Last updated: 2019-03-01
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Knit directory: cropseq/
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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| 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 |
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 1 3.0 3.0
LGALS3 2.00 6.6 15 1.1e-04 0.46 2 5.3 2.6
FGF19 2.00 6.6 14 1.9e-04 0.47 3 6.7 2.2
CWF19L2 -1.10 6.5 15 2.3e-04 0.47 4 7.5 1.9
FIZ1 1.30 6.6 12 6.9e-04 0.73 5 14.0 2.7
LIX1 -1.10 6.7 12 7.4e-04 0.73 6 14.0 2.4
CEP250 -1.20 6.4 14 8.3e-04 0.73 7 15.0 2.2
BTG2 1.30 7.1 11 8.7e-04 0.73 8 16.0 2.0
NSUN2 -1.00 6.5 11 8.8e-04 0.73 9 16.0 1.8
CCND1 0.77 8.0 11 9.1e-04 0.73 10 16.0 1.6
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 1 2.5 2.5
MLLT6 1.70 6.4 21 9.1e-05 0.37 2 5.5 2.8
NIN -1.10 6.9 15 1.7e-04 0.42 3 7.2 2.4
EPS15 1.60 6.4 17 3.0e-04 0.42 4 10.0 2.6
MALAT1 -0.61 14.0 13 3.2e-04 0.42 5 11.0 2.2
RP11-16E18.4 1.50 6.4 18 3.5e-04 0.42 6 11.0 1.9
RAB32 1.60 6.7 13 3.6e-04 0.42 7 12.0 1.7
ARFGAP1 -1.00 6.6 12 7.2e-04 0.59 8 17.0 2.2
NEDD4L 1.50 6.4 16 7.9e-04 0.59 9 18.0 2.0
PIGM -1.10 6.5 14 8.0e-04 0.59 10 18.0 1.8
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 1 4.3 4.3
NRIP1 -1.4 6.4 23 9.6e-05 0.39 2 4.3 2.2
CWF19L2 -1.2 6.5 16 2.2e-04 0.45 3 6.9 2.3
RACGAP1 -1.2 6.6 13 3.1e-04 0.45 4 8.5 2.1
MYC 2.4 7.5 13 3.7e-04 0.45 5 10.0 2.0
ASCL1 1.7 6.9 13 4.8e-04 0.45 6 11.0 1.9
BIN3 1.3 6.8 13 5.0e-04 0.45 7 12.0 1.7
RASSF7 1.6 6.4 16 5.1e-04 0.45 8 12.0 1.5
CDKN1A 1.5 7.9 12 5.6e-04 0.45 9 13.0 1.4
KIF2C -1.2 6.7 12 5.8e-04 0.45 10 13.0 1.3
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 1 6.7 6.7
TMEM88 -1.5 6.5 14 0.00028 0.52 2 8.3 4.2
ERMARD -1.7 6.4 18 0.00034 0.52 3 9.7 3.2
PRR11 -1.4 6.7 13 0.00036 0.52 4 9.9 2.5
TSPAN31 -1.5 6.5 13 0.00052 0.52 5 12.0 2.4
MOK -1.5 6.4 14 0.00062 0.52 6 14.0 2.2
MLXIP 2.3 6.5 14 0.00063 0.52 7 14.0 2.0
ARL6IP1 -1.1 7.9 12 0.00069 0.52 8 15.0 1.8
POMGNT2 2.2 6.5 12 0.00080 0.52 9 16.0 1.8
PTPN18 2.2 6.5 12 0.00080 0.52 10 16.0 1.6
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 1 0.3 0.30
SPP1 -1.9 7.0 24 1.6e-06 4.6e-03 2 0.7 0.35
RGS5 -1.5 6.7 24 1.7e-06 4.6e-03 3 0.7 0.23
PHLDA1 -1.5 7.1 23 2.6e-06 5.4e-03 4 0.7 0.18
TMEM88 -1.5 6.5 22 5.1e-06 8.2e-03 5 0.9 0.18
AXL -1.5 6.6 19 1.7e-05 2.3e-02 6 1.6 0.27
CEBPD -1.4 6.8 18 3.8e-05 4.4e-02 7 2.1 0.30
CDKN2A -1.5 6.7 17 5.0e-05 4.6e-02 8 2.4 0.30
JAG1 -1.3 6.9 17 5.1e-05 4.6e-02 9 2.4 0.27
NT5M 1.7 6.4 21 8.8e-05 7.2e-02 10 3.4 0.34
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 1 1.1 1.1
GGA3 -1.6 6.4 17 2.8e-04 0.81000 2 6.1 3.0
PDE1B -1.5 6.5 13 3.4e-04 0.81000 3 6.8 2.3
NOP2 2.3 6.5 13 5.0e-04 0.81000 4 8.6 2.2
SPEN 2.3 6.5 13 5.2e-04 0.81000 5 8.8 1.8
DUSP1 2.6 6.8 12 6.0e-04 0.81000 6 9.8 1.6
MFSD3 2.2 6.5 12 9.1e-04 0.82000 7 14.0 2.0
TP53I11 2.2 6.5 11 9.1e-04 0.82000 8 14.0 1.8
MGRN1 2.1 6.5 12 1.2e-03 0.82000 9 16.0 1.8
DTNA 2.1 6.5 11 1.3e-03 0.82000 10 18.0 1.8
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 1 1.9 1.9
MT-ND4 -1.4 11.0 12 5.6e-04 0.810 2 7.6 3.8
SEPN1 -2.2 6.5 12 7.5e-04 0.810 3 8.3 2.8
ERBB2 -2.1 6.4 12 1.0e-03 0.810 4 11.0 2.7
FBXW11 -2.1 6.5 11 1.1e-03 0.810 5 11.0 2.3
ARPIN -2.1 6.4 11 1.2e-03 0.810 6 11.0 1.9
NR6A1 -2.0 6.5 10 1.4e-03 0.810 7 13.0 1.8
ABHD17A -2.0 6.7 10 1.4e-03 0.810 8 13.0 1.6
FST -2.3 6.6 10 1.5e-03 0.810 9 13.0 1.4
MTUS1 -2.1 6.4 10 1.6e-03 0.810 10 13.0 1.3
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 1 3.6 3.60
DDB2 -1.5 6.5 18 3.5e-05 0.14 2 4.3 2.20
RP11-46C20.1 -1.4 6.6 17 6.4e-05 0.17 3 5.1 1.70
FIZ1 1.8 6.5 15 1.6e-04 0.25 4 7.1 1.80
PKMYT1 1.8 6.7 14 2.1e-04 0.25 5 8.0 1.60
RCAN1 -1.3 6.7 14 2.8e-04 0.25 6 9.1 1.50
FMR1 -1.3 6.4 16 3.0e-04 0.25 7 9.5 1.40
HOXB3 -1.4 6.4 16 3.0e-04 0.25 8 9.5 1.20
PLPP1 -1.4 6.4 17 3.0e-04 0.25 9 9.5 1.10
KLHL5 -1.2 6.5 13 3.1e-04 0.25 10 9.6 0.96
1e-04 NA NA NA NA NA 3 6.4 2.10
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 1 0.4 0.40
VGF -1.9 6.9 19 1.8e-05 0.075 2 1.0 0.50
RRP9 -1.3 7.0 18 4.0e-05 0.110 3 1.6 0.53
NUP98 -1.6 6.4 18 6.4e-05 0.110 4 2.5 0.62
OXR1 2.4 6.5 16 7.9e-05 0.110 5 3.0 0.60
GDF15 -1.9 6.8 16 9.0e-05 0.110 6 3.1 0.52
AKAP12 -1.3 7.4 16 9.6e-05 0.110 7 3.2 0.46
GLIPR1 -1.5 6.7 15 1.3e-04 0.130 8 3.7 0.46
BTBD1 -1.6 6.3 20 2.1e-04 0.180 9 5.4 0.60
TTC28 2.3 6.5 14 2.3e-04 0.180 10 5.7 0.57
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 1 0.5
S100A10 -2.1 7.1 38 3.9e-09 1.6e-05 2 0.5
LGALS3 -1.7 6.8 25 1.3e-06 3.4e-03 3 1.6
SPP1 -1.8 7.0 24 2.5e-06 4.9e-03 4 1.7
HIST1H2AC -1.5 6.6 23 3.0e-06 4.9e-03 5 1.8
DUSP4 -1.2 6.8 21 7.8e-06 1.1e-02 6 2.7
CTSD -1.0 7.4 19 1.9e-05 2.2e-02 7 3.8
NQO1 -1.3 7.5 19 2.3e-05 2.3e-02 8 4.2
MYC 2.4 7.4 18 3.8e-05 3.4e-02 9 4.4
TAGLN2 -1.3 6.6 17 4.4e-05 3.6e-02 10 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 0.50
S100A10 0.25
LGALS3 0.53
SPP1 0.42
HIST1H2AC 0.36
DUSP4 0.45
CTSD 0.54
NQO1 0.52
MYC 0.49
TAGLN2 0.47
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 1 1.0 1.0
RGS5 -1.40 6.7 25 1.0e-06 4.2e-03 2 1.8 0.9
AXL -1.10 6.6 15 1.7e-04 3.0e-01 3 7.8 2.6
MEG3 -0.95 7.7 15 1.8e-04 3.0e-01 4 7.8 2.0
PGGT1B -0.98 6.5 16 1.9e-04 3.0e-01 5 7.9 1.6
CLN8 0.97 6.6 13 3.6e-04 4.4e-01 6 11.0 1.8
ABL1 -0.93 6.4 14 4.7e-04 4.4e-01 7 12.0 1.7
CASD1 1.10 6.3 19 5.4e-04 4.4e-01 8 13.0 1.6
CSRP1 -0.97 7.3 12 5.4e-04 4.4e-01 9 13.0 1.4
KCTD10 -0.86 6.6 12 5.9e-04 4.4e-01 10 14.0 1.4
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 1 3.2 3.2
LGALS3 2.6 6.5 20 1.5e-05 0.042 2 3.2 1.6
ITGA6 -1.6 6.4 26 1.6e-05 0.042 3 3.2 1.1
NEAT1 1.7 8.1 18 4.2e-05 0.085 4 4.2 1.0
ZBTB8A 1.7 6.4 17 2.8e-04 0.360 5 11.0 2.2
AFF3 1.6 6.4 18 3.6e-04 0.360 6 12.0 2.0
TMEM88 -1.2 6.5 13 3.6e-04 0.360 7 12.0 1.7
PRR11 -1.1 6.7 13 3.7e-04 0.360 8 12.0 1.5
PITRM1 -1.3 6.4 15 4.6e-04 0.360 9 14.0 1.5
RAB32 1.7 6.7 13 4.7e-04 0.360 10 14.0 1.4
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 1 2.4 2.40
SPP1 -1.7 7.0 20 1.2e-05 0.049 2 2.4 1.20
CDKN1C -1.6 7.1 19 1.8e-05 0.049 3 2.9 0.97
RP11-395G23.3 1.8 6.5 18 3.9e-05 0.079 4 3.8 0.95
RPRD2 1.5 6.5 17 2.5e-04 0.330 5 9.0 1.80
PDK2 1.5 6.4 17 2.8e-04 0.330 6 9.6 1.60
SEMA3A -1.2 6.4 15 2.9e-04 0.330 7 9.8 1.40
FAM104B 1.1 6.9 13 3.4e-04 0.350 8 10.0 1.30
DECR1 1.2 6.9 13 5.0e-04 0.450 9 12.0 1.40
AKAP13 1.2 6.6 12 6.4e-04 0.520 10 15.0 1.50
1e-04 NA NA NA NA NA 4 6.2 1.60
1e-05 NA NA NA NA NA 1 2.4 2.40
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 1 1.9 1.90
RGS5 -1.40 6.7 21 8.2e-06 0.033 2 1.9 0.95
ROBO3 -1.40 6.5 20 1.2e-05 0.033 3 2.2 0.73
RACGAP1 -1.20 6.6 16 8.8e-05 0.180 4 5.4 1.40
SAMD4A -1.30 6.4 23 1.2e-04 0.200 5 5.9 1.20
ST7L -0.98 6.6 13 5.0e-04 0.680 6 14.0 2.20
TMEM88 -1.10 6.5 12 6.5e-04 0.750 7 16.0 2.30
SYPL1 0.91 7.1 11 1.0e-03 0.820 8 21.0 2.60
AKT3 -1.00 6.4 13 1.1e-03 0.820 9 22.0 2.50
PUS3 1.10 6.7 11 1.3e-03 0.820 10 26.0 2.60
1e-04 NA NA NA NA NA 4 5.6 1.40
1e-05 NA NA NA NA NA 2 2.0 1.00
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 1 0.9 0.90
MYC 2.8 7.4 27 4.5e-07 0.0018 2 0.9 0.45
NEAT1 -1.3 8.8 22 4.3e-06 0.0120 3 2.1 0.70
RGS5 -1.3 6.7 21 9.4e-06 0.0190 4 2.9 0.72
GRIA1 -1.3 6.5 21 1.2e-05 0.0200 5 3.1 0.62
EML1 1.4 6.5 20 4.2e-05 0.0570 6 4.8 0.80
SLAIN2 1.3 6.4 20 1.2e-04 0.1300 7 7.4 1.10
ARMCX1 -1.1 6.5 15 1.5e-04 0.1300 8 8.1 1.00
PVT1 -1.0 6.5 15 1.6e-04 0.1300 9 8.2 0.91
TADA1 1.3 6.4 18 1.6e-04 0.1300 10 8.2 0.82
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 1 1.4 1.40
MYC 3.5 7.5 20 1.3e-05 0.0420 2 2.8 1.40
LGALS3 2.6 6.6 20 1.5e-05 0.0420 3 2.8 0.93
SHPRH 1.7 6.6 17 6.9e-05 0.1200 4 4.9 1.20
S100A10 2.4 6.7 16 7.3e-05 0.1200 5 5.0 1.00
AP5Z1 -1.2 6.5 16 1.1e-04 0.1400 6 6.1 1.00
CTTNBP2NL 1.6 6.5 15 1.6e-04 0.1700 7 7.5 1.10
SLC20A2 1.6 6.6 15 1.7e-04 0.1700 8 7.6 0.95
BEX2 1.8 6.7 14 2.4e-04 0.2200 9 9.4 1.00
PSTPIP2 1.6 6.4 19 2.7e-04 0.2200 10 10.0 1.00
1e-04 NA NA NA NA NA 5 5.9 1.20
1e-05 NA NA NA NA NA 1 2.8 2.80
1e-06 NA NA NA NA NA 1 1.5 1.50
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 1 0.4 0.40
S100A10 2.6 6.7 22 5.1e-06 0.0170 2 1.2 0.60
RCAN1 2.1 6.6 22 6.2e-06 0.0170 3 1.2 0.40
OPTN 1.9 6.5 19 2.0e-05 0.0340 4 2.0 0.50
MYC 3.0 7.5 19 2.1e-05 0.0340 5 2.1 0.42
KRT8 2.4 7.0 17 4.8e-05 0.0650 6 2.9 0.48
CMTM8 1.9 6.6 17 6.1e-05 0.0710 7 3.4 0.49
LGALS3 2.0 6.6 15 1.2e-04 0.1200 8 5.4 0.68
NINJ1 1.3 6.9 14 2.0e-04 0.1800 9 6.5 0.72
SLC20A2 1.5 6.6 14 2.9e-04 0.2400 10 8.7 0.87
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 1 1.9 1.9
TLE4 -1.4 6.9 16 8.4e-05 0.34 2 4.3 2.2
GEMIN2 -1.3 6.9 14 2.0e-04 0.48 3 6.6 2.2
GDF15 -1.8 6.8 14 2.4e-04 0.48 4 7.4 1.8
GRIA1 -1.5 6.4 15 4.0e-04 0.52 5 10.0 2.1
DBT -1.4 6.4 14 5.5e-04 0.52 6 12.0 2.0
PYCRL 2.1 6.5 14 7.4e-04 0.52 7 14.0 2.0
PPIL2 2.1 6.5 14 7.4e-04 0.52 8 14.0 1.8
YJEFN3 -1.4 6.4 13 7.5e-04 0.52 9 14.0 1.6
IPO9 -1.0 7.1 12 7.7e-04 0.52 10 14.0 1.4
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 1 9.1 9.1
EXOC6 -1.50 6.6 13 0.00039 0.77 2 11.0 5.4
PCDH19 -1.60 6.4 13 0.00055 0.77 3 13.0 4.3
FAM161A 2.40 6.8 12 0.00075 0.77 4 16.0 4.1
CSPP1 2.30 6.5 11 0.00110 0.77 5 22.0 4.4
GMCL1 2.40 6.5 11 0.00110 0.77 6 22.0 3.6
NR6A1 -1.50 6.5 11 0.00130 0.77 7 25.0 3.5
B4GALT5 2.30 6.5 10 0.00150 0.77 8 28.0 3.5
CHAC1 -1.50 6.6 10 0.00160 0.77 9 28.0 3.1
NCSTN 2.30 6.8 10 0.00180 0.77 10 32.0 3.2
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 1 3.3 3.3
QPRT 2.7 6.8 18 4.0e-05 0.16 2 4.3 2.2
CMTM8 2.7 6.6 16 9.9e-05 0.20 3 5.9 2.0
SPP1 -1.8 6.9 16 1.1e-04 0.20 4 6.1 1.5
TEAD1 -1.4 6.6 15 1.5e-04 0.20 5 7.3 1.5
RNF168 2.2 6.7 15 1.5e-04 0.20 6 7.4 1.2
OSGIN1 -1.7 6.9 15 1.8e-04 0.20 7 8.2 1.2
RGS5 -1.4 6.7 14 2.2e-04 0.20 8 9.5 1.2
PRR5 2.1 6.5 14 2.2e-04 0.20 9 9.6 1.1
SEMA3A -1.5 6.5 16 2.6e-04 0.21 10 11.0 1.1
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 1 1.2 1.20
C1orf56 -1.9 6.4 29 1.3e-05 0.052 2 1.2 0.60
ANKRD1 -1.8 6.7 19 2.6e-05 0.070 3 2.3 0.77
PALMD -1.6 6.5 18 3.6e-05 0.073 4 2.5 0.62
BCHE 2.1 6.5 14 2.3e-04 0.320 5 8.8 1.80
COG5 2.1 6.5 16 2.4e-04 0.320 6 8.9 1.50
FDXR -1.3 7.1 14 3.0e-04 0.320 7 11.0 1.50
GPT2 1.8 6.9 13 3.2e-04 0.320 8 11.0 1.40
