Last updated: 2019-03-05
Checks: 6 0
Knit directory: cropseq/
This reproducible R Markdown analysis was created with workflowr (version 1.2.0). The Report tab describes the reproducibility checks that were applied when the results were created. The Past versions tab lists the development history.
Great! Since the R Markdown file has been committed to the Git repository, you know the exact version of the code that produced these results.
Great job! The global environment was empty. Objects defined in the global environment can affect the analysis in your R Markdown file in unknown ways. For reproduciblity it’s best to always run the code in an empty environment.
The command set.seed(20181119) was run prior to running the code in the R Markdown file. Setting a seed ensures that any results that rely on randomness, e.g. subsampling or permutations, are reproducible.
Great job! Recording the operating system, R version, and package versions is critical for reproducibility.
Nice! There were no cached chunks for this analysis, so you can be confident that you successfully produced the results during this run.
Great! You are using Git for version control. Tracking code development and connecting the code version to the results is critical for reproducibility. The version displayed above was the version of the Git repository at the time these results were generated.
Note that you need to be careful to ensure that all relevant files for the analysis have been committed to Git prior to generating the results (you can use wflow_publish or wflow_git_commit). workflowr only checks the R Markdown file, but you know if there are other scripts or data files that it depends on. Below is the status of the Git repository when the results were generated:
Ignored files:
Ignored: .Rproj.user/
Ignored: data/gRNA_edgeR-QLF/
Ignored: data/gRNA_edgeR-QLF_811d97b/
Unstaged changes:
Modified: code/gRNA_edgeR-QLF_run.R
Note that any generated files, e.g. HTML, png, CSS, etc., are not included in this status report because it is ok for generated content to have uncommitted changes.
These are the previous versions of the R Markdown and HTML files. If you’ve configured a remote Git repository (see ?wflow_git_remote), click on the hyperlinks in the table below to view them.
| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | 6283eea | simingz | 2019-03-04 | stricter filtering for gRNA |
| html | 6283eea | simingz | 2019-03-04 | stricter filtering for gRNA |
| html | 811d97b | simingz | 2019-03-01 | gNNA-de |
| html | c912143 | simingz | 2019-03-01 | gRNA-de |
| html | 9809320 | simingz | 2019-02-28 | gRNA_edgeR-QLF |
| Rmd | 0dffd41 | simingz | 2019-02-28 | gRNA_edgeR-QLF |
| html | 0dffd41 | simingz | 2019-02-28 | gRNA_edgeR-QLF |
| Rmd | 2fd9ad6 | simingz | 2019-02-28 | gRNA_edgeR-QLF |
