.1500 7 2.8 0.40
DHX8 1.50 6.2 20 2.1e-04 0.1900 8 3.6 0.45
CTNNA1 0.80 7.2 13 2.8e-04 0.2200 9 4.7 0.52
1e-04 NA NA NA NA NA 5 2.3 0.46
1e-05 NA NA NA NA NA 2 0.8 0.40
1e-06 NA NA NA NA NA 2 0.2 0.10
1e-07 NA NA NA NA NA 2 0.1 0.05
1e-08 NA NA NA NA NA 0 0.1 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "LOC105376975_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
PLP1 -1.10 6.4 19 1.4e-05 0.063 0 0.7 Inf
SLC7A11 1.70 6.6 19 1.6e-05 0.063 1 0.8 0.80
CHAC1 1.70 6.4 17 4.2e-05 0.091 2 1.5 0.75
NQO1 1.60 7.4 17 4.5e-05 0.091 3 1.6 0.53
NAT9 0.98 6.7 16 6.7e-05 0.110 4 2.1 0.52
AGPS 1.20 6.3 16 1.0e-04 0.140 5 3.1 0.62
MRPS34 -0.40 8.4 14 1.5e-04 0.160 6 3.7 0.62
ATF5 1.40 6.9 14 1.6e-04 0.160 7 3.8 0.54
ARHGEF2 1.20 6.3 15 2.0e-04 0.180 8 4.2 0.52
FHL1 -0.60 7.1 13 2.9e-04 0.240 9 5.9 0.66
1e-04 NA NA NA NA NA 5 3.0 0.60
1e-05 NA NA NA NA NA 0 0.6 Inf
1e-06 NA NA NA NA NA 0 0.4 Inf
1e-07 NA NA NA NA NA 0 0.1 Inf
1e-08 NA NA NA NA NA 0 0.1 Inf
1e-09 NA NA NA NA NA 0 0.0 NaN
1e-10 NA NA NA NA NA 0 0.0 NaN
[1] "LOC105376975_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
RP11-46C20.1 -2.3 6.4 22.0 2.7e-06 0.022 0 0.8
CMTM8 -2.1 6.3 17.0 4.5e-05 0.180 1 1.9
ACBD3 -1.6 6.6 13.0 3.8e-04 0.760 2 4.5
FNBP4 3.4 6.7 13.0 3.9e-04 0.760 3 4.5
PLGRKT 3.4 6.7 12.0 6.6e-04 0.760 4 6.4
KIF5C 2.5 7.2 11.0 1.1e-03 0.760 5 9.7
RIF1 3.3 6.7 10.0 1.2e-03 0.760 6 10.0
METTL15 -1.8 6.2 13.0 1.3e-03 0.760 7 10.0
PPP2R1B 3.0 6.6 10.0 1.6e-03 0.760 8 13.0
RQCD1 3.1 6.6 9.9 1.7e-03 0.760 9 13.0
1e-04 NA NA NA NA NA 2 2.8
1e-05 NA NA NA NA NA 1 0.9
1e-06 NA NA NA NA NA 0 0.5
1e-07 NA NA NA NA NA 0 0.3
1e-08 NA NA NA NA NA 0 0.3
1e-09 NA NA NA NA NA 0 0.1
1e-10 NA NA NA NA NA 0 0.0
EmpiricalFDR
RP11-46C20.1 Inf
CMTM8 1.9
ACBD3 2.2
FNBP4 1.5
PLGRKT 1.6
KIF5C 1.9
RIF1 1.7
METTL15 1.5
PPP2R1B 1.6
RQCD1 1.5
1e-04 1.4
1e-05 0.9
1e-06 Inf
1e-07 Inf
1e-08 Inf
1e-09 Inf
1e-10 NaN
[1] "miR137_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
EXTL3 1.40 6.3 18 9.6e-05 0.58 0 2.4 Inf
YWHAZ 0.51 8.3 14 1.5e-04 0.58 1 3.1 3.1
HERPUD2 -0.86 6.3 14 2.4e-04 0.58 2 4.0 2.0
LGALS3 1.90 6.6 13 3.9e-04 0.58 3 5.4 1.8
ABHD5 1.20 6.4 13 4.4e-04 0.58 4 5.9 1.5
DPH2 0.87 6.8 12 5.7e-04 0.58 5 7.3 1.5