MARCH9 2.0 6.4 14 4.6e-04 0.420 9 14.0 1.50
KCTD1 -1.2 6.7 12 5.7e-04 0.460 10 16.0 1.60
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 1 0.8 0.80
MYC 3.20 7.4 27 5.3e-07 0.00220 2 1.2 0.60
MALAT1 -0.63 14.0 20 1.4e-05 0.03700 3 2.5 0.83
PKMYT1 1.50 6.7 19 2.2e-05 0.04500 4 3.2 0.80
SPP1 2.00 6.6 17 4.3e-05 0.06900 5 4.1 0.82
FKBP1B 1.30 6.7 15 1.3e-04 0.17000 6 6.7 1.10
CTB-31O20.2 1.40 6.4 18 3.1e-04 0.36000 7 11.0 1.50
CAMKK2 1.40 6.3 20 3.5e-04 0.36000 8 12.0 1.40
SMAD1 -0.98 6.5 13 5.8e-04 0.53000 9 16.0 1.80
SPIN2B 1.20 6.4 13 6.9e-04 0.56000 10 18.0 1.80
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 1 1.1 1.10
TP53I3 -1.2 7.0 19 2.3e-05 0.075 2 2.2 1.10
GDF15 -1.6 6.8 18 3.3e-05 0.075 3 2.2 0.73
TRIO -1.4 6.4 22 3.7e-05 0.075 4 2.3 0.58
TUBA1C 2.0 6.7 17 6.9e-05 0.110 5 3.6 0.72
TMEM200C 1.7 6.4 22 9.5e-05 0.130 6 4.0 0.67
SRD5A1 1.4 6.6 14 2.9e-04 0.340 7 8.4 1.20
MAFB 1.8 6.6 13 3.6e-04 0.350 8 9.6 1.20
KCTD9 1.5 6.5 13 3.9e-04 0.350 9 9.9 1.10
SRFBP1 1.3 6.5 12 6.9e-04 0.560 10 15.0 1.50
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 1 0.8 0.80
CDC25A 1.5 6.5 21 7.0e-06 0.02800 2 2.4 1.20
DLL3 2.0 6.9 20 1.4e-05 0.02900 3 3.0 1.00
CDKN1C 1.8 6.7 19 1.7e-05 0.02900 4 3.1 0.78
MIAT 1.8 6.9 19 2.2e-05 0.02900 5 3.1 0.62
SEMA3A -1.2 6.4 19 2.2e-05 0.02900 6 3.1 0.52
RGS5 -1.2 6.7 17 4.4e-05 0.04800 7 3.8 0.54
SPP1 -1.5 7.0 17 4.7e-05 0.04800 8 4.0 0.50
TPM2 -1.4 7.4 17 5.3e-05 0.04800 9 4.5 0.50
TNFRSF12A -1.1 7.9 15 1.4e-04 0.11000 10 6.4 0.64
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 1 0.9 0.90
TPM2 -2.1 7.3 24 2.1e-06 0.0085 2 1.1 0.55
S100A10 -2.1 6.9 23 3.7e-06 0.0100 3 1.1 0.37
CDKN1C -2.1 7.0 22 6.5e-06 0.0130 4 1.4 0.35
GADD45G -2.3 7.9 21 9.1e-06 0.0150 5 1.5 0.30
CCND2 -1.6 7.1 19 2.5e-05 0.0340 6 2.1 0.35
THAP5 -1.6 6.5 18 2.9e-05 0.0340 7 2.3 0.33
ANAPC10 2.3 6.5 15 1.6e-04 0.1700 8 4.3 0.54
DPY19L3 -1.5 6.4 18 2.8e-04 0.2500 9 6.0 0.67
LAMC1 -1.4 6.4 13 4.3e-04 0.3500 10 8.4 0.84
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 1 0.3 0.30
TIMP2 -1.9 6.5 31 7.4e-08 3.0e-04 2 0.3 0.15
S100A16 -1.8 6.8 29 1.9e-07 5.1e-04 3 0.5 0.17
S100A10 -1.9 7.0 23 2.6e-06 5.2e-03 4 1.3 0.32
SEMA3A -1.5 6.4 22 7.8e-06 1.3e-02 5 1.9 0.38
S100A13 -1.3 7.1 20 1.4e-05 1.9e-02 6 2.3 0.38
AXL -1.5 6.6 19 2.7e-05 2.7e-02 7 2.5 0.36
DHRS7 -1.3 6.7 18 2.7e-05 2.7e-02 8 2.5 0.31
ANKRD1 -1.6 6.8 17 5.5e-05 5.0e-02 9 3.7 0.41
SPOCK1 -1.3 6.7 16 7.7e-05 6.2e-02 10 4.0 0.40
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 1 0.3 0.30
DDIT4 -1.40 8.1 26 7.8e-07 0.00320 2 0.8 0.40
SPP1 -1.80 7.1 23 3.8e-06 0.01000 3 1.4 0.47
EEF2 -0.41 11.0 14 2.4e-04 0.49000 4 6.8 1.70
TRIB3 -1.10 7.3 13 4.0e-04 0.55000 5 10.0 2.00
HUS1 -0.94 6.5 12 5.5e-04 0.55000 6 12.0 2.00
CYP2R1 -1.10 6.4 15 6.4e-04 0.55000 7 14.0 2.00
SHMT2 -0.72 7.6 12 6.4e-04 0.55000 8 14.0 1.70
WARS -0.79 7.4 12 7.3e-04 0.55000 9 14.0 1.60
TAF6 -0.66 7.2 12 7.5e-04 0.55000 10 15.0 1.50
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 1 0.9 0.9
NEFM -1.6 7.9 18 3.0e-05 0.1200 2 3.5 1.8
MYC 2.6 7.5 17 6.9e-05 0.1900 3 4.6 1.5
DHX8 1.5 6.4 20 2.1e-04 0.3700 4 9.0 2.2
TPM2 -1.3 7.3 14 2.7e-04 0.3700 5 10.0 2.0
STMN2 -1.6 7.7 14 2.7e-04 0.3700 6 10.0 1.7
CSPP1 1.3 6.5 12 6.0e-04 0.6400 7 15.0 2.1
FNDC3A 1.2 6.6 12 6.3e-04 0.6400 8 15.0 1.8
CDK20 1.4 6.5 13 7.1e-04 0.6400 9 16.0 1.8
PLCD1 -1.1 6.5 11 1.1e-03 0.8400 10 22.0 2.2
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 1 5.5 5.5
CHAC1 1.40 6.4 15 1.7e-04 0.38 2 6.2 3.1
SLC7A11 1.40 6.6 14 2.0e-04 0.38 3 6.7 2.2
PSAT1 0.77 8.3 14 2.5e-04 0.38 4 7.1 1.8
MCM5 0.99 7.1 14 2.7e-04 0.38 5 7.4 1.5
PHGDH 0.75 8.6 14 2.8e-04 0.38 6 7.7 1.3
MTHFD2 0.91 7.3 13 4.3e-04 0.41 7 9.5 1.4
TRMO -0.99 6.5 13 4.3e-04 0.41 8 9.6 1.2
CEBPB 1.30 6.8 12 5.7e-04 0.41 9 11.0 1.3
EIF5AL1 -1.10 6.4 16 5.8e-04 0.41 10 11.0 1.1
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 1 0.5 0.5
ACBD3 -1.7 6.8 13 3.5e-04 0.8400 2 5.0 2.5
SPOCK1 -1.9 6.6 13 3.6e-04 0.8400 3 5.0 1.7
SDC2 -1.4 7.7 13 4.2e-04 0.8400 4 5.9 1.5
METTL15 -1.9 6.4 14 8.9e-04 0.8400 5 9.0 1.8
KIF5C 2.4 7.3 11 1.1e-03 0.8400 6 11.0 1.8
TOP2A 4.4 7.4 11 1.2e-03 0.8400 7 11.0 1.6
HES4 2.3 7.7 11 1.2e-03 0.8400 8 12.0 1.4
A2M -1.8 6.6 10 1.5e-03 0.8400 9 14.0 1.6
FNBP4 3.1 6.8 10 1.5e-03 0.8400 10 14.0 1.4
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 1 0.7 0.70
FAM228B -1.3 6.5 23 2.7e-05 0.1100 2 2.6 1.30
PKMYT1 1.4 6.7 16 7.6e-05 0.1700 3 3.5 1.20
KRT18 1.9 7.2 16 8.2e-05 0.1700 4 3.5 0.88
CDC6 1.3 6.9 13 3.6e-04 0.3500 5 7.7 1.50
EXTL3 1.4 6.4 18 4.0e-04 0.3500 6 7.9 1.30
APMAP 0.7 7.4 13 4.2e-04 0.3500 7 8.3 1.20
HERPUD2 -1.0 6.5 13 4.6e-04 0.3500 8 8.9 1.10
GADD45G 1.9 7.4 13 4.6e-04 0.3500 9 8.9 0.99
LGALS3 1.5 6.6 13 4.7e-04 0.3500 10 9.1 0.91
1e-04 NA NA NA NA NA 4 3.6 0.90
1e-05 NA NA NA NA NA 1 1.9 1.90
1e-06 NA NA NA NA NA 1 0.9 0.90
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 1 5.1 5.1
MYC 2.6 7.5 15 1.2e-04 0.28 2 6.0 3.0
SLC4A1AP 1.6 6.6 15 1.4e-04 0.28 3 6.6 2.2
FAM105A 1.6 6.4 19 2.0e-04 0.28 4 8.2 2.0
SEMA3A -1.3 6.4 16 2.1e-04 0.28 5 8.2 1.6
TUBD1 -1.2 6.5 14 2.1e-04 0.28 6 8.2 1.4
IRS1 -1.1 6.6 14 2.6e-04 0.30 7 8.6 1.2
GAS2L3 -1.2 6.4 14 3.2e-04 0.33 8 9.4 1.2
FRZB 1.7 6.9 13 3.8e-04 0.34 9 10.0 1.1
SLC30A6 1.5 6.3 18 4.9e-04 0.40 10 12.0 1.2
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 1 1.4 1.40
SPP1 -1.7 7.1 23 2.9e-06 0.012 2 1.6 0.80
RGS5 -1.3 6.7 21 8.4e-06 0.023 3 1.8 0.60
DST -1.1 6.7 20 1.2e-05 0.024 4 2.1 0.52
ZNF660 1.5 6.4 25 1.8e-05 0.029 5 2.2 0.44
NQO1 -1.2 7.5 18 4.0e-05 0.054 6 3.4 0.57
SLC2A3 -1.0 6.6 16 7.3e-05 0.085 7 4.3 0.61
S100A16 -1.1 6.7 16 9.2e-05 0.093 8 4.6 0.58
SAMD4A -1.2 6.3 21 1.2e-04 0.110 9 5.1 0.57
PDLIM7 -0.6 8.4 15 1.5e-04 0.120 10 5.5 0.55
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 1 0.8 0.80
DDX10 -1.5 6.7 23 3.3e-06 0.013 2 0.8 0.40
ZBTB20 -1.3 6.6 19 2.6e-05 0.070 3 2.6 0.87
WNT7B 1.8 6.6 16 7.0e-05 0.140 4 4.6 1.20
DTNA 1.6 6.5 18 1.3e-04 0.210 5 6.8 1.40
TBKBP1 1.6 6.4 19 2.1e-04 0.280 6 8.4 1.40
SEMA3A -1.2 6.4 15 2.5e-04 0.290 7 9.2 1.30
SMIM14 -1.1 6.5 14 3.1e-04 0.320 8 9.9 1.20
CUEDC1 1.3 6.5 13 4.3e-04 0.390 9 12.0 1.30
CMTM8 1.5 6.6 13 4.8e-04 0.390 10 12.0 1.20
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 1 0.2
S100A10 -2.5 7.1 46 1.4e-10 5.8e-07 2 0.2
NQO1 -1.9 7.5 36 8.9e-09 2.4e-05 3 0.5
LGALS3 -2.1 6.8 32 4.8e-08 9.7e-05 4 0.6
GAP43 -1.7 8.2 31 1.0e-07 1.7e-04 5 0.7
FTH1 -1.1 12.0 28 2.9e-07 4.0e-04 6 1.0
ETV1 -1.6 6.4 26 1.0e-05 1.2e-02 7 1.7
GNG3 -1.7 6.5 20 1.3e-05 1.3e-02 8 1.8
CTD-2006C1.2 -1.2 7.0 19 2.0e-05 1.8e-02 9 2.4
IFI27L1 -1.2 6.7 18 3.4e-05 2.7e-02 10 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 0.20
S100A10 0.10
NQO1 0.17
LGALS3 0.15
GAP43 0.14
FTH1 0.17
ETV1 0.24
GNG3 0.22
CTD-2006C1.2 0.27
IFI27L1 0.33
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 1 0.7 0.7
SLC19A1 2.00 6.4 20 4.2e-05 0.170 2 2.5 1.2
CWF19L2 -1.30 6.5 18 6.6e-05 0.180 3 3.4 1.1
EVA1B -1.20 6.6 14 1.9e-04 0.390 4 5.9 1.5
MT-ATP6 -0.63 11.0 14 3.0e-04 0.430 5 7.3 1.5
PKMYT1 1.70 6.7 13 3.3e-04 0.430 6 8.1 1.4
APPL2 1.70 6.4 17 3.7e-04 0.430 7 8.4 1.2
ARHGAP21 1.60 6.6 12 5.7e-04 0.470 8 12.0 1.6
RANBP9 1.60 6.4 17 5.7e-04 0.470 9 12.0 1.4
AP5S1 1.70 6.4 16 5.9e-04 0.470 10 13.0 1.3
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 1 4.5 4.5
KMT5A -1.7 6.5 15 1.3e-04 0.53 2 5.6 2.8
PLPP3 -1.5 6.5 14 2.6e-04 0.61 3 7.1 2.4
CTTN -1.4 6.9 13 3.3e-04 0.61 4 7.7 1.9
SPP1 -1.8 6.9 13 4.6e-04 0.61 5 9.2 1.8
CNTROB -1.6 6.4 16 5.8e-04 0.61 6 11.0 1.8
AKAP8L 2.7 6.6 12 6.0e-04 0.61 7 11.0 1.5
CMBL 2.4 6.8 12 6.5e-04 0.61 8 12.0 1.5
TPX2 -1.4 7.0 12 6.7e-04 0.61 9 12.0 1.3
CCNF -1.5 6.5 12 8.4e-04 0.65 10 14.0 1.4
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 1 1.6 1.60
CDCA2 -2.9 6.5 20 1.7e-05 0.069 2 1.9 0.95
BORA -2.9 6.4 18 2.9e-05 0.079 3 2.1 0.70
C2orf69 -2.7 6.6 16 1.1e-04 0.190 4 3.1 0.78
TTK -2.7 6.5 16 1.1e-04 0.190 5 3.1 0.62
CCNF -2.5 6.5 13 3.4e-04 0.460 6 6.2 1.00
RP11-343C2.12 -2.6 6.4 14 4.3e-04 0.500 7 7.1 1.00
MSANTD2 -2.5 6.5 12 5.5e-04 0.550 8 8.0 1.00
SGO2 -2.4 6.8 12 6.7e-04 0.550 9 8.8 0.98
EMG1 -1.8 7.7 12 6.8e-04 0.550 10 8.8 0.88
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 1 2.5
NDC80 -2.6 6.7 22 4.6e-06 0.019 2 2.6
CDC25B -2.4 7.2 17 6.0e-05 0.140 3 5.5
RP11-339B21.12 -2.2 7.0 16 7.7e-05 0.140 4 5.7
DLL1 -2.7 7.0 16 8.6e-05 0.140 5 5.8
JUN -1.8 7.8 15 1.4e-04 0.180 6 7.0
TPX2 -2.1 7.0 14 2.5e-04 0.280 7 9.0
PTTG1 -1.9 8.5 13 3.2e-04 0.280 8 9.9
NEK2 -2.2 6.5 13 3.4e-04 0.280 9 9.9
DLGAP5 -2.2 6.7 13 3.5e-04 0.280 10 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 2.50
NDC80 1.30
CDC25B 1.80
RP11-339B21.12 1.40
DLL1 1.20
JUN 1.20
TPX2 1.30
PTTG1 1.20
NEK2 1.10
DLGAP5 0.99
1e-04 1.20
1e-05 1.50
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 1 1.7 1.70
IFITM3 -1.6 8.7 18 4.4e-05 0.14 2 2.3 1.20
TPM2 -1.9 7.2 17 5.4e-05 0.14 3 2.4 0.80
INTU -1.5 6.8 16 7.7e-05 0.14 4 2.5 0.62
EFCAB11 -1.7 6.4 19 8.9e-05 0.14 5 2.5 0.50
MED13 -1.6 6.4 16 2.2e-04 0.28 6 4.3 0.72
PRC1 -1.5 6.7 14 2.9e-04 0.28 7 4.9 0.70
RGS5 -1.5 6.6 14 3.1e-04 0.28 8 5.1 0.64
ZNF134 -1.6 6.4 16 3.2e-04 0.28 9 5.4 0.60
ITGA6 -1.7 6.4 19 3.9e-04 0.32 10 6.1 0.61
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 1 0.1 0.10
RGS5 -3.0 6.7 33 4.1e-08 1.6e-04 2 0.3 0.15
TPPP3 -3.1 6.6 29 2.5e-07 6.9e-04 3 0.5 0.17
SPARC -1.6 8.5 20 1.4e-05 2.6e-02 4 0.8 0.20
SESN3 -2.6 6.5 20 1.6e-05 2.6e-02 5 0.8 0.16
CCND2 -2.3 7.1 16 9.1e-05 1.2e-01 6 1.6 0.27
HDAC2 2.0 8.5 15 1.2e-04 1.4e-01 7 1.6 0.23
HEBP1 -1.9 6.9 14 2.1e-04 1.8e-01 8 2.1 0.26
CEBPD -2.4 6.7 14 2.1e-04 1.8e-01 9 2.1 0.23
SCD -1.7 7.6 14 2.3e-04 1.8e-01 10 2.1 0.21
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 1 0.9 0.90
SEMA3A -1.40 6.4 26 6.9e-07 0.0028 2 1.0 0.50
GRIA1 -1.30 6.4 23 2.6e-06 0.0070 3 1.3 0.43
SPP1 2.00 6.6 22 5.4e-06 0.0110 4 1.5 0.38
ARMCX6 -0.90 7.0 17 5.1e-05 0.0820 5 3.8 0.76
C2orf49 -1.00 6.5 17 9.7e-05 0.1100 6 4.7 0.78
C1orf56 -1.20 6.4 21 9.8e-05 0.1100 7 4.7 0.67
NUP58 1.20 6.6 16 1.1e-04 0.1100 8 5.1 0.64
GAP43 -0.92 8.1 14 2.3e-04 0.1700 9 6.9 0.77
PHLDA1 -1.10 7.0 14 2.5e-04 0.1700 10 7.5 0.75