| html | 2fd9ad6 | simingz | 2019-02-28 | gRNA_edgeR-QLF |
| Rmd | a9f9f26 | simingz | 2019-02-27 | gRNA-de |
| html | a9f9f26 | simingz | 2019-02-27 | gRNA-de |
source("code/empiricalFDR.R")
pbins <- 10** (-4:-10)
for (gRNAfile in list.files("data/gRNA_edgeR-QLF/", "*edgeR-qlf_Neg1.Rd")){
print(gRNAfile)
load(paste0("data/gRNA_edgeR-QLF/", 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
CCND1 0.76 8.1 10.0 0.0015 1 1 9.200 9.2
BTG2 1.30 7.1 10.0 0.0015 1 2 9.300 4.6
UFM1 0.97 7.2 9.5 0.0025 1 3 13.000 4.4
ARF4 0.70 8.4 9.3 0.0026 1 4 14.000 3.5
MPZL1 -0.75 6.9 8.9 0.0032 1 5 17.000 3.3
LARP1 0.78 7.3 8.8 0.0034 1 6 18.000 2.9
IER2 0.93 7.2 8.8 0.0034 1 7 18.000 2.5
NUB1 -0.82 6.8 8.7 0.0036 1 8 19.000 2.3
EMP2 1.10 6.8 8.4 0.0042 1 9 22.000 2.4
KIF22 -0.68 7.6 8.3 0.0046 1 10 23.000 2.3
1e-04 NA NA NA NA NA 0 1.400 Inf
1e-05 NA NA NA NA NA 0 0.300 Inf
1e-06 NA NA NA NA NA 0 0.100 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "BAG5_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NIN -1.10 6.9 15.0 0.00014 0.60 1 0.800 0.8
MALAT1 -0.62 14.0 13.0 0.00051 0.88 2 2.400 1.2
BAG1 -0.56 7.8 11.0 0.00110 0.88 3 4.600 1.5
DUT 0.79 8.4 9.9 0.00190 0.88 4 8.000 2.0
DHFR 0.85 7.8 9.9 0.00190 0.88 5 8.000 1.6
MIAT -1.30 7.3 9.6 0.00230 0.88 6 9.100 1.5
ARID5B -0.93 6.9 9.6 0.00230 0.88 7 9.500 1.4
BAALC 1.30 6.8 9.1 0.00290 0.88 8 12.000 1.5
SNRNP25 0.62 8.2 9.0 0.00310 0.88 9 13.000 1.4
OS9 -0.80 7.3 9.0 0.00310 0.88 10 13.000 1.3
1e-04 NA NA NA NA NA 0 0.570 Inf
1e-05 NA NA NA NA NA 0 0.130 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "BAG5_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CDKN3 -1.20 7.0 15.0 0.00014 0.59 1 1.300 1.30
BIN3 1.30 6.9 12.0 0.00054 0.70 2 3.000 1.50
KIF2C -1.20 6.8 12.0 0.00061 0.70 3 3.200 1.10
ASCL1 1.70 6.9 12.0 0.00080 0.70 4 4.000 1.00
DFFA -0.78 7.2 12.0 0.00083 0.70 5 4.100 0.83
NQO1 -1.20 7.5 11.0 0.00100 0.71 6 5.100 0.85
CDKN1A 1.40 8.0 11.0 0.00120 0.72 7 6.000 0.86
ARL6IP1 -0.84 8.0 11.0 0.00140 0.72 8 6.800 0.85
CAV1 -1.20 7.4 10.0 0.00180 0.83 9 8.400 0.93
ARL5A 1.00 6.9 9.4 0.00250 1.00 10 11.000 1.10
1e-04 NA NA NA NA NA 0 1.100 Inf
1e-05 NA NA NA NA NA 0 0.300 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "BCL11B_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ARL6IP1 -1.1 8.0 11.0 0.0013 0.99 1 4.80 4.80
UNG 2.2 6.9 11.0 0.0014 0.99 2 5.00 2.50
UXS1 2.0 6.8 11.0 0.0014 0.99 3 5.00 1.70
IMPA2 2.1 6.9 10.0 0.0016 0.99 4 5.60 1.40
CADM4 -1.3 6.8 10.0 0.0019 0.99 5 6.50 1.30
TPX2 -1.2 7.1 9.6 0.0023 0.99 6 7.90 1.30
SMCO4 1.9 6.8 9.5 0.0025 0.99 7 8.40 1.20
ADI1 1.5 7.3 9.3 0.0027 0.99 8 9.30 1.20
AURKA -1.4 7.1 9.3 0.0027 0.99 9 9.30 1.00
ATF5 2.6 7.1 9.3 0.0027 0.99 10 9.30 0.93
1e-04 NA NA NA NA NA 0 0.73 Inf
1e-05 NA NA NA NA NA 0 0.10 Inf
1e-06 NA NA NA NA NA 0 0.10 Inf
1e-07 NA NA NA NA NA 0 0.00 NaN