APMAP 0.60 7.3 11 7.2e-04 0.58 6 8.9 1.5
CORO1C 0.92 6.6 11 8.3e-04 0.58 7 10.0 1.4
SLC12A9 1.20 6.3 14 9.2e-04 0.58 8 11.0 1.3
RBM45 -0.85 6.2 13 9.9e-04 0.58 9 11.0 1.3
1e-04 NA NA NA NA NA 1 2.4 2.4
1e-05 NA NA NA NA NA 0 0.7 Inf
1e-06 NA NA NA NA NA 0 0.4 Inf
1e-07 NA NA NA NA NA 0 0.2 Inf
1e-08 NA NA NA NA NA 0 0.2 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "miR137_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SLC4A1AP 1.60 6.6 17 3.7e-05 0.16 0 1.1 Inf
SLC30A6 1.70 6.3 23 4.1e-05 0.16 1 1.1 1.10
RCAN1 -1.00 6.5 14 1.9e-04 0.41 2 3.5 1.80
TOMM5 -0.87 6.6 14 2.2e-04 0.41 3 3.8 1.30
PATL1 -1.00 6.3 16 2.5e-04 0.41 4 4.2 1.00
HAUS6 1.30 6.5 13 3.5e-04 0.47 5 5.3 1.10
NDEL1 1.40 6.3 14 4.7e-04 0.53 6 6.4 1.10
KHDRBS3 1.40 6.4 12 5.5e-04 0.53 7 7.4 1.10
SAMD1 1.40 6.3 13 6.3e-04 0.53 8 7.9 0.99
PRKAB1 1.10 6.7 11 7.8e-04 0.53 9 9.7 1.10
1e-04 NA NA NA NA NA 2 2.2 1.10
1e-05 NA NA NA NA NA 0 0.7 Inf
1e-06 NA NA NA NA NA 0 0.4 Inf
1e-07 NA NA NA NA NA 0 0.4 Inf
1e-08 NA NA NA NA NA 0 0.2 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.0 NaN
[1] "miR137_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ADAM15 -0.78 6.4 15 0.00012 0.48 0 3.1 Inf
IER3 -0.81 6.3 13 0.00030 0.48 1 5.6 5.60
LCMT2 -0.83 6.2 17 0.00032 0.48 2 5.9 2.90
TUBB2A -0.51 8.8 13 0.00035 0.48 3 6.5 2.20
NDUFB11 0.27 9.1 13 0.00037 0.48 4 6.5 1.60
SOD2 0.96 6.4 13 0.00044 0.48 5 6.8 1.40
S100A16 -0.75 6.6 12 0.00046 0.48 6 6.9 1.20
ZNF660 1.10 6.2 16 0.00052 0.48 7 7.2 1.00
TTLL5 1.10 6.2 16 0.00059 0.48 8 8.2 1.00
DST -0.66 6.6 12 0.00059 0.48 9 8.3 0.92
1e-04 NA NA NA NA NA 0 2.7 Inf
1e-05 NA NA NA NA NA 0 1.0 Inf
1e-06 NA NA NA NA NA 0 0.6 Inf
1e-07 NA NA NA NA NA 0 0.2 Inf
1e-08 NA NA NA NA NA 0 0.2 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
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
loaded via a namespace (and not attached):
[1] locfit_1.5-9.1 workflowr_1.2.0 Rcpp_1.0.0 lattice_0.20-38
[5] digest_0.6.18 rprojroot_1.3-2 grid_3.5.1 backports_1.1.2
[9] git2r_0.23.0 magrittr_1.5 evaluate_0.12 stringi_1.3.1
[13] fs_1.2.6 whisker_0.3-2 rmarkdown_1.10 tools_3.5.1
[17] stringr_1.4.0 glue_1.3.0 yaml_2.2.0 compiler_3.5.1
[21] htmltools_0.3.6 knitr_1.20