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 1 0.1 0.10
LGALS3 -1.60 6.9 22 4.9e-06 2.0e-02 2 1.8 0.90
SAMD4A -1.20 6.4 24 2.7e-05 7.2e-02 3 3.2 1.10
SNAPC1 -1.20 6.7 17 4.8e-05 9.7e-02 4 3.9 0.98
KCTD10 -0.96 6.6 16 8.6e-05 1.4e-01 5 5.4 1.10
KMT5A -1.00 6.5 15 1.3e-04 1.7e-01 6 6.2 1.00
CTGF -0.85 8.5 14 1.9e-04 2.2e-01 7 7.0 1.00
CDCA7 1.00 6.6 14 2.2e-04 2.2e-01 8 7.7 0.96
CITED1 1.10 6.4 16 3.4e-04 3.1e-01 9 9.9 1.10
ZNF660 1.10 6.4 16 4.9e-04 3.2e-01 10 11.0 1.10
1e-04 NA NA NA NA NA 5 5.7 1.10
1e-05 NA NA NA NA NA 2 2.0 1.00
1e-06 NA NA NA NA NA 1 1.4 1.40
1e-07 NA NA NA NA NA 1 1.2 1.20
1e-08 NA NA NA NA NA 1 0.8 0.80
1e-09 NA NA NA NA NA 1 0.3 0.30
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 1 0.2 0.20
SMG1 -1.00 6.6 17 5.2e-05 1.8e-01 2 3.3 1.60
STMN2 1.80 7.1 16 6.7e-05 1.8e-01 3 3.5 1.20
CNPY4 -1.10 6.4 19 9.3e-05 1.9e-01 4 4.3 1.10
GPM6B -0.49 8.5 15 1.2e-04 2.0e-01 5 5.0 1.00
NCAPG -1.00 6.6 14 1.8e-04 2.5e-01 6 5.7 0.95
PTPN11 -0.86 6.6 14 2.3e-04 2.7e-01 7 6.5 0.93
CYP2R1 -1.00 6.4 16 2.9e-04 3.0e-01 8 7.4 0.92
NRDC 0.80 6.9 13 3.8e-04 3.5e-01 9 9.1 1.00
HIST1H2AC 1.10 6.4 13 4.6e-04 3.7e-01 10 10.0 1.00
1e-04 NA NA NA NA NA 4 4.5 1.10
1e-05 NA NA NA NA NA 1 1.6 1.60
1e-06 NA NA NA NA NA 1 1.2 1.20
1e-07 NA NA NA NA NA 1 0.6 0.60
1e-08 NA NA NA NA NA 1 0.6 0.60
1e-09 NA NA NA NA NA 1 0.3 0.30
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 1 4.9 4.9
TRMO -2.2 6.4 10.0 0.00140 0.83 2 12.0 6.0
EDC3 -2.2 6.5 9.9 0.00200 0.83 3 15.0 5.0
UPRT -2.5 6.4 14.0 0.00220 0.83 4 16.0 4.0
TCF19 -2.2 6.5 10.0 0.00260 0.83 5 19.0 3.8
NHLRC3 -2.1 6.6 9.2 0.00280 0.83 6 20.0 3.3
GUF1 -2.1 6.5 9.1 0.00290 0.83 7 20.0 2.9
DTX3 -2.1 6.6 8.9 0.00320 0.83 8 23.0 2.8
TDG 4.1 7.2 8.8 0.00350 0.83 9 24.0 2.7
EFCC1 -2.1 6.5 8.4 0.00430 0.83 10 29.0 2.9
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 1 3.2 3.2
ELMO1 1.50 6.4 21 2.4e-05 0.085 2 5.0 2.5
FGF19 1.80 6.5 18 3.1e-05 0.085 3 5.3 1.8
CAV1 -1.30 7.4 16 8.6e-05 0.170 4 6.7 1.7
ZNF273 1.30 6.4 17 1.7e-04 0.270 5 9.4 1.9
CEP250 -1.10 6.4 15 3.1e-04 0.390 6 13.0 2.2
POLR3A 1.20 6.5 13 3.4e-04 0.390 7 13.0 1.9
PLS3 1.20 6.4 15 5.7e-04 0.570 8 17.0 2.1
ATF2 -0.98 6.4 12 8.3e-04 0.570 9 21.0 2.4
LAMP5 1.20 6.4 12 8.6e-04 0.570 10 21.0 2.1
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 1 2.3 2.30
MYC 2.90 7.5 18 3.7e-05 0.095 2 3.4 1.70
TMEM88 -1.40 6.5 18 4.0e-05 0.095 3 3.4 1.10
HIST1H1C -1.50 6.6 17 4.7e-05 0.095 4 3.7 0.92
GDF15 -1.60 6.8 15 1.2e-04 0.190 5 5.9 1.20
ATF2 -1.20 6.5 16 2.8e-04 0.370 6 8.7 1.40
GADD45G -1.60 7.9 13 4.4e-04 0.440 7 10.0 1.50
PMP22 1.50 6.5 13 4.6e-04 0.440 8 11.0 1.30
EZR -0.83 7.5 12 5.5e-04 0.440 9 12.0 1.30
NKAIN3 -1.10 6.4 13 5.8e-04 0.440 10 12.0 1.20
1e-04 NA NA NA NA NA 4 5.4 1.40
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 1 1.3 1.30
EIF4ENIF1 1.6 6.5 19 7.3e-05 0.23 2 3.4 1.70
LGALS3 1.8 6.5 15 1.6e-04 0.23 3 6.2 2.10
FAM83D 1.6 6.5 15 1.7e-04 0.23 4 6.5 1.60
FGF19 1.8 6.6 15 1.7e-04 0.23 5 6.6 1.30
PROM1 1.6 6.5 16 1.9e-04 0.23 6 7.0 1.20
ASCL1 -1.3 7.2 14 2.0e-04 0.23 7 7.2 1.00
VGF 1.8 6.7 14 2.3e-04 0.24 8 7.8 0.98
CASP9 1.5 6.4 19 3.0e-04 0.27 9 8.8 0.98
PTRF 1.7 6.9 12 5.0e-04 0.39 10 12.0 1.20
1e-04 NA NA NA NA NA 2 4.0 2.00
1e-05 NA NA NA NA NA 1 2.2 2.20
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 1 1.6 1.60
TSC22D4 1.60 6.5 22 7.5e-06 0.030 2 2.0 1.00
MYC 2.40 7.5 19 1.9e-05 0.051 3 2.9 0.97
STMN2 2.00 7.2 15 1.7e-04 0.350 4 6.1 1.50
EIF1AD 1.30 6.5 13 3.1e-04 0.510 5 9.4 1.90
TPX2 -0.96 7.1 13 4.3e-04 0.530 6 12.0 2.00
S100A10 1.50 6.7 12 5.2e-04 0.530 7 14.0 2.00
ASGR1 1.20 6.7 12 6.2e-04 0.530 8 16.0 1.90
NDC80 -0.97 6.8 12 7.2e-04 0.530 9 17.0 1.90
SNX27 -0.85 6.7 12 7.5e-04 0.530 10 17.0 1.70
1e-04 NA NA NA NA NA 3 5.0 1.70
1e-05 NA NA NA NA NA 2 2.4 1.20
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 1 0.7 0.70
MYC 3.20 7.5 28 3.1e-07 1.2e-03 2 1.0 0.50
SH3KBP1 1.40 6.4 16 2.4e-04 5.5e-01 3 8.5 2.80
USMG5 0.46 8.7 14 2.7e-04 5.5e-01 4 9.2 2.30
KDELR2 0.60 8.0 13 4.6e-04 6.3e-01 5 12.0 2.40
FBXO5 1.20 6.9 12 5.1e-04 6.3e-01 6 13.0 2.20
KCTD10 -0.99 6.6 12 5.9e-04 6.3e-01 7 13.0 1.90
TAGLN3 -1.20 7.4 12 6.3e-04 6.3e-01 8 13.0 1.70
HIST1H1C -1.10 6.6 12 7.2e-04 6.4e-01 9 15.0 1.60
GCHFR -1.10 6.5 12 8.0e-04 6.4e-01 10 16.0 1.60
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 1 1.0 1.00
MAFF 2.50 6.5 20 1.7e-05 0.069 2 1.7 0.85
HIST1H2AC 2.10 6.4 16 8.1e-05 0.200 3 3.8 1.30
GLIPR1 -1.40 6.7 15 1.2e-04 0.200 4 4.7 1.20
AC093323.3 1.70 6.6 16 1.2e-04 0.200 5 4.7 0.94
GNG10 1.70 6.4 18 4.6e-04 0.520 6 11.0 1.90
BRCA1 -1.20 6.7 13 4.7e-04 0.520 7 12.0 1.70
FGF19 2.00 6.6 12 7.5e-04 0.520 8 16.0 2.00
HIPK2 -0.94 7.0 12 8.3e-04 0.520 9 17.0 1.90
SLC2A3 -1.10 6.6 11 9.2e-04 0.520 10 19.0 1.90
1e-04 NA NA NA NA NA 3 4.0 1.30
1e-05 NA NA NA NA NA 1 1.7 1.70
1e-06 NA NA NA NA NA 1 1.1 1.10
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 1 2.2 2.20
CNN1 -1.6 6.6 18 4.3e-05 0.17 2 3.5 1.80
ZNF33A 2.0 6.5 17 6.4e-05 0.17 3 3.9 1.30
DLL3 3.1 7.0 16 1.1e-04 0.19 4 4.9 1.20
QSER1 2.0 6.4 18 1.2e-04 0.19 5 5.0 1.00
KLHL8 1.9 6.4 17 2.1e-04 0.25 6 6.8 1.10
AGPAT2 1.9 6.6 14 2.4e-04 0.25 7 7.0 1.00
PLXNB1 -1.4 6.4 18 2.5e-04 0.25 8 7.0 0.88
ANKRD1 2.1 6.6 13 5.0e-04 0.40 9 11.0 1.20
JAKMIP2 1.7 6.5 13 5.0e-04 0.40 10 11.0 1.10
1e-04 NA NA NA NA NA 3 4.5 1.50
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 1 0.7 0.70
S100A10 -2.10 7.0 32 4.9e-08 2.0e-04 2 1.3 0.65
TAGLN2 -1.70 6.7 25 1.3e-06 3.5e-03 3 2.6 0.87
RGS5 -1.60 6.7 24 1.9e-06 3.7e-03 4 2.7 0.68
SERPINE2 -1.60 6.7 24 2.3e-06 3.7e-03 5 2.8 0.56
RAB13 -0.83 7.9 20 1.3e-05 1.3e-02 6 4.3 0.72
KCTD10 -1.30 6.5 20 1.3e-05 1.3e-02 7 4.3 0.61
CALD1 -1.10 8.1 20 1.3e-05 1.3e-02 8 4.3 0.54
TPM2 -1.60 7.3 19 2.4e-05 2.2e-02 9 4.8 0.53
MMP2 -1.30 6.5 18 3.0e-05 2.4e-02 10 5.2 0.52
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 1 1.9 1.90
FXYD6 3.6 8.0 15 1.2e-04 0.50 2 2.7 1.40
BEX2 -2.2 6.9 12 5.7e-04 0.77 3 5.5 1.80
CST3 2.3 8.2 12 7.1e-04 0.77 4 6.2 1.60
COX11 4.1 7.2 12 8.1e-04 0.77 5 6.8 1.40
MSTO1 -2.1 6.5 11 8.7e-04 0.77 6 6.8 1.10
PTN -1.8 8.0 11 1.1e-03 0.77 7 8.1 1.20
ARHGEF2 -2.2 6.5 11 1.1e-03 0.77 8 8.3 1.00
NOL11 4.1 7.2 11 1.1e-03 0.77 9 8.6 0.96
CREB3 4.0 7.2 11 1.3e-03 0.77 10 9.4 0.94
1e-04 NA NA NA NA NA 1 2.7 2.70
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 1 1.8 1.8
MYC 3.5 7.5 18 3.0e-05 0.12 2 2.4 1.2
TOR1AIP1 1.7 6.4 18 2.7e-04 0.72 3 8.5 2.8
NUP98 -1.2 6.4 15 3.6e-04 0.73 4 10.0 2.6
DHODH -1.2 6.6 13 5.0e-04 0.81 5 13.0 2.5
EMP3 1.7 6.7 12 6.8e-04 0.90 6 17.0 2.8
DCAF6 1.5 6.3 16 1.0e-03 0.90 7 22.0 3.1
KCTD2 -1.2 6.4 15 1.1e-03 0.90 8 23.0 2.8
RAB11FIP2 1.6 6.4 13 1.2e-03 0.90 9 24.0 2.7
SERGEF 1.6 6.4 14 1.2e-03 0.90 10 24.0 2.4
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 1 0.5 0.50
LGALS3 -1.70 6.8 23 2.5e-06 1.0e-02 2 1.9 0.95
IMPA2 1.50 6.8 17 6.2e-05 1.5e-01 3 4.2 1.40
TP53I3 -1.20 7.0 16 7.2e-05 1.5e-01 4 4.4 1.10
DHFR 0.98 7.7 16 1.1e-04 1.7e-01 5 5.1 1.00
ZNF561 1.40 6.5 15 1.3e-04 1.7e-01 6 5.2 0.87
STMN2 2.10 7.2 14 1.9e-04 2.2e-01 7 6.3 0.90
LTBP1 1.50 6.4 18 2.1e-04 2.2e-01 8 6.7 0.84
CYFIP2 -0.92 6.8 13 4.1e-04 3.6e-01 9 9.9 1.10
ENHO 1.20 6.7 13 4.5e-04 3.6e-01 10 11.0 1.10
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 1 1.7 1.7
SEMA3A -1.20 6.4 18 5.7e-05 0.19 2 4.0 2.0
PIF1 1.40 6.4 16 7.1e-05 0.19 3 4.1 1.4
GADD45G -1.60 8.0 15 1.3e-04 0.25 4 4.9 1.2
TACC3 1.10 6.8 14 2.8e-04 0.43 5 6.9 1.4
SPTY2D1 1.20 6.4 13 4.1e-04 0.43 6 8.9 1.5
MPZL1 -0.79 6.8 13 4.3e-04 0.43 7 9.2 1.3
RILPL2 1.30 6.4 21 4.4e-04 0.43 8 9.5 1.2
LTN1 -1.00 6.4 15 5.3e-04 0.43 9 11.0 1.2
LIX1 -0.99 6.7 12 5.5e-04 0.43 10 11.0 1.1
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 1 1.0 1.00
TSPAN15 1.50 6.7 19 1.7e-05 0.07000 2 2.2 1.10
SPP1 2.00 6.7 18 2.7e-05 0.07400 3 2.9 0.97
GOLGA8B 1.40 6.4 24 8.9e-05 0.16000 4 5.0 1.20
ANKRD1 1.50 6.6 15 1.1e-04 0.16000 5 5.6 1.10
IDI1 0.67 8.2 15 1.2e-04 0.16000 6 5.8 0.97
SLC20A2 1.20 6.6 15 1.6e-04 0.19000 7 7.2 1.00
TRIO -1.10 6.5 15 2.8e-04 0.25000 8 10.0 1.20
SCD5 1.20 6.5 15 2.8e-04 0.25000 9 10.0 1.10
FAM111B 1.20 6.5 13 3.5e-04 0.28000 10 11.0 1.10
1e-04 NA NA NA NA NA 4 5.4 1.40
1e-05 NA NA NA NA NA 1 2.1 2.10
1e-06 NA NA NA NA NA 1 1.5 1.50
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 1 0.9 0.90
RGS5 -1.30 6.7 19 1.7e-05 0.0480 2 1.8 0.90
STMN2 2.40 7.2 19 1.8e-05 0.0480 3 1.8 0.60
NFXL1 1.40 6.4 19 2.3e-04 0.3100 4 5.6 1.40
NNAT 1.40 6.5 14 2.7e-04 0.3100 5 6.5 1.30
CMTR2 1.30 6.4 16 3.0e-04 0.3100 6 6.9 1.20
GADD45G 1.90 7.4 14 3.0e-04 0.3100 7 6.9 0.99
ATPIF1 -0.51 8.3 13 3.1e-04 0.3100 8 7.1 0.89
JAKMIP2 1.20 6.5 14 4.2e-04 0.3800 9 8.2 0.91
FAT3 -0.98 6.5 12 5.0e-04 0.4100 10 9.1 0.91
1e-04 NA NA NA NA NA 3 3.0 1.00
1e-05 NA NA NA NA NA 1 1.7 1.70
1e-06 NA NA NA NA NA 1 1.0 1.00
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 1 0.2 0.20
BORA -1.7 6.5 14 2.6e-04 6.1e-01 2 4.3 2.20
CLN8 2.8 6.7 14 3.0e-04 6.1e-01 3 5.0 1.70
CCDC84 -1.6 6.5 13 4.1e-04 6.1e-01 4 6.0 1.50
SLC7A11 -1.7 6.8 13 5.1e-04 6.1e-01 5 6.6 1.30
RNF25 2.7 6.6 13 5.2e-04 6.1e-01 6 6.6 1.10
MRPS28 2.4 6.8 12 6.1e-04 6.1e-01 7 7.5 1.10
CHMP4A 2.6 6.6 12 6.6e-04 6.1e-01 8 8.2 1.00
DIO3 -1.5 7.3 12 6.8e-04 6.1e-01 9 8.5 0.94
PTRH1 2.5 6.6 12 7.9e-04 6.2e-01 10 9.5 0.95
1e-04 NA NA NA NA NA 1 2.6 2.60
1e-05 NA NA NA NA NA 1 0.5 0.50
1e-06 NA NA NA NA NA 1 0.3 0.30
1e-07 NA NA NA NA NA 1 0.2 0.20
1e-08 NA NA NA NA NA 1 0.2 0.20
1e-09 NA NA NA NA NA 1 0.2 0.20
1e-10 NA NA NA NA NA 1 0.2 0.20
[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 1 1.9 1.9
KRT18 -2.7 7.5 13.0 4.6e-04 0.85 2 4.3 2.2
METTL18 -2.5 6.5 14.0 4.8e-04 0.85 3 4.5 1.5
HMGCS1 -1.6 8.1 11.0 9.2e-04 0.85 4 6.3 1.6
SDF2L1 -1.9 7.3 11.0 1.3e-03 0.85 5 8.6 1.7
CKAP2L -2.2 6.6 10.0 1.7e-03 0.85 6 10.0 1.7
ACVR2A -2.2 6.5 10.0 1.8e-03 0.85 7 11.0 1.5
MRPS34 1.9 8.4 9.7 2.2e-03 0.85 8 12.0 1.5
INIP -1.8 6.9 9.6 2.3e-03 0.85 9 13.0 1.5
PYCR1 -2.2 6.9 9.5 2.3e-03 0.85 10 14.0 1.4
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 1 3.7 3.7
CDKN1C -1.7 7.0 15 0.00014 0.53 2 5.0 2.5
MYC 3.8 7.6 14 0.00020 0.53 3 6.1 2.0