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "BCL11B_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
PHLDA1 -1.60 7.2 23 3.4e-06 0.015 1 0.100 0.10
JAG1 -1.40 7.0 17 5.6e-05 0.120 2 0.330 0.17
RMI2 1.50 6.8 15 1.8e-04 0.130 3 0.830 0.28
RPRML 1.60 6.8 15 1.9e-04 0.130 4 0.870 0.22
CDC6 1.60 7.0 14 2.3e-04 0.130 5 1.100 0.22
ZNF24 -0.88 7.1 14 2.5e-04 0.130 6 1.200 0.19
CACYBP 0.70 8.1 14 2.7e-04 0.130 7 1.300 0.19
SKP2 1.20 6.9 14 2.8e-04 0.130 8 1.300 0.17
GAP43 -1.10 8.2 14 2.8e-04 0.130 9 1.300 0.15
VOPP1 1.10 7.0 13 3.3e-04 0.140 10 1.500 0.15
1e-04 NA NA NA NA NA 2 0.530 0.27
1e-05 NA NA NA NA NA 1 0.170 0.17
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "BCL11B_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
DUSP1 2.60 6.9 11.0 0.0011 1 1 5.500 5.5
DKK3 -1.20 6.9 11.0 0.0012 1 2 6.000 3.0
FAAP20 1.10 7.4 8.9 0.0032 1 3 15.000 5.0
MED24 1.60 6.9 8.6 0.0039 1 4 18.000 4.4
SCML1 1.80 6.8 8.5 0.0042 1 5 19.000 3.7
ITM2C 1.30 7.1 8.4 0.0043 1 6 20.000 3.3
FASTK 1.40 7.0 8.4 0.0043 1 7 20.000 2.8
POLR1D -0.63 8.2 8.4 0.0044 1 8 20.000 2.4
TCF7L1 -1.10 6.8 8.1 0.0050 1 9 22.000 2.4
GOLGA7 0.94 7.5 7.8 0.0059 1 10 26.000 2.6
1e-04 NA NA NA NA NA 0 0.930 Inf
1e-05 NA NA NA NA NA 0 0.330 Inf
1e-06 NA NA NA NA NA 0 0.170 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "CHRNA3_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MT-ND4 -1.3 11.0 11.0 0.0012 0.85 1 3.600 3.6
ABHD17A -1.9 6.7 11.0 0.0012 0.85 2 3.700 1.8
SCAMP3 3.6 7.0 9.5 0.0025 0.85 3 7.200 2.4
AP1S2 2.8 7.5 9.4 0.0026 0.85 4 7.400 1.8
PHAX 2.7 7.4 9.1 0.0030 0.85 5 8.500 1.7
NUDCD2 -1.4 7.5 8.9 0.0034 0.85 6 9.400 1.6
KPNA2 -1.4 8.7 8.2 0.0047 0.85 7 13.000 1.9
PLK1 -2.0 7.4 8.2 0.0049 0.85 8 13.000 1.7
MIIP -1.8 6.8 8.1 0.0051 0.85 9 14.000 1.6
BRIX1 2.4 7.7 8.0 0.0054 0.85 10 15.000 1.5
1e-04 NA NA NA NA NA 0 0.770 Inf
1e-05 NA NA NA NA NA 0 0.170 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "CHRNA3_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
PKMYT1 1.80 6.8 14.0 0.00026 1 1 1.700 1.7
SLC25A26 1.50 6.7 12.0 0.00066 1 2 3.500 1.8
PRDX1 -0.43 9.6 11.0 0.00120 1 3 6.000 2.0
NDN -0.79 7.5 10.0 0.00150 1 4 7.300 1.8
HADHB -0.85 7.2 10.0 0.00170 1 5 8.000 1.6
TCF7L2 -0.86 7.1 9.8 0.00210 1 6 9.600 1.6
PRKAR1A -0.72 7.3 9.4 0.00250 1 7 11.000 1.6
ZNF503 -1.00 7.0 9.1 0.00300 1 8 13.000 1.6
AUTS2 -0.76 7.2 8.9 0.00330 1 9 14.000 1.6
GRSF1 -0.60 7.7 8.8 0.00340 1 10 15.000 1.5
1e-04 NA NA NA NA NA 0 0.800 Inf
1e-05 NA NA NA NA NA 0 0.200 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "CHRNA3_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CDC42EP3 -1.80 6.8 22 5.5e-06 0.024 1 0.230 0.23
RRP9 -1.30 7.1 18 3.6e-05 0.055 2 0.600 0.30
VGF -1.90 7.0 18 3.8e-05 0.055 3 0.630 0.21
AKAP12 -1.20 7.4 15 2.0e-04 0.210 4 1.800 0.45
NANS -1.30 7.1 14 2.9e-04 0.250 5 2.300 0.45