AC084018.1 -1.3 6.5 14 0.00026 0.53 4 7.4 1.8
WWP2 -1.3 6.4 15 0.00066 0.83 5 14.0 2.9
EXD2 1.8 6.4 14 0.00075 0.83 6 16.0 2.6
LOXL1 1.9 6.6 11 0.00085 0.83 7 17.0 2.4
APC2 -1.3 6.5 12 0.00089 0.83 8 17.0 2.1
IGF1R -1.2 6.6 11 0.00110 0.83 9 19.0 2.1
MANEAL -1.3 6.4 15 0.00130 0.83 10 22.0 2.2
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 1 0.2 0.20
ATF7IP2 1.20 6.4 18 3.1e-05 1.2e-01 2 2.7 1.40
TAMM41 -1.10 6.4 20 4.3e-05 1.2e-01 3 2.9 0.97
IER3 1.20 6.4 16 9.8e-05 2.0e-01 4 4.3 1.10
NUP155 1.10 6.4 16 1.6e-04 2.6e-01 5 5.1 1.00
DOLK -0.85 6.5 13 4.3e-04 5.8e-01 6 8.4 1.40
KCTD10 -0.85 6.5 12 6.6e-04 6.9e-01 7 12.0 1.70
CLK3 -0.76 6.7 12 6.8e-04 6.9e-01 8 12.0 1.50
RPUSD1 0.78 6.7 11 9.1e-04 7.2e-01 9 14.0 1.60
ATOH8 -0.97 6.4 13 1.0e-03 7.2e-01 10 16.0 1.60
1e-04 NA NA NA NA NA 4 4.3 1.10
1e-05 NA NA NA NA NA 1 2.1 2.10
1e-06 NA NA NA NA NA 1 1.1 1.10
1e-07 NA NA NA NA NA 1 1.0 1.00
1e-08 NA NA NA NA NA 1 0.5 0.50
1e-09 NA NA NA NA NA 1 0.2 0.20
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 1 0.3 0.30
SPP1 -2.4 6.9 26 7.4e-07 0.0030 2 0.3 0.15
S100A10 -2.1 6.9 20 1.3e-05 0.0340 3 1.2 0.40
NQO1 -1.7 7.3 17 6.9e-05 0.1400 4 3.0 0.75
TPM2 -1.9 7.2 16 1.2e-04 0.1800 5 4.3 0.86
SERPINH1 -1.1 7.8 15 1.3e-04 0.1800 6 4.7 0.78
SHPRH 2.6 6.6 15 1.6e-04 0.1900 7 5.5 0.79
SGO1 2.6 6.8 15 1.9e-04 0.1900 8 6.0 0.75
NRSN2 2.5 6.5 14 2.5e-04 0.2100 9 6.7 0.74
RP11-75C9.1 -1.7 6.4 17 2.6e-04 0.2100 10 6.8 0.68
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 1 0.0 0.00
PCDH9 -2.30 6.4 23 6.0e-06 2.4e-02 2 1.7 0.85
TERF2IP -1.50 7.4 16 9.2e-05 2.4e-01 3 3.6 1.20
AFF4 -1.80 6.6 16 1.2e-04 2.4e-01 4 3.8 0.95
SPOCK1 -1.80 6.6 15 1.6e-04 2.6e-01 5 4.4 0.88
MALAT1 -0.91 14.0 13 3.4e-04 4.6e-01 6 6.7 1.10
KCTD2 -1.90 6.4 17 4.0e-04 4.7e-01 7 7.9 1.10
UFSP2 2.50 6.9 12 6.9e-04 6.2e-01 8 10.0 1.30
SFRP1 3.80 7.0 12 7.1e-04 6.2e-01 9 11.0 1.20
ATP5B -0.75 9.6 12 8.3e-04 6.2e-01 10 12.0 1.20
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 1 2.5 2.5
NAV1 -1.5 6.8 16 9.0e-05 0.250 2 5.3 2.6
RHBDL3 -1.8 6.4 17 9.1e-05 0.250 3 5.3 1.8
RALGAPA1 -1.6 6.4 15 2.5e-04 0.510 4 8.5 2.1
MAP3K4 -1.6 6.4 15 3.3e-04 0.540 5 9.6 1.9
HERC1 -1.6 6.4 14 5.2e-04 0.680 6 12.0 2.1
GNG12 2.7 6.6 12 8.0e-04 0.680 7 17.0 2.4
A2M -1.5 6.6 12 8.5e-04 0.680 8 17.0 2.1
ZNF496 -1.5 6.4 13 9.0e-04 0.680 9 18.0 2.0
METTL8 2.5 6.6 11 9.4e-04 0.680 10 18.0 1.8
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 1 0.1 0.100
IFITM3 -2.1 8.9 40 1.9e-09 7.9e-06 2 0.1 0.050
PTN -1.9 8.1 31 9.1e-08 2.5e-04 3 0.2 0.067
CLU -1.8 7.6 28 3.2e-07 6.1e-04 4 0.4 0.100
GPM6B -1.2 8.5 28 3.7e-07 6.1e-04 5 0.4 0.080
LGALS3 -2.3 6.8 25 1.2e-06 1.6e-03 6 0.6 0.100
S100A10 -2.0 6.9 19 2.6e-05 3.0e-02 7 1.5 0.210
SULF2 -1.7 6.7 18 3.3e-05 3.2e-02 8 1.5 0.190
TIMP2 -1.7 6.4 18 4.1e-05 3.2e-02 9 1.6 0.180
WLS -1.4 7.1 17 4.5e-05 3.2e-02 10 1.6 0.160
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 1 0.5 0.50
SPP1 -2.7 6.9 25 1.4e-06 0.00580 2 0.7 0.35
NKAIN4 -2.1 7.0 18 2.9e-05 0.07800 3 1.5 0.50
WDR26 -1.9 6.5 18 8.0e-05 0.16000 4 2.2 0.55
PCGF2 3.5 6.9 16 9.6e-05 0.16000 5 2.6 0.52
TXNRD1 -1.6 7.2 14 2.8e-04 0.38000 6 4.1 0.68
JUNB -1.8 6.7 13 4.1e-04 0.43000 7 4.9 0.70
GNPDA1 -1.7 6.9 13 4.3e-04 0.43000 8 5.1 0.64
UCK2 2.9 6.7 13 5.0e-04 0.45000 9 5.4 0.60
TSC1 -1.7 6.5 13 6.7e-04 0.50000 10 7.0 0.70
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 1 7.5 7.5
LARP1 0.85 7.2 13 0.00028 0.54 2 7.5 3.8
FAXC 1.50 6.3 14 0.00028 0.54 3 7.5 2.5
ARPC3 0.45 8.4 13 0.00032 0.54 4 8.1 2.0
LGALS3 2.50 6.6 13 0.00034 0.54 5 8.2 1.6
SIN3A 1.50 6.3 15 0.00044 0.60 6 9.3 1.6
CNOT11 1.10 6.7 12 0.00055 0.63 7 11.0 1.5
PCF11 1.20 6.5 12 0.00064 0.65 8 12.0 1.5
USP36 1.30 6.3 12 0.00080 0.68 9 14.0 1.6
SBK1 1.30 6.5 11 0.00086 0.68 10 15.0 1.5
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 1 4.0 4.0
MLLT6 1.60 6.2 21 1.0e-04 0.42 2 5.0 2.5
SLC39A9 1.50 6.3 15 2.5e-04 0.47 3 7.8 2.6
ZDHHC2 1.50 6.3 16 3.4e-04 0.47 4 8.3 2.1
MIAT -1.20 7.0 13 3.7e-04 0.47 5 9.0 1.8
RAB32 1.60 6.6 13 3.8e-04 0.47 6 9.0 1.5
EPS15 1.50 6.3 15 4.8e-04 0.47 7 10.0 1.5
NIN -0.87 6.7 12 5.0e-04 0.47 8 11.0 1.3
FKBP5 1.40 6.4 12 5.2e-04 0.47 9 11.0 1.2
ADAT1 -0.90 6.3 12 6.1e-04 0.49 10 12.0 1.2
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 1 3.1 3.1
ASCL1 2.20 7.0 14 2.1e-04 0.60 2 5.7 2.8
KRT8 -1.40 7.0 14 2.4e-04 0.60 3 6.1 2.0
RASSF7 1.60 6.3 15 3.7e-04 0.60 4 9.0 2.2
ZYG11B 1.40 6.4 13 3.7e-04 0.60 5 9.0 1.8
CDKN1A 1.60 8.1 12 6.5e-04 0.72 6 12.0 2.0
MED4 0.68 7.3 11 7.8e-04 0.72 7 13.0 1.9
DLL1 2.10 6.8 11 8.5e-04 0.72 8 14.0 1.7
LAMTOR5 0.50 8.2 11 8.6e-04 0.72 9 14.0 1.6
RP11-220I1.1 1.30 6.4 11 9.9e-04 0.72 10 16.0 1.6
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 1 5.7 5.7
ERMARD -1.5 6.2 17 0.00046 0.8 2 7.2 3.6
ZCCHC8 2.4 6.4 13 0.00047 0.8 3 7.3 2.4
POMGNT2 2.3 6.4 13 0.00059 0.8 4 9.4 2.3
UBR7 2.3 6.4 12 0.00069 0.8 5 11.0 2.1
ATF7IP2 2.3 6.4 11 0.00082 0.8 6 13.0 2.1
ZHX1 2.2 6.3 12 0.00120 0.8 7 17.0 2.5
CADM4 -1.2 6.5 10 0.00130 0.8 8 18.0 2.2
SFT2D2 2.2 6.3 11 0.00130 0.8 9 19.0 2.1
FNDC4 -1.3 6.3 10 0.00140 0.8 10 19.0 1.9
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 1 0.1 0.10
S100A10 -1.6 6.8 24 9.5e-07 3.8e-03 2 0.4 0.20
CDKN2A -1.4 6.5 22 3.3e-06 8.8e-03 3 0.6 0.20
SLC12A2 -1.1 6.4 20 7.9e-06 1.6e-02 4 1.2 0.30
CCP110 1.7 6.4 17 4.0e-05 5.5e-02 5 2.4 0.48
FLRT3 1.7 6.2 21 4.1e-05 5.5e-02 6 2.4 0.40
JAG1 -1.1 6.8 16 5.9e-05 6.1e-02 7 2.9 0.41
HIST1H2AC -1.2 6.3 16 6.1e-05 6.1e-02 8 2.9 0.36
DHRS12 1.6 6.2 21 8.6e-05 6.6e-02 9 3.3 0.37
PHLDA1 -1.1 6.9 15 8.6e-05 6.6e-02 10 3.3 0.33
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 1 8.0 8.0
MGRN1 2.4 6.4 13 0.00036 0.8 2 8.7 4.4
DKK3 -1.2 6.6 12 0.00055 0.8 3 11.0 3.8
SPEN 2.3 6.4 12 0.00075 0.8 4 14.0 3.4
CCP110 2.3 6.4 12 0.00083 0.8 5 14.0 2.8
EIF5 0.8 8.9 11 0.00110 0.8 6 17.0 2.9
PDE1B -1.3 6.3 11 0.00110 0.8 7 18.0 2.5
MXRA7 2.1 6.5 10 0.00130 0.8 8 20.0 2.4
FASTK 1.5 6.9 10 0.00140 0.8 9 20.0 2.2
DYRK2 2.2 6.3 12 0.00140 0.8 10 20.0 2.0
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 1 0.5 0.50
FST -2.4 6.3 13.0 3.9e-04 0.79 2 1.9 0.95
ARPIN -2.2 6.2 13.0 5.4e-04 0.79 3 2.4 0.80
ERBB2 -2.1 6.3 11.0 9.1e-04 0.79 4 3.8 0.95
ABHD17A -1.9 6.5 10.0 1.5e-03 0.79 5 6.5 1.30
ACVR2B -1.9 6.4 9.7 1.9e-03 0.79 6 7.9 1.30
BTBD7 -2.0 6.3 9.7 1.9e-03 0.79 7 7.9 1.10
FBXW11 -1.9 6.3 9.4 2.2e-03 0.79 8 8.7 1.10
PHF12 -2.1 6.2 11.0 2.8e-03 0.79 9 11.0 1.30
PHAX 2.8 7.3 8.6 3.5e-03 0.79 10 14.0 1.40
1e-04 NA NA NA NA NA 1 0.9 0.90
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 1 1.1 1.10
TOP3A 1.9 6.3 18 8.5e-05 0.21 2 3.1 1.60
RP11-46C20.1 -1.2 6.4 15 9.0e-05 0.21 3 3.1 1.00
DDB2 -1.2 6.3 15 1.0e-04 0.21 4 3.4 0.85
ARFGAP3 1.8 6.4 14 1.6e-04 0.27 5 4.1 0.82
SLC25A26 1.5 6.6 14 2.0e-04 0.27 6 4.7 0.78
MKNK1 1.6 6.4 13 3.2e-04 0.33 7 6.3 0.90
JOSD1 1.7 6.3 14 3.3e-04 0.33 8 6.5 0.81
TPD52 -1.1 6.4 13 3.9e-04 0.35 9 7.2 0.80
KRT18 -1.5 7.1 12 5.2e-04 0.37 10 8.7 0.87
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 1 0.2 0.20
ARF4 -1.1 8.2 26 3.9e-07 0.0016 2 0.2 0.10
NANS -1.4 6.8 22 2.7e-06 0.0073 3 0.4 0.13
CDC42EP3 -1.5 6.6 21 5.1e-06 0.0100 4 0.6 0.15
TFPI2 -1.7 6.5 20 1.0e-05 0.0170 5 0.9 0.18
GDF15 -1.9 6.5 18 2.0e-05 0.0270 6 1.1 0.18
OXR1 2.6 6.4 18 2.7e-05 0.0320 7 1.6 0.23
ALG3 -1.1 7.0 15 8.8e-05 0.0880 8 2.5 0.31
TTC28 2.4 6.4 15 9.8e-05 0.0880 9 2.6 0.29
CITED4 -1.4 6.2 16 1.3e-04 0.0960 10 3.1 0.31
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] "DPYD_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
CTD-2006C1.2 -1.8 6.8 120 1.1e-27 8.8e-24 1 0.0
HIST1H2AC -1.7 6.3 65 1.1e-15 4.3e-12 2 0.1
TAGLN2 -1.4 6.4 37 1.3e-09 3.6e-06 3 0.1
S100A10 -1.6 6.9 31 2.9e-08 5.9e-05 4 0.2
DUSP4 -1.2 6.6 30 4.0e-08 6.4e-05 5 0.2
RCAN1 -1.1 6.5 28 1.1e-07 1.5e-04 6 0.3
TACC1 -1.2 6.4 28 1.3e-07 1.5e-04 7 0.3
LGALS3 -1.4 6.6 27 2.6e-07 2.6e-04 8 0.4
EPHX1 -1.1 6.3 26 3.1e-07 2.8e-04 9 0.4
TUBA1C -1.2 6.8 25 5.6e-07 4.6e-04 10 0.4
1e-04 NA NA NA NA NA 33 3.3
1e-05 NA NA NA NA NA 12 0.7
1e-06 NA NA NA NA NA 11 0.4
1e-07 NA NA NA NA NA 5 0.3
1e-08 NA NA NA NA NA 3 0.1
1e-09 NA NA NA NA NA 2 0.1
1e-10 NA NA NA NA NA 2 0.1
EmpiricalFDR
CTD-2006C1.2 0.000
HIST1H2AC 0.050
TAGLN2 0.033
S100A10 0.050
DUSP4 0.040
RCAN1 0.050
TACC1 0.043
LGALS3 0.050
EPHX1 0.044
TUBA1C 0.040
1e-04 0.100
1e-05 0.058
1e-06 0.036
1e-07 0.060
1e-08 0.033
1e-09 0.050
1e-10 0.050
[1] "DPYD_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MEG3 -0.83 7.5 26 3.3e-07 0.0026 1 0.8 0.80
CSRP1 -0.92 7.0 23 1.8e-06 0.0072 2 1.3 0.65
SMPD4 0.84 6.6 17 4.1e-05 0.1100 3 2.9 0.97
NUDT3 0.77 6.8 15 9.0e-05 0.1800 4 3.5 0.88
CCDC80 -0.77 6.4 15 1.2e-04 0.1900 5 4.1 0.82
CRNDE 0.47 8.3 14 1.4e-04 0.1900 6 5.0 0.83
SPP1 1.60 6.9 14 2.0e-04 0.2300 7 6.0 0.86
WASL 0.82 6.4 13 4.0e-04 0.3400 8 9.0 1.10
MRFAP1 0.24 8.9 12 4.2e-04 0.3400 9 9.0 1.00
MYL9 -0.74 7.5 12 4.8e-04 0.3400 10 9.8 0.98
1e-04 NA NA NA NA NA 4 3.6 0.90
1e-05 NA NA NA NA NA 2 2.0 1.00
1e-06 NA NA NA NA NA 1 1.2 1.20
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 0.2 Inf
[1] "DPYD_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NEAT1 2.00 8.5 17 3.8e-05 0.26 1 3.2 3.2
LGALS3 3.00 6.6 16 6.5e-05 0.26 2 4.1 2.0
AFF3 1.70 6.3 19 9.7e-05 0.26 3 5.2 1.7
AGTPBP1 1.60 6.2 19 2.1e-04 0.37 4 7.7 1.9
ZBTB8A 1.60 6.3 16 2.3e-04 0.37 5 7.7 1.5
DUSP16 1.50 6.4 12 4.2e-04 0.49 6 9.8 1.6
SPRED1 1.60 6.3 15 4.3e-04 0.49 7 9.8 1.4
GPR107 1.50 6.3 14 5.7e-04 0.56 8 12.0 1.5
C4orf48 0.63 7.9 11 7.3e-04 0.56 9 14.0 1.5
CEP164 1.30 6.5 11 7.7e-04 0.56 10 14.0 1.4
1e-04 NA NA NA NA NA 3 5.3 1.8
1e-05 NA NA NA NA NA 0 1.6 Inf
1e-06 NA NA NA NA NA 0 1.0 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 0.2 Inf
1e-10 NA NA NA NA NA 0 0.2 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 1 0.8 0.80
CDKN1C -1.40 6.8 18 1.8e-05 0.071 2 1.1 0.55
NNAT -1.20 6.3 17 3.7e-05 0.099 3 1.5 0.50
RP11-395G23.3 1.60 6.3 16 6.2e-05 0.130 4 1.7 0.42
FAM104B 1.00 6.8 15 1.2e-04 0.190 5 2.9 0.58
FAM110A -1.00 6.3 13 3.2e-04 0.300 6 5.4 0.90
ZNF784 1.40 6.3 17 3.3e-04 0.300 7 5.5 0.79
PRAG1 1.40 6.3 13 3.3e-04 0.300 8 5.5 0.69
SRD5A1 -0.83 6.5 13 3.8e-04 0.300 9 6.0 0.67
MED7 1.20 6.4 13 4.1e-04 0.300 10 6.7 0.67
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 1 1.7 1.7
STMN2 -1.60 7.1 16 6.8e-05 0.280 2 5.5 2.8
RALYL -1.00 6.3 15 1.4e-04 0.370 3 7.5 2.5
IRF7 -0.91 6.3 14 2.1e-04 0.420 4 9.6 2.4
FAAP100 1.40 6.3 16 2.9e-04 0.460 5 11.0 2.2
TFE3 -0.87 6.4 13 3.7e-04 0.460 6 12.0 2.0
ZSCAN16 1.40 6.3 15 4.0e-04 0.460 7 12.0 1.7
MAP2K6 -0.88 6.3 11 7.7e-04 0.730 8 18.0 2.2
MFSD2A 1.30 6.3 12 8.1e-04 0.730 9 18.0 2.0
ST7L -0.77 6.4 10 1.5e-03 1.000 10 27.0 2.7
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 1 3.1 3.1
NEAT1 -0.97 8.5 17 4.2e-05 0.12 2 3.6 1.8
STMN2 2.50 7.1 17 4.8e-05 0.12 3 4.0 1.3
EML1 1.30 6.3 18 5.9e-05 0.12 4 4.1 1.0
CHAF1B -0.82 6.5 14 1.5e-04 0.24 5 5.7 1.1
CASK 1.20 6.2 18 2.4e-04 0.33 6 7.0 1.2
SCAF4 0.98 6.4 12 4.6e-04 0.53 7 8.9 1.3
ARHGEF12 1.10 6.3 14 6.2e-04 0.56 8 11.0 1.3
GADD45G -1.10 7.5 11 7.5e-04 0.56 9 12.0 1.3
CUTC -0.67 6.5 11 7.8e-04 0.56 10 12.0 1.2
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 1 0.7 0.70
AP5Z1 -1.20 6.3 19 1.5e-05 0.060 2 0.8 0.40
SLC25A39 0.85 7.5 16 5.2e-05 0.089 3 1.4 0.47
LGALS3 3.10 6.6 16 5.7e-05 0.089 4 1.5 0.38
CTTNBP2NL 1.70 6.4 16 6.3e-05 0.089 5 1.7 0.34
FUOM -1.10 6.4 16 6.5e-05 0.089 6 1.7 0.28
DMTF1 1.70 6.3 16 1.8e-04 0.150 7 3.0 0.43
S100A10 3.10 6.9 14 1.9e-04 0.150 8 3.2 0.40
NDUFB2 0.50 8.7 14 2.0e-04 0.150 9 3.5 0.39
TMSB10 0.68 12.0 14 2.0e-04 0.150 10 3.6 0.36
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 1 1.4 1.40
OPTN 2.1 6.4 18 2.2e-05 0.079 2 1.6 0.80
KRT18 3.6 7.1 17 3.8e-05 0.079 3 2.2 0.73
S100A10 3.4 6.9 17 3.9e-05 0.079 4 2.3 0.58
LPP 1.5 6.7 15 1.4e-04 0.220 5 4.0 0.80
TENM3 1.4 6.6 14 2.0e-04 0.240 6 4.8 0.80
EPN2 1.6 6.3 16 2.1e-04 0.240 7 4.9 0.70
RPS6KA3 1.5 6.3 16 3.4e-04 0.300 8 6.7 0.84
EFCC1 1.5 6.3 13 3.4e-04 0.300 9 6.7 0.74
LGALS3 2.5 6.6 13 3.8e-04 0.300 10 7.2 0.72
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 1 1.4 1.40
GEMIN2 -1.1 6.7 13 3.5e-04 0.51 2 5.1 2.60
ALKBH8 -1.3 6.2 15 3.6e-04 0.51 3 5.1 1.70
MAP3K4 -1.3 6.3 13 3.9e-04 0.51 4 5.4 1.40
GINM1 2.1 6.5 12 4.1e-04 0.51 5 5.6 1.10
FAM35A -1.4 6.2 16 4.7e-04 0.51 6 5.9 0.98
YJEFN3 -1.4 6.2 14 4.9e-04 0.51 7 6.0 0.86
GRK4 -1.3 6.2 14 5.0e-04 0.51 8 6.1 0.76
JOSD2 2.1 6.3 12 7.1e-04 0.62 9 8.5 0.94
STK24 -1.1 6.5 11 8.2e-04 0.62 10 9.2 0.92
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 1 3.5 3.5
ZMYND11 2.6 6.4 12 0.00057 0.76 2 6.3 3.2
NCSTN 2.3 6.6 11 0.00073 0.76 3 7.7 2.6
CNRIP1 -1.3 6.6 11 0.00077 0.76 4 8.2 2.0
GMCL1 2.5 6.4 11 0.00079 0.76 5 8.4 1.7
FAM161A 2.4 6.7 11 0.00086 0.76 6 9.5 1.6
BIN1 -1.3 6.6 10 0.00130 0.76 7 14.0 2.0
B4GALT5 2.3 6.4 10 0.00150 0.76 8 16.0 2.0
BET1 1.8 6.8 10 0.00160 0.76 9 17.0 1.9
UCKL1 2.3 6.4 11 0.00160 0.76 10 17.0 1.7
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 1 3.3 3.30
OSGIN1 -1.6 6.6 16 5.8e-05 0.16 2 3.4 1.70
RNF168 2.3 6.5 16 5.8e-05 0.16 3 3.4 1.10
RAB8A 1.6 6.9 15 1.2e-04 0.16 4 4.4 1.10
CCDC28B 2.1 6.6 15 1.2e-04 0.16 5 4.4 0.88
DCLK1 2.2 6.3 15 1.4e-04 0.16 6 4.4 0.73
CSNK1D 1.4 7.1 14 1.5e-04 0.16 7 4.5 0.64
PRR5 2.2 6.3 15 1.6e-04 0.16 8 4.6 0.58
QPRT 2.8 6.7 13 2.5e-04 0.22 9 6.1 0.68
SLC2A3 2.0 6.5 13 3.5e-04 0.29 10 7.6 0.76
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 1 1.4 1.4
MARCH9 2.2 6.3 17 9.3e-05 0.38 2 2.8 1.4
TP53I3 -1.2 6.8 14 2.0e-04 0.53 3 4.8 1.6
GPT2 1.7 6.7 13 3.4e-04 0.53 4 6.7 1.7
RECQL 2.0 6.3 14 3.8e-04 0.53 5 7.2 1.4
NCSTN 1.7 6.6 13 3.9e-04 0.53 6 7.4 1.2
DEDD -1.1 6.4 12 4.8e-04 0.55 7 8.7 1.2
BCHE 1.9 6.3 13 5.7e-04 0.55 8 9.4 1.2
LRP3 1.9 6.3 14 6.3e-04 0.55 9 10.0 1.1
ARHGAP1 1.8 6.3 14 8.0e-04 0.55 10 13.0 1.3
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] "LINC00637_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
HSP90AA1 -0.82 10.0 67 3.0e-16 2.4e-12 1 0.0 0.00
HSPH1 -0.81 7.2 26 3.6e-07 1.5e-03 2 1.0 0.50
SPP1 2.70 6.9 17 3.9e-05 1.0e-01 3 2.7 0.90
HSPD1 -0.38 9.6 16 7.3e-05 1.5e-01 4 3.4 0.85
RXRA -0.97 6.3 18 1.1e-04 1.8e-01 5 3.8 0.76
NEFM -1.00 7.5 15 1.3e-04 1.8e-01 6 4.2 0.70
FKBP1B 1.00 6.6 13 3.0e-04 3.5e-01 7 7.7 1.10
SPECC1L 1.30 6.3 16 3.8e-04 3.8e-01 8 8.0 1.00
CAMKK2 1.30 6.2 17 4.4e-04 4.0e-01 9 9.2 1.00
PPRC1 1.10 6.4 12 5.2e-04 4.0e-01 10 10.0 1.00
1e-04 NA NA NA NA NA 4 3.7 0.92
1e-05 NA NA NA NA NA 2 2.0 1.00
1e-06 NA NA NA NA NA 2 1.2 0.60
1e-07 NA NA NA NA NA 1 0.5 0.50
1e-08 NA NA NA NA NA 1 0.4 0.40
1e-09 NA NA NA NA NA 1 0.3 0.30
1e-10 NA NA NA NA NA 1 0.1 0.10
[1] "LINC00637_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
GDF15 -1.6 6.6 26 2.9e-07 0.0023 1 1.9 1.9
TP53I3 -1.1 6.8 17 4.0e-05 0.1600 2 5.1 2.6
TMEM200C 1.6 6.2 21 8.5e-05 0.1600 3 6.3 2.1
STAG2 1.5 6.5 15 8.9e-05 0.1600 4 6.4 1.6
SRFBP1 1.5 6.5 15 9.6e-05 0.1600 5 6.7 1.3
TUBA1C 2.1 6.8 14 1.8e-04 0.2500 6 8.5 1.4
COASY 1.2 6.6 13 3.0e-04 0.3500 7 11.0 1.5
KCTD9 1.4 6.4 13 3.6e-04 0.3700 8 12.0 1.4
UHMK1 1.3 6.5 12 4.7e-04 0.4200 9 14.0 1.5
NCK2 1.4 6.3 13 5.4e-04 0.4200 10 15.0 1.5
1e-04 NA NA NA NA NA 5 6.8 1.4
1e-05 NA NA NA NA NA 1 3.5 3.5
1e-06 NA NA NA NA NA 1 2.1 2.1
1e-07 NA NA NA NA NA 0 1.9 Inf
1e-08 NA NA NA NA NA 0 1.3 Inf
1e-09 NA NA NA NA NA 0 0.9 Inf
1e-10 NA NA NA NA NA 0 0.8 Inf
[1] "LINC00637_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
GADD45G 3.1 7.5 25 6.0e-07 0.0049 1 0.6 0.60
MIAT 1.9 7.0 19 1.1e-05 0.0320 2 1.3 0.65
CDKN1C 2.1 6.8 19 1.2e-05 0.0320 3 1.3 0.43
CDC25A 1.2 6.4 18 2.9e-05 0.0540 4 1.9 0.48
ZNHIT6 -0.8 6.5 17 3.3e-05 0.0540 5 1.9 0.38
TPM2 -1.0 7.2 15 1.1e-04 0.1400 6 2.9 0.48
DLL3 1.9 7.0 15 1.2e-04 0.1400 7 3.0 0.43
SMOC1 1.1 7.0 14 1.7e-04 0.1800 8 3.5 0.44
ATOH8 1.1 6.3 14 2.5e-04 0.2300 9 4.8 0.53
DIO3 1.2 7.0 13 3.0e-04 0.2400 10 5.2 0.52
1e-04 NA NA NA NA NA 5 2.8 0.56
1e-05 NA NA NA NA NA 1 1.3 1.30
1e-06 NA NA NA NA NA 1 0.7 0.70
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 0.2 Inf
[1] "LOC100507431_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
S100A16 -1.70 6.5 26 3.5e-07 0.0021 1 0.2 0.20
GADD45G -2.30 7.5 25 5.1e-07 0.0021 2 0.2 0.10
THAP5 -1.50 6.3 20 1.2e-05 0.0320 3 1.6 0.53
CCND2 -1.40 6.9 18 2.7e-05 0.0550 4 1.9 0.48
CDKN1C -1.80 6.8 17 3.6e-05 0.0590 5 2.0 0.40
TPM2 -1.70 7.2 15 1.1e-04 0.1300 6 3.6 0.60
ANAPC10 2.40 6.4 16 1.1e-04 0.1300 7 3.6 0.51
SIGIRR 2.30 6.4 13 2.9e-04 0.3000 8 7.5 0.94
JOSD1 2.20 6.3 14 3.4e-04 0.3100 9 8.3 0.92
C4orf48 0.96 7.9 13 3.9e-04 0.3200 10 9.3 0.93
1e-04 NA NA NA NA NA 5 3.5 0.70
1e-05 NA NA NA NA NA 2 1.5 0.75
1e-06 NA NA NA NA NA 2 0.5 0.25
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] "LOC100507431_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
LGALS3 -2.2 6.6 51 8.7e-13 7.0e-09 1 0.2 0.20
TIMP2 -1.7 6.3 49 3.0e-12 1.2e-08 2 0.3 0.15
S100A16 -1.5 6.5 33 1.1e-08 3.0e-05 3 0.6 0.20
S100A13 -1.2 6.9 24 1.2e-06 2.4e-03 4 1.5 0.38
ANKRD1 -1.4 6.5 20 7.5e-06 1.2e-02 5 2.1 0.42
FNDC3B -1.1 6.4 20 8.7e-06 1.2e-02 6 2.2 0.37
HTRA1 -1.1 6.3 16 7.8e-05 9.0e-02 7 4.0 0.57
AK1 1.8 6.2 19 9.2e-05 9.4e-02 8 4.2 0.52
SLC36A4 1.4 6.5 14 2.0e-04 1.8e-01 9 6.1 0.68
BAIAP2-AS1 1.6 6.2 18 2.5e-04 1.8e-01 10 7.4 0.74
1e-04 NA NA NA NA NA 8 4.3 0.54
1e-05 NA NA NA NA NA 6 2.2 0.37
1e-06 NA NA NA NA NA 3 1.5 0.50
1e-07 NA NA NA NA NA 3 1.2 0.40
1e-08 NA NA NA NA NA 2 0.6 0.30
1e-09 NA NA NA NA NA 2 0.5 0.25
1e-10 NA NA NA NA NA 2 0.3 0.15
[1] "LOC100507431_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
DDIT4 -1.00 7.9 22 3.4e-06 0.016 1 1.0 1.00
HERPUD1 -0.97 7.1 21 4.0e-06 0.016 2 1.0 0.50
PCK2 -1.00 6.4 19 1.6e-05 0.043 3 1.4 0.47
ATF5 -1.00 6.9 18 2.5e-05 0.050 4 1.6 0.40
TRIB3 -1.00 7.1 15 1.4e-04 0.230 5 3.8 0.76
SPP1 -1.10 6.9 13 3.1e-04 0.340 6 6.6 1.10
WARS -0.68 7.3 13 3.1e-04 0.340 7 6.6 0.94
RAP2A 1.10 6.2 16 3.9e-04 0.340 8 7.4 0.92
KCTD9 -0.75 6.4 13 4.0e-04 0.340 9 7.4 0.82
CEBPB -0.88 6.8 12 4.3e-04 0.340 10 7.8 0.78
1e-04 NA NA NA NA NA 4 2.9 0.72
1e-05 NA NA NA NA NA 2 1.3 0.65
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 0.3 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 1 0.1 0.10
STMN2 -2.00 7.1 29 7.4e-08 0.0003 2 0.1 0.05
SH3KBP1 -1.20 6.3 19 1.4e-05 0.0390 3 1.1 0.37
PLCD1 -1.10 6.3 18 1.9e-05 0.0390 4 1.1 0.28
SCML1 -0.97 6.5 16 5.6e-05 0.0910 5 1.5 0.30
FNDC3A 1.30 6.6 15 1.0e-04 0.1400 6 2.3 0.38
SPP1 -1.40 6.9 15 1.2e-04 0.1400 7 2.5 0.36
PSMB7 0.45 9.1 14 1.5e-04 0.1500 8 2.8 0.35
DHX8 1.50 6.2 20 2.1e-04 0.1900 9 3.6 0.40
CTNNA1 0.80 7.2 13 2.8e-04 0.2200 10 4.7 0.47
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 1 0.7 0.70
SLC7A11 1.70 6.6 19 1.6e-05 0.063 2 0.8 0.40
CHAC1 1.70 6.4 17 4.2e-05 0.091 3 1.5 0.50
NQO1 1.60 7.4 17 4.5e-05 0.091 4 1.6 0.40
NAT9 0.98 6.7 16 6.7e-05 0.110 5 2.1 0.42
AGPS 1.20 6.3 16 1.0e-04 0.140 6 3.1 0.52
MRPS34 -0.40 8.4 14 1.5e-04 0.160 7 3.7 0.53
ATF5 1.40 6.9 14 1.6e-04 0.160 8 3.8 0.48
ARHGEF2 1.20 6.3 15 2.0e-04 0.180 9 4.2 0.47
FHL1 -0.60 7.1 13 2.9e-04 0.240 10 5.9 0.59
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 1 0.8
CMTM8 -2.1 6.3 17.0 4.5e-05 0.180 2 1.9
ACBD3 -1.6 6.6 13.0 3.8e-04 0.760 3 4.5
FNBP4 3.4 6.7 13.0 3.9e-04 0.760 4 4.5
PLGRKT 3.4 6.7 12.0 6.6e-04 0.760 5 6.4
KIF5C 2.5 7.2 11.0 1.1e-03 0.760 6 9.7
RIF1 3.3 6.7 10.0 1.2e-03 0.760 7 10.0
METTL15 -1.8 6.2 13.0 1.3e-03 0.760 8 10.0
PPP2R1B 3.0 6.6 10.0 1.6e-03 0.760 9 13.0
RQCD1 3.1 6.6 9.9 1.7e-03 0.760 10 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 0.80
CMTM8 0.95
ACBD3 1.50
FNBP4 1.10
PLGRKT 1.30
KIF5C 1.60
RIF1 1.50
METTL15 1.30
PPP2R1B 1.40
RQCD1 1.30
1e-04 1.40
1e-05 0.90
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 1 2.4 2.4
YWHAZ 0.51 8.3 14 1.5e-04 0.58 2 3.1 1.6
HERPUD2 -0.86 6.3 14 2.4e-04 0.58 3 4.0 1.3
LGALS3 1.90 6.6 13 3.9e-04 0.58 4 5.4 1.4
ABHD5 1.20 6.4 13 4.4e-04 0.58 5 5.9 1.2
DPH2 0.87 6.8 12 5.7e-04 0.58 6 7.3 1.2
APMAP 0.60 7.3 11 7.2e-04 0.58 7 8.9 1.3
CORO1C 0.92 6.6 11 8.3e-04 0.58 8 10.0 1.3
SLC12A9 1.20 6.3 14 9.2e-04 0.58 9 11.0 1.2
RBM45 -0.85 6.2 13 9.9e-04 0.58 10 11.0 1.1
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 1 1.1 1.10
SLC30A6 1.70 6.3 23 4.1e-05 0.16 2 1.1 0.55
RCAN1 -1.00 6.5 14 1.9e-04 0.41 3 3.5 1.20
TOMM5 -0.87 6.6 14 2.2e-04 0.41 4 3.8 0.95
PATL1 -1.00 6.3 16 2.5e-04 0.41 5 4.2 0.84
HAUS6 1.30 6.5 13 3.5e-04 0.47 6 5.3 0.88
NDEL1 1.40 6.3 14 4.7e-04 0.53 7 6.4 0.91
KHDRBS3 1.40 6.4 12 5.5e-04 0.53 8 7.4 0.92
SAMD1 1.40 6.3 13 6.3e-04 0.53 9 7.9 0.88
PRKAB1 1.10 6.7 11 7.8e-04 0.53 10 9.7 0.97
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 1 3.1 3.10
IER3 -0.81 6.3 13 0.00030 0.48 2 5.6 2.80
LCMT2 -0.83 6.2 17 0.00032 0.48 3 5.9 2.00
TUBB2A -0.51 8.8 13 0.00035 0.48 4 6.5 1.60
NDUFB11 0.27 9.1 13 0.00037 0.48 5 6.5 1.30
SOD2 0.96 6.4 13 0.00044 0.48 6 6.8 1.10
S100A16 -0.75 6.6 12 0.00046 0.48 7 6.9 0.99
ZNF660 1.10 6.2 16 0.00052 0.48 8 7.2 0.90
TTLL5 1.10 6.2 16 0.00059 0.48 9 8.2 0.91
DST -0.66 6.6 12 0.00059 0.48 10 8.3 0.83
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
[1] "NAB2_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
DDX10 -1.30 6.5 30 5.7e-08 0.00046 1 1.2 1.20
PRPF39 1.70 6.2 24 1.9e-05 0.07300 2 3.2 1.60
ZBTB20 -1.10 6.4 18 2.7e-05 0.07300 3 3.6 1.20
WNT7B 1.70 6.5 15 8.7e-05 0.14000 4 5.0 1.20
CUEDC1 1.40 6.4 15 8.9e-05 0.14000 5 5.0 1.00
PRKAB1 1.20 6.7 14 1.6e-04 0.21000 6 5.6 0.93
TBKBP1 1.50 6.3 17 2.1e-04 0.24000 7 6.3 0.90
EIF2B2 0.94 6.9 13 3.0e-04 0.30000 8 7.4 0.92
TMEM248 1.20 6.5 13 4.0e-04 0.36000 9 9.0 1.00
EEF2KMT 1.00 6.7 12 5.5e-04 0.38000 10 11.0 1.10
1e-04 NA NA NA NA NA 5 5.1 1.00
1e-05 NA NA NA NA NA 1 2.6 2.60
1e-06 NA NA NA NA NA 1 1.6 1.60
1e-07 NA NA NA NA NA 1 1.3 1.30
1e-08 NA NA NA NA NA 0 1.1 Inf
1e-09 NA NA NA NA NA 0 1.0 Inf
1e-10 NA NA NA NA NA 0 0.9 Inf
[1] "NAB2_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CLU -1.80 7.3 64 1.7e-15 1.4e-11 1 0.1 0.100
HIST1H2AC -1.60 6.3 33 7.8e-09 3.2e-05 2 0.2 0.100
S100A10 -1.90 6.9 32 1.6e-08 3.3e-05 3 0.2 0.067
DTNA -1.50 6.3 32 1.6e-08 3.3e-05 4 0.2 0.050
LGALS3 -1.70 6.6 27 1.7e-07 2.8e-04 5 0.2 0.040
GNG3 -1.50 6.3 26 3.8e-07 4.8e-04 6 0.2 0.033
STMN2 -2.20 7.1 26 4.1e-07 4.8e-04 7 0.2 0.029
PTGR1 -1.40 6.3 25 7.4e-07 7.5e-04 8 0.2 0.025
NQO1 -1.50 7.4 23 2.1e-06 1.9e-03 9 0.2 0.022
FTH1 -0.98 12.0 21 4.6e-06 3.7e-03 10 0.3 0.030
1e-04 NA NA NA NA NA 18 2.5 0.140
1e-05 NA NA NA NA NA 10 0.4 0.040
1e-06 NA NA NA NA NA 8 0.2 0.025
1e-07 NA NA NA NA NA 4 0.2 0.050
1e-08 NA NA NA NA NA 2 0.2 0.100
1e-09 NA NA NA NA NA 1 0.2 0.200
1e-10 NA NA NA NA NA 1 0.1 0.100
[1] "NAB2_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
PAK3 -1.5 6.3 23 1.8e-06 0.014 1 0.7 0.70
SLC19A1 1.9 6.3 19 7.3e-05 0.300 2 3.1 1.60
IRF2BP1 1.7 6.3 15 2.6e-04 0.420 3 5.9 2.00
RANBP9 1.7 6.2 17 2.7e-04 0.420 4 6.1 1.50
PPP1R14C -1.2 6.6 13 3.5e-04 0.420 5 6.9 1.40
APPL2 1.7 6.2 17 3.8e-04 0.420 6 7.4 1.20
ZNF331 -1.0 6.3 13 4.3e-04 0.420 7 7.8 1.10
GTF3C4 1.5 6.4 12 4.4e-04 0.420 8 7.9 0.99
NT5M -1.1 6.2 16 4.6e-04 0.420 9 8.2 0.91
TMCO3 1.5 6.4 12 5.9e-04 0.450 10 9.3 0.93
1e-04 NA NA NA NA NA 2 3.3 1.60
1e-05 NA NA NA NA NA 1 1.3 1.30
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 0.1 Inf
1e-09 NA NA NA NA NA 0 0.0 NaN
1e-10 NA NA NA NA NA 0 0.0 NaN
[1] "neg_CTRL_00018_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
FAM181B -1.9 6.3 33 1.2e-08 9.7e-05 1 0.4 0.40
SCPEP1 2.3 6.4 15 1.2e-04 2.3e-01 2 2.7 1.40
FTL 2.0 12.0 15 1.3e-04 2.3e-01 3 3.2 1.10
ZBTB20 2.6 6.4 14 1.5e-04 2.3e-01 4 3.2 0.80
CDC45 -1.3 6.4 14 1.6e-04 2.3e-01 5 3.8 0.76
RPUSD2 2.3 6.4 16 1.7e-04 2.3e-01 6 4.2 0.70
BRI3 1.0 8.4 13 2.9e-04 3.3e-01 7 5.6 0.80
CSRNP3 2.2 6.3 13 3.4e-04 3.3e-01 8 6.7 0.84
GAP43 2.2 8.1 13 3.6e-04 3.3e-01 9 6.9 0.77
WDR76 -1.3 6.4 12 4.1e-04 3.3e-01 10 7.5 0.75
1e-04 NA NA NA NA NA 1 2.5 2.50
1e-05 NA NA NA NA NA 1 1.2 1.20
1e-06 NA NA NA NA NA 1 0.8 0.80
1e-07 NA NA NA NA NA 1 0.4 0.40
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] "neg_CTRL_00022_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ADAM9 -1.20 6.3 18 4.1e-05 0.33 1 1.8 1.8
NEFM -1.30 7.5 14 1.8e-04 0.48 2 4.7 2.3
PDLIM2 1.10 7.4 13 2.4e-04 0.48 3 6.6 2.2
ZBTB22 1.60 6.2 18 3.5e-04 0.48 4 8.1 2.0
STMN2 -1.60 7.1 13 4.1e-04 0.48 5 8.9 1.8
ATAD2 -0.99 6.5 13 4.1e-04 0.48 6 8.9 1.5
VGF -1.20 6.6 12 4.4e-04 0.48 7 9.3 1.3
SMOX -0.99 6.5 12 4.7e-04 0.48 8 10.0 1.2
ARAF 1.40 6.5 12 6.1e-04 0.55 9 12.0 1.3
KHNYN 1.50 6.2 17 8.0e-04 0.59 10 14.0 1.4
1e-04 NA NA NA NA NA 1 2.7 2.7
1e-05 NA NA NA NA NA 0 1.3 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 0.1 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "neg_EGFP_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC -3.5 6.7 42.0 1.0e-10 8.2e-07 1 0.1 0.10
SLF2 -2.3 6.3 23.0 4.9e-06 2.0e-02 2 0.8 0.40
CHCHD10 -1.4 7.7 15.0 1.3e-04 3.6e-01 3 2.4 0.80
ATF7IP2 -1.9 6.4 13.0 3.1e-04 6.4e-01 4 3.2 0.80
ROCK1 3.4 6.7 11.0 9.4e-04 7.8e-01 5 7.1 1.40
KLHL9 -1.7 6.5 11.0 1.1e-03 7.8e-01 6 7.3 1.20
ID3 -2.0 7.9 10.0 1.2e-03 7.8e-01 7 8.2 1.20
CNBD2 -1.8 6.3 11.0 1.8e-03 7.8e-01 8 10.0 1.30
PPP1R1A 3.9 6.9 9.7 1.9e-03 7.8e-01 9 11.0 1.20
COQ4 -1.1 7.2 9.7 1.9e-03 7.8e-01 10 11.0 1.10
1e-04 NA NA NA NA NA 2 1.8 0.90
1e-05 NA NA NA NA NA 2 1.1 0.55
1e-06 NA NA NA NA NA 1 0.8 0.80
1e-07 NA NA NA NA NA 1 0.4 0.40
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] "neg_EGFP_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
PPP3CA 2.00 6.3 21 1.7e-05 0.13 1 2.0 2.00
UBE2E2 1.60 6.6 15 8.7e-05 0.23 2 3.0 1.50
TAX1BP1 0.98 7.3 15 1.2e-04 0.23 3 3.6 1.20
SYMPK 1.50 6.6 14 1.4e-04 0.23 4 3.8 0.95
C1orf56 1.70 6.2 16 2.4e-04 0.23 5 5.3 1.10
FLRT3 1.70 6.2 16 2.7e-04 0.23 6 5.4 0.90
ATAD5 -1.00 6.5 13 2.8e-04 0.23 7 5.4 0.77
C19orf10 0.71 8.4 13 2.8e-04 0.23 8 5.5 0.69
CBL 1.60 6.4 13 3.1e-04 0.23 9 5.9 0.66
NEFM 2.00 7.5 13 3.2e-04 0.23 10 6.0 0.60
1e-04 NA NA NA NA NA 2 3.2 1.60
1e-05 NA NA NA NA NA 0 1.9 Inf
1e-06 NA NA NA NA NA 0 1.2 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 0.3 Inf
[1] "neg_EGFP_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC -2.90 6.7 140 3.9e-32 3.2e-28 1 0.0 0.00
ARF4 -0.70 8.2 22 3.1e-06 1.2e-02 2 1.3 0.65
PTRF -1.10 6.7 14 1.4e-04 3.9e-01 3 3.2 1.10
NCAPG 1.40 6.5 13 2.8e-04 4.8e-01 4 4.7 1.20
SPTY2D1 -0.91 6.3 13 3.0e-04 4.8e-01 5 4.7 0.94
SAMD4A 1.40 6.2 15 5.2e-04 6.5e-01 6 7.4 1.20
TGDS -0.91 6.3 13 6.6e-04 6.5e-01 7 9.6 1.40
SPIN2B -0.89 6.3 12 7.7e-04 6.5e-01 8 11.0 1.30
NDC80 1.40 6.6 11 8.0e-04 6.5e-01 9 11.0 1.20
FBN2 1.30 6.3 13 8.2e-04 6.5e-01 10 11.0 1.10
1e-04 NA NA NA NA NA 2 2.6 1.30
1e-05 NA NA NA NA NA 2 1.8 0.90
1e-06 NA NA NA NA NA 1 1.1 1.10
1e-07 NA NA NA NA NA 1 0.7 0.70
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 1 0.5 0.50
[1] "NGEF_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SKP1 0.78 8.9 16 5.9e-05 0.48 1 1.4 1.4
HSD17B10 0.98 7.9 13 3.9e-04 0.65 2 4.1 2.0
TTC39C -1.40 6.3 12 4.3e-04 0.65 3 4.3 1.4
CNTROB -1.60 6.2 16 4.4e-04 0.65 4 4.5 1.1
AKAP8L 2.70 6.5 12 6.1e-04 0.65 5 6.1 1.2
MRPL49 1.50 7.3 11 8.7e-04 0.65 6 7.9 1.3
PIDD1 2.60 6.4 11 8.7e-04 0.65 7 7.9 1.1
PHLDA3 2.00 7.8 11 9.1e-04 0.65 8 8.4 1.0
PARD6A 2.40 6.4 11 1.0e-03 0.65 9 10.0 1.2
TMEM167A 1.10 7.5 11 1.2e-03 0.65 10 11.0 1.1
1e-04 NA NA NA NA NA 1 1.9 1.9
1e-05 NA NA NA NA NA 0 0.9 Inf
1e-06 NA NA NA NA NA 0 0.2 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] "NGEF_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
PIF1 -3.2 6.4 17.0 3.8e-05 0.29 1 1.0
BORA -2.8 6.3 15.0 9.2e-05 0.29 2 1.3
C2orf69 -2.6 6.5 15.0 1.2e-04 0.29 3 1.4
TTK -2.7 6.3 15.0 1.4e-04 0.29 4 1.8
RP11-343C2.12 -2.5 6.2 13.0 5.4e-04 0.79 5 3.9
CDCA2 -2.6 6.4 12.0 6.4e-04 0.79 6 4.3
ZXDC -2.4 6.3 11.0 1.1e-03 0.79 7 6.8
EMG1 -1.8 7.5 11.0 1.2e-03 0.79 8 7.4
FAM83D -2.6 6.4 10.0 1.4e-03 0.79 9 7.8
MSANTD2 -2.3 6.3 9.8 1.7e-03 0.79 10 9.3
1e-04 NA NA NA NA NA 2 1.3
1e-05 NA NA NA NA NA 0 0.7
1e-06 NA NA NA NA NA 0 0.5
1e-07 NA NA NA NA NA 0 0.1
1e-08 NA NA NA NA NA 0 0.1
1e-09 NA NA NA NA NA 0 0.1
1e-10 NA NA NA NA NA 0 0.1
EmpiricalFDR
PIF1 1.00
BORA 0.65
C2orf69 0.47
TTK 0.45
RP11-343C2.12 0.78
CDCA2 0.72
ZXDC 0.97
EMG1 0.92
FAM83D 0.87
MSANTD2 0.93
1e-04 0.65
1e-05 Inf
1e-06 Inf
1e-07 Inf
1e-08 Inf
1e-09 Inf
1e-10 Inf
[1] "PBRM1_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
CDC25B -2.5 6.9 20 8.5e-06 0.069 1 2.4
RP11-339B21.12 -2.4 6.7 18 2.2e-05 0.091 2 3.2
RP11-32K4.2 -2.3 6.2 16 9.6e-05 0.260 3 4.5
NDC80 -2.2 6.6 14 2.3e-04 0.450 4 6.9
DLL1 -2.6 6.8 13 2.8e-04 0.450 5 7.4
PLK1 -2.3 7.4 13 3.7e-04 0.500 6 9.3
YWHAB 1.5 8.7 12 4.5e-04 0.520 7 10.0
JUN -1.7 7.8 12 6.8e-04 0.690 8 12.0
CHEK2 -2.1 6.3 11 7.7e-04 0.700 9 12.0
SMARCAL1 -2.0 6.3 11 1.1e-03 0.760 10 15.0
1e-04 NA NA NA NA NA 3 4.6
1e-05 NA NA NA NA NA 1 2.4
1e-06 NA NA NA NA NA 0 1.6
1e-07 NA NA NA NA NA 0 1.1
1e-08 NA NA NA NA NA 0 0.7
1e-09 NA NA NA NA NA 0 0.4
1e-10 NA NA NA NA NA 0 0.2
EmpiricalFDR
CDC25B 2.4
RP11-339B21.12 1.6
RP11-32K4.2 1.5
NDC80 1.7
DLL1 1.5
PLK1 1.6
YWHAB 1.5
JUN 1.5
CHEK2 1.4
SMARCAL1 1.5
1e-04 1.5
1e-05 2.4
1e-06 Inf
1e-07 Inf
1e-08 Inf
1e-09 Inf
1e-10 Inf
[1] "PBRM1_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CD9 -1.6 6.5 14 0.00016 0.52 1 3.2 3.2
EFCAB11 -1.5 6.2 17 0.00017 0.52 2 3.4 1.7
RP4-758J18.2 2.4 6.6 14 0.00019 0.52 3 3.7 1.2
EDNRB -1.4 6.3 12 0.00041 0.62 4 6.0 1.5
NRDE2 -1.3 6.3 12 0.00046 0.62 5 6.6 1.3
TFPT 2.1 6.7 12 0.00050 0.62 6 6.9 1.2
IFITM3 -1.5 8.5 12 0.00058 0.62 7 7.9 1.1
AZI2 1.8 6.7 11 0.00083 0.62 8 10.0 1.3
INTU -1.2 6.7 11 0.00091 0.62 9 11.0 1.2
TMEM14A -1.1 6.7 11 0.00096 0.62 10 12.0 1.2
1e-04 NA NA NA NA NA 0 1.9 Inf
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] "PBRM1_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TPPP3 -3.3 6.3 43 6.3e-11 5.1e-07 1 0.3 0.30
TPM2 -3.5 7.1 32 1.8e-08 7.4e-05 2 0.6 0.30
SPARC -1.5 8.5 18 2.1e-05 4.7e-02 3 2.4 0.80
CEBPD -2.6 6.4 18 2.3e-05 4.7e-02 4 2.4 0.60
HDAC2 2.1 8.5 17 4.4e-05 7.2e-02 5 2.6 0.52
HEBP1 -2.0 6.7 16 7.6e-05 1.0e-01 6 3.2 0.53
PNP -2.3 6.3 14 1.4e-04 1.7e-01 7 3.9 0.56
CCND2 -2.2 6.9 14 2.4e-04 2.4e-01 8 4.7 0.59
LRRC47 4.4 7.2 13 3.0e-04 2.6e-01 9 6.0 0.67
SESN3 -2.2 6.4 13 3.4e-04 2.6e-01 10 6.1 0.61
1e-04 NA NA NA NA NA 6 3.4 0.57
1e-05 NA NA NA NA NA 2 1.9 0.95
1e-06 NA NA NA NA NA 2 1.1 0.55
1e-07 NA NA NA NA NA 2 0.8 0.40
1e-08 NA NA NA NA NA 1 0.4 0.40
1e-09 NA NA NA NA NA 1 0.4 0.40
1e-10 NA NA NA NA NA 1 0.3 0.30
[1] "PCDHA123_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SPP1 2.70 6.9 23 2.1e-06 0.017 1 1.4 1.40
RNF111 1.40 6.2 28 6.5e-06 0.024 2 1.6 0.80
BPNT1 1.40 6.3 24 9.0e-06 0.024 3 1.6 0.53
NUP58 0.95 6.5 13 2.5e-04 0.370 4 7.2 1.80
PFDN4 -0.40 8.1 13 2.6e-04 0.370 5 7.3 1.50
FSIP1 1.10 6.3 15 2.7e-04 0.370 6 7.5 1.20
SIAH1 0.83 6.6 12 4.7e-04 0.520 7 9.6 1.40
RAB33A -0.77 6.3 12 5.1e-04 0.520 8 10.0 1.20
FANCA 0.93 6.5 12 6.1e-04 0.550 9 11.0 1.20
ZCCHC7 0.90 6.4 12 7.1e-04 0.580 10 11.0 1.10
1e-04 NA NA NA NA NA 3 4.6 1.50
1e-05 NA NA NA NA NA 3 1.6 0.53
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 0.5 Inf
1e-09 NA NA NA NA NA 0 0.5 Inf
1e-10 NA NA NA NA NA 0 0.3 Inf
[1] "PCDHA123_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
LGALS3 -1.30 6.6 27 2.0e-07 0.0017 1 0.7 0.70
SNAPC1 -0.90 6.5 19 1.2e-05 0.0410 2 1.7 0.85
CTGF -0.82 8.2 19 1.5e-05 0.0410 3 1.7 0.57
MYC 1.80 6.7 17 4.8e-05 0.0980 4 2.4 0.60
CYR61 -0.64 7.7 14 1.5e-04 0.2100 5 3.8 0.76
NAT8L 1.00 6.3 17 1.5e-04 0.2100 6 3.9 0.65
PHF12 1.10 6.3 19 1.9e-04 0.2200 7 4.7 0.67
GPR107 0.98 6.3 15 2.8e-04 0.2900 8 5.6 0.70
TMEM194A 0.97 6.2 16 5.4e-04 0.4700 9 8.4 0.93
AKT3 0.93 6.3 15 6.7e-04 0.4700 10 9.9 0.99
1e-04 NA NA NA NA NA 4 3.0 0.75
1e-05 NA NA NA NA NA 1 1.7 1.70
1e-06 NA NA NA NA NA 1 0.7 0.70
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] "PCDHA123_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
FAM105A -0.88 6.3 21 2.9e-05 0.23 1 3.1 3.1
MYC 1.80 6.7 16 5.7e-05 0.23 2 4.1 2.0
SOX4 0.84 8.6 15 1.3e-04 0.33 3 5.4 1.8
CMTM8 -0.79 6.4 14 2.0e-04 0.33 4 6.3 1.6
ARHGEF9 1.00 6.3 16 2.0e-04 0.33 5 6.3 1.3
PTPN11 -0.63 6.5 12 5.6e-04 0.51 6 11.0 1.8
HIST1H2AC 1.00 6.3 12 6.5e-04 0.51 7 11.0 1.6
SERPINH1 -0.44 7.6 11 7.8e-04 0.51 8 13.0 1.6
CDKN1C 1.30 6.9 11 8.1e-04 0.51 9 13.0 1.5
SMIM8 -0.59 6.5 11 9.0e-04 0.51 10 14.0 1.4
1e-04 NA NA NA NA NA 2 4.9 2.4
1e-05 NA NA NA NA NA 0 2.7 Inf
1e-06 NA NA NA NA NA 0 1.8 Inf
1e-07 NA NA NA NA NA 0 1.3 Inf
1e-08 NA NA NA NA NA 0 1.1 Inf
1e-09 NA NA NA NA NA 0 0.9 Inf
1e-10 NA NA NA NA NA 0 0.8 Inf
[1] "pos_SNAP91_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
HYOU1 -2.5 6.3 14.0 0.00024 0.77 1 6.0 6.0
TDG 4.5 7.3 12.0 0.00066 0.77 2 9.1 4.6
LLPH 4.3 7.2 11.0 0.00120 0.77 3 14.0 4.6
NHLRC3 -2.1 6.5 10.0 0.00150 0.77 4 17.0 4.2
TCF19 -2.2 6.3 9.5 0.00210 0.77 5 20.0 4.0
USP16 4.2 7.1 9.3 0.00230 0.77 6 22.0 3.6
EFCC1 -2.2 6.3 9.3 0.00240 0.77 7 22.0 3.2
CCAR1 2.8 7.5 9.0 0.00280 0.77 8 25.0 3.1
UPRT -2.4 6.2 12.0 0.00300 0.77 9 26.0 2.9
FOXB1 -1.9 6.7 8.7 0.00320 0.77 10 27.0 2.7
1e-04 NA NA NA NA NA 0 4.5 Inf
1e-05 NA NA NA NA NA 0 2.1 Inf
1e-06 NA NA NA NA NA 0 1.3 Inf
1e-07 NA NA NA NA NA 0 0.9 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] "pos_SNAP91_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
WDFY1 -1.80 6.3 53 3.2e-13 2.6e-09 1 0.1 0.1
GNG3 1.90 6.3 15 9.6e-05 3.2e-01 2 2.9 1.4
SLC25A17 1.60 6.5 15 1.2e-04 3.2e-01 3 3.5 1.2
ADI1 -0.82 7.0 14 2.0e-04 3.3e-01 4 5.0 1.2
PHYKPL 1.60 6.4 14 2.1e-04 3.3e-01 5 5.2 1.0
SPP1 3.40 6.9 13 3.1e-04 3.9e-01 6 7.1 1.2
SCARA3 1.70 6.2 17 3.4e-04 3.9e-01 7 7.2 1.0
ZFP62 1.60 6.3 14 5.1e-04 5.2e-01 8 9.5 1.2
COMMD10 1.30 6.6 12 6.6e-04 5.9e-01 9 10.0 1.2
LONP1 1.10 7.0 11 8.0e-04 6.5e-01 10 12.0 1.2
1e-04 NA NA NA NA NA 2 2.9 1.4
1e-05 NA NA NA NA NA 1 0.7 0.7
1e-06 NA NA NA NA NA 1 0.3 0.3
1e-07 NA NA NA NA NA 1 0.1 0.1
1e-08 NA NA NA NA NA 1 0.1 0.1
1e-09 NA NA NA NA NA 1 0.1 0.1
1e-10 NA NA NA NA NA 1 0.1 0.1
[1] "PPP1R16B_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NEFM -1.20 7.5 19 1.1e-05 0.092 1 2.0 2.0
CAV1 -1.00 7.2 15 8.5e-05 0.250 2 3.8 1.9
SRPK2 -0.58 7.2 15 9.2e-05 0.250 3 3.8 1.3
GNG3 -0.93 6.3 13 2.9e-04 0.500 4 6.2 1.6
ELMO1 1.20 6.3 13 3.1e-04 0.500 5 6.6 1.3
POLR3A 1.00 6.4 13 4.1e-04 0.560 6 7.9 1.3
ZNF273 1.10 6.3 13 5.2e-04 0.560 7 9.1 1.3
YIF1B 0.83 6.8 12 5.5e-04 0.560 8 9.4 1.2
CLUAP1 0.98 6.5 12 6.6e-04 0.590 9 11.0 1.2
FGF19 1.40 6.4 11 7.2e-04 0.590 10 12.0 1.2
1e-04 NA NA NA NA NA 3 4.0 1.3
1e-05 NA NA NA NA NA 0 1.8 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 0.5 Inf
1e-09 NA NA NA NA NA 0 0.5 Inf
1e-10 NA NA NA NA NA 0 0.4 Inf
[1] "PPP1R16B_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
GDF15 -1.7 6.5 25 4.8e-07 0.0029 1 0.5 0.50
DDX10 -1.2 6.5 25 7.3e-07 0.0029 2 0.5 0.25
HIST1H1C -1.4 6.4 22 2.3e-06 0.0062 3 1.1 0.37
GADD45G -1.6 7.5 18 1.9e-05 0.0390 4 1.5 0.38
CYP2R1 1.7 6.2 22 5.0e-05 0.0810 5 2.8 0.56
ALS2 -1.1 6.2 20 1.0e-04 0.1400 6 3.9 0.65
PMP22 1.6 6.4 12 4.9e-04 0.5700 7 10.0 1.40
CDKN2A 1.8 6.5 11 7.3e-04 0.7100 8 12.0 1.50
TAOK1 1.1 6.6 11 8.5e-04 0.7100 9 14.0 1.50
MPHOSPH9 1.4 6.3 13 8.7e-04 0.7100 10 14.0 1.40
1e-04 NA NA NA NA NA 5 3.9 0.78
1e-05 NA NA NA NA NA 3 1.4 0.47
1e-06 NA NA NA NA NA 2 0.6 0.30
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] "PPP1R16B_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
FST -1.30 6.4 24 1.2e-06 0.0055 1 0.6 0.60
STMN2 -1.80 7.1 23 1.4e-06 0.0055 2 0.6 0.30
PROM1 1.60 6.3 17 6.2e-05 0.1700 3 2.0 0.67
STK33 1.60 6.3 18 9.8e-05 0.2000 4 2.7 0.68
LIX1 1.70 6.5 15 1.2e-04 0.2000 5 3.0 0.60
VGF 1.80 6.6 14 2.3e-04 0.2600 6 4.8 0.80
FAM46A 1.50 6.3 13 2.6e-04 0.2600 7 5.0 0.71
GPC2 -0.97 6.5 13 3.1e-04 0.2600 8 5.7 0.71
LGALS3 2.30 6.6 13 3.1e-04 0.2600 9 5.8 0.64
FAM83D 1.60 6.4 13 3.5e-04 0.2600 10 6.5 0.65
1e-04 NA NA NA NA NA 4 2.8 0.70
1e-05 NA NA NA NA NA 2 0.9 0.45
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 0.4 Inf
1e-09 NA NA NA NA NA 0 0.4 Inf
1e-10 NA NA NA NA NA 0 0.4 Inf
[1] "RERE_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TSC22D4 1.50 6.4 20 8.4e-06 0.068 1 1.3 1.3
S100A10 2.20 6.9 14 1.6e-04 0.460 2 3.7 1.8
C1orf56 -0.96 6.2 16 1.7e-04 0.460 3 3.8 1.3
CCDC18 -0.86 6.3 13 2.6e-04 0.510 4 4.6 1.2
EIF1AD 1.20 6.4 13 3.8e-04 0.510 5 6.5 1.3
C6orf203 0.99 6.6 12 4.4e-04 0.510 6 7.2 1.2
RIOK3 1.10 6.5 12 4.6e-04 0.510 7 7.7 1.1
FSTL1 1.10 6.6 12 5.1e-04 0.510 8 8.2 1.0
KBTBD2 1.20 6.2 15 7.4e-04 0.530 9 11.0 1.3
EXOC1 1.10 6.4 11 8.8e-04 0.530 10 13.0 1.3
1e-04 NA NA NA NA NA 1 3.3 3.3
1e-05 NA NA NA NA NA 1 1.4 1.4
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 0.3 Inf
1e-09 NA NA NA NA NA 0 0.2 Inf
1e-10 NA NA NA NA NA 0 0.2 Inf
[1] "RERE_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SPP1 -1.70 6.9 34 5.2e-09 4.2e-05 1 0.9 0.90
TAGLN3 -1.30 7.0 25 6.5e-07 2.6e-03 2 1.9 0.95
FLNA 0.82 7.7 18 2.4e-05 6.2e-02 3 3.5 1.20
USMG5 0.47 8.7 17 3.1e-05 6.2e-02 4 3.9 0.98
KDELR2 0.56 7.9 16 7.4e-05 1.2e-01 5 4.7 0.94
TMEM8A 1.30 6.3 16 1.4e-04 1.6e-01 6 5.6 0.93
GDF15 -1.10 6.5 15 1.4e-04 1.6e-01 7 5.7 0.81
GADD45G -1.20 7.5 12 6.3e-04 3.7e-01 8 13.0 1.60
ANO10 1.20 6.3 14 6.7e-04 3.7e-01 9 13.0 1.40
SEMA5B 0.96 6.7 11 7.5e-04 3.7e-01 10 14.0 1.40
1e-04 NA NA NA NA NA 5 5.1 1.00
1e-05 NA NA NA NA NA 2 3.0 1.50
1e-06 NA NA NA NA NA 2 2.1 1.00
1e-07 NA NA NA NA NA 1 1.4 1.40
1e-08 NA NA NA NA NA 1 0.9 0.90
1e-09 NA NA NA NA NA 0 0.9 Inf
1e-10 NA NA NA NA NA 0 0.7 Inf
[1] "RERE_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MAFF 2.5 6.4 20 7.1e-06 0.057 1 2.7 2.7
AC093323.3 1.8 6.5 17 3.1e-05 0.130 2 3.5 1.8
TOP3B 1.9 6.3 18 1.0e-04 0.280 3 5.7 1.9
HIST1H2AC 2.1 6.3 14 1.7e-04 0.340 4 6.5 1.6
S100A10 -1.4 6.9 13 2.9e-04 0.480 5 7.8 1.6
TOB1 1.7 6.3 13 4.0e-04 0.530 6 9.5 1.6
GLIPR1 -1.1 6.5 12 4.5e-04 0.530 7 10.0 1.4
BRCA1 -1.0 6.5 11 7.2e-04 0.730 8 13.0 1.7
PCGF1 1.6 6.2 15 9.1e-04 0.820 9 16.0 1.7
LRRIQ1 1.6 6.2 15 1.1e-03 0.910 10 19.0 1.9
1e-04 NA NA NA NA NA 2 5.7 2.8
1e-05 NA NA NA NA NA 1 2.9 2.9
1e-06 NA NA NA NA NA 0 1.7 Inf
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 0.7 Inf
1e-10 NA NA NA NA NA 0 0.7 Inf
[1] "SETD1A_1st_exon_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
QSER1 2.4 6.4 22 4.8e-06 0.039 1 0.7 0.70
CNN1 -1.5 6.4 18 2.9e-05 0.120 2 1.3 0.65
CUX1 1.9 6.5 15 8.6e-05 0.180 3 2.1 0.70
AGPAT2 2.0 6.5 15 1.1e-04 0.180 4 2.5 0.62
ZNF33A 1.9 6.4 15 1.3e-04 0.180 5 2.9 0.58
BORA 1.9 6.3 15 1.6e-04 0.180 6 3.4 0.57
KLHL8 1.9 6.3 17 1.6e-04 0.180 7 3.4 0.49
EMP3 2.6 6.6 14 1.8e-04 0.190 8 3.5 0.44
FGF19 -1.3 6.4 13 3.2e-04 0.280 9 4.3 0.48
GNG3 1.9 6.3 13 3.4e-04 0.280 10 4.4 0.44
1e-04 NA NA NA NA NA 3 2.3 0.77
1e-05 NA NA NA NA NA 1 1.0 1.00
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 0.2 Inf
1e-09 NA NA NA NA NA 0 0.1 Inf
1e-10 NA NA NA NA NA 0 0.1 Inf
[1] "SETD1A_1st_exon_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TAGLN2 -1.7 6.4 50 1.9e-12 1.5e-08 1 1.1 1.10
SPP1 -2.1 6.9 44 3.1e-11 1.2e-07 2 1.6 0.80
LOXL2 -1.4 6.2 36 4.1e-09 1.1e-05 3 1.7 0.57
SLC2A6 -1.4 6.2 34 1.7e-08 3.5e-05 4 1.8 0.45
CALD1 -1.1 7.9 31 2.9e-08 4.8e-05 5 2.0 0.40
EMP3 -1.5 6.6 29 6.6e-08 8.9e-05 6 2.1 0.35
SERPINE2 -1.3 6.5 29 7.8e-08 9.0e-05 7 2.1 0.30
TNIP1 -1.1 6.5 25 6.6e-07 6.7e-04 8 2.4 0.30
MYL9 -1.3 7.5 23 1.3e-06 1.2e-03 9 2.8 0.31
S100A10 -1.6 6.8 23 1.5e-06 1.2e-03 10 2.9 0.29
1e-04 NA NA NA NA NA 21 9.2 0.44
1e-05 NA NA NA NA NA 12 4.5 0.38
1e-06 NA NA NA NA NA 8 2.7 0.34
1e-07 NA NA NA NA NA 7 2.3 0.33
1e-08 NA NA NA NA NA 3 1.8 0.60
1e-09 NA NA NA NA NA 2 1.7 0.85
1e-10 NA NA NA NA NA 2 1.6 0.80
[1] "SETD1A_1st_exon_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
UBB 4.3 9.6 24 9.8e-07 0.0079 1 1.0 1.0
BEX2 -2.4 6.6 14 2.3e-04 0.7200 2 3.8 1.9
ARHGEF2 -2.3 6.3 13 3.3e-04 0.7200 3 5.4 1.8
COX11 4.2 7.1 12 6.2e-04 0.7200 4 8.4 2.1
CREB3 4.2 7.1 11 7.7e-04 0.7200 5 9.3 1.9
RAB6B -2.2 6.3 11 9.1e-04 0.7200 6 11.0 1.8
CST3 2.2 8.2 11 9.1e-04 0.7200 7 11.0 1.5
PPP1R12A 4.1 7.1 11 9.5e-04 0.7200 8 11.0 1.4
NPDC1 4.3 7.2 11 9.8e-04 0.7200 9 11.0 1.2
MSTO1 -2.0 6.3 11 9.9e-04 0.7200 10 11.0 1.1
1e-04 NA NA NA NA NA 1 3.1 3.1
1e-05 NA NA NA NA NA 1 1.8 1.8
1e-06 NA NA NA NA NA 1 1.0 1.0
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 0.2 Inf
[1] "STAT6_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
S100A10 3.70 6.8 16 7.3e-05 0.59 1 5.0 5.0
TOR1AIP1 1.60 6.2 17 4.3e-04 1.00 2 14.0 6.8
DCAF6 1.60 6.2 17 4.8e-04 1.00 3 14.0 4.7
EIF2D 1.10 6.8 12 6.6e-04 1.00 4 18.0 4.6
SNX13 1.50 6.2 16 8.0e-04 1.00 5 21.0 4.1
DHX32 -0.93 6.3 11 1.2e-03 1.00 6 26.0 4.4
IREB2 1.30 6.5 11 1.2e-03 1.00 7 26.0 3.8
SERGEF 1.50 6.3 13 1.3e-03 1.00 8 28.0 3.5
ZNF420 -1.00 6.2 12 1.6e-03 1.00 9 32.0 3.5
TMEM184C 1.50 6.3 12 1.9e-03 1.00 10 36.0 3.6
1e-04 NA NA NA NA NA 1 5.7 5.7
1e-05 NA NA NA NA NA 0 2.5 Inf
1e-06 NA NA NA NA NA 0 0.8 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 0.2 Inf
[1] "STAT6_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC -2.50 6.7 84 9.1e-20 7.4e-16 1 0.1 0.10
SPP1 -1.80 6.9 36 2.0e-09 8.0e-06 2 0.2 0.10
LGALS3 -1.40 6.6 22 2.2e-06 5.9e-03 3 0.4 0.13
TP53I3 -1.00 6.8 17 3.4e-05 6.9e-02 4 1.6 0.40
ZNF561 1.40 6.4 16 6.3e-05 1.0e-01 5 2.4 0.48
EFNB3 1.40 6.3 15 1.3e-04 1.7e-01 6 3.6 0.60
LTBP1 1.40 6.3 15 2.8e-04 3.1e-01 7 5.6 0.80
NUDT14 -0.71 6.9 13 3.0e-04 3.1e-01 8 6.4 0.80
MOAP1 -0.82 6.4 13 4.0e-04 3.5e-01 9 7.5 0.83
CLUH 1.30 6.3 15 4.4e-04 3.5e-01 10 7.9 0.79
1e-04 NA NA NA NA NA 5 3.4 0.68
1e-05 NA NA NA NA NA 3 1.0 0.33
1e-06 NA NA NA NA NA 2 0.2 0.10
1e-07 NA NA NA NA NA 2 0.2 0.10
1e-08 NA NA NA NA NA 2 0.2 0.10
1e-09 NA NA NA NA NA 1 0.2 0.20
1e-10 NA NA NA NA NA 1 0.2 0.20
[1] "STAT6_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
GADD45G -1.60 7.5 29 8.6e-08 0.0007 1 0.8 0.8
RILPL2 1.40 6.3 24 1.2e-05 0.0510 2 3.3 1.6
PLK1 1.50 7.4 18 2.4e-05 0.0650 3 4.7 1.6
PIF1 1.60 6.4 17 3.2e-05 0.0660 4 4.9 1.2
PPP1R12C 1.20 6.3 18 1.2e-04 0.1900 5 8.4 1.7
OMA1 1.20 6.2 19 1.8e-04 0.2200 6 9.3 1.6
ALPL -0.73 6.8 14 1.9e-04 0.2200 7 9.4 1.3
CCNB1 1.10 7.4 14 2.3e-04 0.2400 8 10.0 1.3
OLMALINC 1.00 6.4 13 3.8e-04 0.3400 9 12.0 1.3
UBE2C 1.20 8.2 12 4.9e-04 0.3700 10 14.0 1.4
1e-04 NA NA NA NA NA 4 7.9 2.0
1e-05 NA NA NA NA NA 1 3.1 3.1
1e-06 NA NA NA NA NA 1 2.0 2.0
1e-07 NA NA NA NA NA 1 0.8 0.8
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] "TCF4-ITF2_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MYC -2.80 6.7 190 1.1e-41 9.0e-38 1 0.0 0.00
MT1X -2.00 6.3 110 2.1e-25 8.4e-22 2 0.1 0.05
GOLGA8B 1.50 6.2 29 7.0e-06 1.9e-02 3 2.3 0.77
TSPAN15 1.50 6.6 19 1.7e-05 3.4e-02 4 3.2 0.80
SPP1 2.70 6.9 18 2.5e-05 4.0e-02 5 3.5 0.70
SLC35B3 1.40 6.3 19 3.0e-05 4.1e-02 6 4.1 0.68
TAGLN 1.20 9.3 15 9.1e-05 9.8e-02 7 6.0 0.86
RPL27A 0.30 12.0 15 9.6e-05 9.8e-02 8 6.0 0.75
GLRX -0.97 6.3 15 1.2e-04 9.8e-02 9 6.6 0.73
CDKN2A -1.00 6.5 15 1.4e-04 9.8e-02 10 6.9 0.69
1e-04 NA NA NA NA NA 8 6.1 0.76
1e-05 NA NA NA NA NA 3 2.8 0.93
1e-06 NA NA NA NA NA 2 1.3 0.65
1e-07 NA NA NA NA NA 2 1.0 0.50
1e-08 NA NA NA NA NA 2 0.8 0.40
1e-09 NA NA NA NA NA 2 0.7 0.35
1e-10 NA NA NA NA NA 2 0.6 0.30
[1] "TCF4-ITF2_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
DMTF1 1.20 6.3 15 0.00024 0.55 1 7.0 7.0
TMEM136 1.10 6.4 13 0.00030 0.55 2 7.4 3.7
ZKSCAN1 0.79 7.0 13 0.00030 0.55 3 7.4 2.5
TRRAP 1.20 6.3 15 0.00037 0.55 4 8.2 2.0
CMTR2 1.20 6.3 14 0.00046 0.55 5 9.6 1.9
GADD45G 2.00 7.5 12 0.00059 0.55 6 11.0 1.8
FOS -0.83 6.7 12 0.00063 0.55 7 12.0 1.7
STMN2 2.10 7.1 12 0.00067 0.55 8 12.0 1.5
PHLDA1 1.30 7.0 12 0.00067 0.55 9 12.0 1.3
THAP4 0.93 6.6 12 0.00068 0.55 10 12.0 1.2
1e-04 NA NA NA NA NA 0 4.7 Inf
1e-05 NA NA NA NA NA 0 1.5 Inf
1e-06 NA NA NA NA NA 0 1.3 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 0.4 Inf
1e-10 NA NA NA NA NA 0 0.4 Inf
[1] "TCF4-ITF2_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SNAPC1 -3.0 6.5 69 1.6e-16 1.3e-12 1 0.0 0.00
RNF25 2.9 6.5 14 2.2e-04 6.4e-01 2 3.4 1.70
CLN6 -1.6 6.2 16 3.6e-04 6.4e-01 3 4.7 1.60
LMO4 2.1 6.9 12 5.1e-04 6.4e-01 4 6.0 1.50
CHMP4A 2.6 6.4 12 5.4e-04 6.4e-01 5 6.2 1.20
BORA -1.5 6.3 12 5.6e-04 6.4e-01 6 6.2 1.00
CLN8 2.7 6.5 12 5.6e-04 6.4e-01 7 6.2 0.89
DIO3 -1.5 7.0 11 9.0e-04 6.4e-01 8 9.0 1.10
MRPS28 2.3 6.6 11 9.3e-04 6.4e-01 9 9.4 1.00
COA5 2.0 6.7 11 9.5e-04 6.4e-01 10 9.4 0.94
1e-04 NA NA NA NA NA 1 2.0 2.00
1e-05 NA NA NA NA NA 1 0.7 0.70
1e-06 NA NA NA NA NA 1 0.2 0.20
1e-07 NA NA NA NA NA 1 0.2 0.20
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 0.0 0.00
[1] "TRANK1_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SDF2L1 -2.1 7.1 15.0 9.4e-05 0.77 1 0.5 0.50
KRT18 -3.1 7.1 13.0 2.4e-04 0.81 2 1.6 0.80
METTL18 -2.6 6.3 14.0 4.1e-04 0.81 3 2.3 0.77
INIP -1.9 6.8 12.0 6.8e-04 0.81 4 3.5 0.88
ACVR2A -2.4 6.2 13.0 7.4e-04 0.81 5 3.7 0.74
NRIP1 -2.3 6.2 12.0 7.7e-04 0.81 6 4.2 0.70
PYCR1 -2.3 6.8 10.0 1.5e-03 0.81 7 7.1 1.00
FAM13B -2.3 6.3 11.0 1.5e-03 0.81 8 7.3 0.91
CDH11 -2.2 6.3 9.6 2.0e-03 0.81 9 9.3 1.00
SEC11C -1.4 7.4 8.8 3.0e-03 0.81 10 14.0 1.40
1e-04 NA NA NA NA NA 1 0.5 0.50
1e-05 NA NA NA NA NA 0 0.3 Inf
1e-06 NA NA NA NA NA 0 0.3 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] "TRANK1_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CDKN1C -1.50 6.8 12 0.00048 0.8 1 12.0 12.0
LOXL1 2.20 6.6 12 0.00053 0.8 2 13.0 6.3
DIRC2 -1.20 6.3 13 0.00053 0.8 3 13.0 4.2
TMEM230 0.66 8.0 12 0.00065 0.8 4 15.0 3.7
WWP2 -1.20 6.2 15 0.00072 0.8 5 16.0 3.2
UGP2 1.10 7.1 11 0.00088 0.8 6 20.0 3.2
BTBD7 1.70 6.4 12 0.00110 0.8 7 22.0 3.1
EXD2 1.70 6.2 13 0.00120 0.8 8 24.0 3.0
CXXC4 1.70 6.4 10 0.00120 0.8 9 24.0 2.7
YEATS2 1.70 6.2 14 0.00140 0.8 10 27.0 2.7
1e-04 NA NA NA NA NA 0 5.0 Inf
1e-05 NA NA NA NA NA 0 2.1 Inf
1e-06 NA NA NA NA NA 0 1.2 Inf
1e-07 NA NA NA NA NA 0 0.9 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] "TRANK1_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ATF7IP2 1.30 6.4 22 2.4e-06 0.019 1 1.4 1.40
TAMM41 -0.76 6.3 17 1.2e-04 0.360 2 3.4 1.70
ZNF280D 1.10 6.2 19 1.4e-04 0.360 3 3.5 1.20
OPTN 1.10 6.4 14 1.8e-04 0.360 4 3.8 0.95
CNN1 -0.82 6.4 14 2.3e-04 0.370 5 4.8 0.96
MYC 1.50 6.7 13 3.3e-04 0.440 6 6.0 1.00
MEX3B 0.94 6.3 14 5.8e-04 0.510 7 9.9 1.40
FST 1.00 6.4 12 6.2e-04 0.510 8 10.0 1.30
IL6ST 0.89 6.3 13 6.3e-04 0.510 9 10.0 1.20
TPD52 -0.67 6.4 11 7.6e-04 0.510 10 12.0 1.20
1e-04 NA NA NA NA NA 1 2.8 2.80
1e-05 NA NA NA NA NA 1 1.8 1.80
1e-06 NA NA NA NA NA 0 1.1 Inf
1e-07 NA NA NA NA NA 0 0.8 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] "UBE2Q2P1_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
JAG1 -1.90 6.8 21 3.8e-06 0.031 1 1.5 1.50
SERPINH1 -1.20 7.6 19 1.3e-05 0.053 2 1.8 0.90
RCN1 -0.92 8.6 16 7.0e-05 0.190 3 2.5 0.83
IMMP2L -1.50 6.3 15 1.8e-04 0.340 4 4.1 1.00
LDLR 2.60 6.4 13 3.1e-04 0.340 5 6.0 1.20
LINC00461 2.70 6.5 13 3.5e-04 0.340 6 6.4 1.10
DBX2 -1.60 6.3 13 4.0e-04 0.340 7 6.7 0.96
NRSN2 2.40 6.4 13 4.4e-04 0.340 8 7.0 0.88
FANCG 2.50 6.4 12 4.7e-04 0.340 9 7.7 0.86
MGST1 -1.10 7.7 12 6.0e-04 0.340 10 8.7 0.87
1e-04 NA NA NA NA NA 3 2.7 0.90
1e-05 NA NA NA NA NA 1 1.6 1.60
1e-06 NA NA NA NA NA 0 1.3 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 0.6 Inf
1e-10 NA NA NA NA NA 0 0.5 Inf
[1] "UBE2Q2P1_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
LGALS3 -3.50 6.6 58 3.3e-14 2.7e-10 1 0.0 0.00
PCDH9 -2.00 6.3 18 4.8e-05 1.9e-01 2 1.7 0.85
TERF2IP -1.40 7.3 13 2.5e-04 6.0e-01 3 3.6 1.20
UFSP2 2.60 6.8 13 3.0e-04 6.0e-01 4 4.2 1.00
PABPC1 0.80 10.0 12 4.6e-04 6.2e-01 5 6.3 1.30
SFRP1 4.10 7.1 12 4.8e-04 6.2e-01 6 6.3 1.00
TTLL12 2.90 6.5 12 5.4e-04 6.2e-01 7 6.7 0.96
ATP5B -0.67 9.4 11 7.4e-04 6.2e-01 8 8.3 1.00
CDK20 -1.70 6.2 13 7.9e-04 6.2e-01 9 9.3 1.00
ALDH2 3.40 6.7 11 8.7e-04 6.2e-01 10 10.0 1.00
1e-04 NA NA NA NA NA 2 2.4 1.20
1e-05 NA NA NA NA NA 1 0.7 0.70
1e-06 NA NA NA NA NA 1 0.6 0.60
1e-07 NA NA NA NA NA 1 0.5 0.50
1e-08 NA NA NA NA NA 1 0.2 0.20
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_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TAF1A -2.1 6.3 33 4.8e-08 0.00039 1 0.4 0.4
NAV1 -1.4 6.6 14 1.7e-04 0.48000 2 4.0 2.0
RHBDL3 -1.6 6.3 14 1.8e-04 0.48000 3 4.2 1.4
RALGAPA1 -1.5 6.2 14 3.4e-04 0.69000 4 5.7 1.4
NSUN2 2.5 6.4 12 8.0e-04 0.85000 5 10.0 2.1
GNG12 2.7 6.5 11 9.0e-04 0.85000 6 12.0 1.9
METTL8 2.4 6.4 11 9.1e-04 0.85000 7 12.0 1.6
CAMLG 1.1 7.6 11 9.2e-04 0.85000 8 12.0 1.5
PUS7 -1.4 6.3 12 9.7e-04 0.85000 9 12.0 1.4
ARFIP1 2.4 6.4 11 1.0e-03 0.85000 10 13.0 1.3
1e-04 NA NA NA NA NA 1 3.0 3.0
1e-05 NA NA NA NA NA 1 1.7 1.7
1e-06 NA NA NA NA NA 1 0.8 0.8
1e-07 NA NA NA NA NA 1 0.4 0.4
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] "VPS45_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
A2M -2.40 6.6 50 2.3e-12 1.8e-08 1 0.2 0.200
PTN -1.90 7.8 34 7.3e-09 3.0e-05 2 0.2 0.100
IFITM3 -2.00 8.5 30 4.6e-08 1.2e-04 3 0.2 0.067
CLU -1.70 7.3 26 3.8e-07 7.6e-04 4 0.2 0.050
CTSC -1.70 6.6 25 4.7e-07 7.6e-04 5 0.2 0.040
GPM6B -1.00 8.4 22 3.4e-06 4.6e-03 6 0.5 0.083
CD47 -1.40 6.9 19 1.1e-05 1.2e-02 7 0.5 0.071
SULF2 -1.60 6.5 19 1.7e-05 1.6e-02 8 0.6 0.075
RCN1 -0.94 8.6 18 1.8e-05 1.6e-02 9 0.6 0.067
WLS -1.40 7.0 18 2.9e-05 2.3e-02 10 1.0 0.100
1e-04 NA NA NA NA NA 14 2.0 0.140
1e-05 NA NA NA NA NA 6 0.5 0.083
1e-06 NA NA NA NA NA 5 0.2 0.040
1e-07 NA NA NA NA NA 3 0.2 0.067
1e-08 NA NA NA NA NA 2 0.2 0.100
1e-09 NA NA NA NA NA 1 0.2 0.200
1e-10 NA NA NA NA NA 1 0.2 0.200
[1] "VPS45_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
GLRX -1.30 6.3 43 7.6e-11 6.2e-07 1 0.4 0.40
DLL3 -1.30 7.0 28 1.1e-07 4.7e-04 2 0.8 0.40
SYT1 -0.97 6.4 24 8.3e-07 2.3e-03 3 0.9 0.30
STMN2 -1.30 7.1 22 3.4e-06 6.8e-03 4 1.2 0.30
MT1X -0.89 6.3 22 7.0e-06 1.1e-02 5 1.3 0.26
SUMO3 0.44 7.9 17 4.1e-05 5.5e-02 6 1.9 0.32
DLL1 -0.93 6.8 15 1.0e-04 1.2e-01 7 3.1 0.44
RNF19A -0.73 6.2 17 2.1e-04 2.1e-01 8 4.4 0.55
SLF2 0.92 6.3 16 2.3e-04 2.1e-01 9 4.5 0.50
CYC1 0.32 8.7 13 2.7e-04 2.2e-01 10 5.7 0.57
1e-04 NA NA NA NA NA 6 3.0 0.50
1e-05 NA NA NA NA NA 5 1.3 0.26
1e-06 NA NA NA NA NA 3 1.0 0.33
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 1 0.5 0.50
[1] "VPS45_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
LAMP5 -3.0 6.3 58 3.9e-14 3.2e-10 1 0.0 0.00
PCGF2 3.8 6.9 21 3.8e-06 1.5e-02 2 1.4 0.70
NKAIN4 -1.9 6.8 17 3.1e-05 8.5e-02 3 2.7 0.90
ARG2 -1.7 6.5 16 6.2e-05 1.3e-01 4 3.2 0.80
JUNB -1.8 6.4 14 1.5e-04 2.5e-01 5 5.3 1.10
CHTF8 1.8 7.1 12 4.7e-04 4.7e-01 6 9.5 1.60
NELFE 1.3 7.7 12 5.1e-04 4.7e-01 7 10.0 1.50
UCK2 3.0 6.6 12 5.7e-04 4.7e-01 8 12.0 1.40
NADK 2.9 6.6 12 5.8e-04 4.7e-01 9 12.0 1.30
TXNRD1 -1.5 7.0 12 7.0e-04 4.7e-01 10 13.0 1.30
1e-04 NA NA NA NA NA 4 3.8 0.95
1e-05 NA NA NA NA NA 2 1.7 0.85
1e-06 NA NA NA NA NA 1 0.9 0.90
1e-07 NA NA NA NA NA 1 0.3 0.30
1e-08 NA NA NA NA NA 1 0.0 0.00
1e-09 NA NA NA NA NA 1 0.0 0.00
1e-10 NA NA NA NA NA 1 0.0 0.00
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