LPP -1.30 6.9 13 4.5e-04 0.300 6 3.200 0.54
CIB1 -1.00 7.3 12 5.5e-04 0.300 7 3.600 0.51
SPTLC1 -1.30 6.9 12 5.5e-04 0.300 8 3.600 0.45
CBWD1 -1.20 6.7 12 6.3e-04 0.300 9 4.000 0.45
MALAT1 -0.77 14.0 12 7.5e-04 0.300 10 4.500 0.45
1e-04 NA NA NA NA NA 3 1.100 0.36
1e-05 NA NA NA NA NA 1 0.300 0.30
1e-06 NA NA NA NA NA 0 0.100 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "DPYD_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
CTD-2006C1.2 -1.90 7.3 45 3.1e-10 1.3e-06 1 0.27
DUSP4 -1.20 6.9 21 9.3e-06 2.0e-02 2 0.90
CTSD -1.00 7.5 18 2.9e-05 4.2e-02 3 1.20
NQO1 -1.30 7.5 17 5.9e-05 6.3e-02 4 1.40
NTRK2 1.20 7.2 15 1.2e-04 1.0e-01 5 2.30
RHNO1 1.10 7.1 14 2.1e-04 1.4e-01 6 3.30
TUBA1C -1.20 7.1 14 2.4e-04 1.4e-01 7 3.50
CDC20 1.40 7.6 13 4.0e-04 1.9e-01 8 4.60
GADD45A -0.98 7.7 13 4.3e-04 1.9e-01 9 4.90
FASN 0.95 7.0 13 4.4e-04 1.9e-01 10 5.00
1e-04 NA NA NA NA NA 4 1.90
1e-05 NA NA NA NA NA 2 0.90
1e-06 NA NA NA NA NA 1 0.50
1e-07 NA NA NA NA NA 1 0.37
1e-08 NA NA NA NA NA 1 0.27
1e-09 NA NA NA NA NA 1 0.27
1e-10 NA NA NA NA NA 0 0.27
EmpiricalFDR
CTD-2006C1.2 0.27
DUSP4 0.45
CTSD 0.41
NQO1 0.35
NTRK2 0.45
RHNO1 0.55
TUBA1C 0.50
CDC20 0.57
GADD45A 0.54
FASN 0.50
1e-04 0.48
1e-05 0.45
1e-06 0.50
1e-07 0.37
1e-08 0.27
1e-09 0.27
1e-10 Inf
[1] "DPYD_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MEG3 -0.98 7.8 14.0 0.00030 0.9 1 1.800 1.8
CSRP1 -0.97 7.4 12.0 0.00080 0.9 2 3.800 1.9
RP11-995C19.3 0.89 6.8 11.0 0.00093 0.9 3 4.100 1.4
TAGLN -0.79 9.4 11.0 0.00130 0.9 4 5.800 1.5
SPAG7 -0.36 8.3 11.0 0.00140 0.9 5 6.000 1.2
CCDC184 -0.66 7.1 9.6 0.00220 0.9 6 8.700 1.4
ABCD4 -0.68 6.8 9.6 0.00220 0.9 7 8.900 1.3
NUDT3 0.72 6.9 9.3 0.00260 0.9 8 10.000 1.3
ACO2 -0.53 7.2 9.3 0.00260 0.9 9 11.000 1.2
SMPD4 0.74 6.7 9.0 0.00300 0.9 10 12.000 1.2
1e-04 NA NA NA NA NA 0 0.870 Inf
1e-05 NA NA NA NA NA 0 0.230 Inf
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.100 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "DPYD_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NEAT1 1.70 8.2 16.0 0.00011 0.49 1 1.100 1.10
PRR11 -1.10 6.7 14.0 0.00028 0.60 2 2.000 0.98
EMC9 -1.00 6.8 12.0 0.00071 1.00 3 3.500 1.20
SERINC2 1.20 6.8 10.0 0.00170 1.00 4 7.400 1.80
MAX -0.87 6.8 9.9 0.00190 1.00 5 8.500 1.70
APEX1 -0.43 9.1 9.9 0.00200 1.00 6 8.600 1.40
SHMT2 -0.78 7.7 9.4 0.00260 1.00 7 11.000 1.50
IFT81 -0.82 6.8 9.2 0.00280 1.00 8 11.000 1.40
SOCS3 -0.98 6.8 9.0 0.00300 1.00 9 12.000 1.40
LARP6 0.99 7.0 8.8 0.00350 1.00 10 14.000 1.40
1e-04 NA NA NA NA NA 0 1.000 Inf
1e-05 NA NA NA NA NA 0 0.200 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "GALNT10_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
FAM104B 1.10 7.0 13.0 0.00036 0.87 1 2.000 2.00
DECR1 1.20 7.0 12.0 0.00061 0.87 2 2.800 1.40
AKAP13 1.20 6.7 12.0 0.00061 0.87 3 2.900 0.98
ASRGL1 1.00 7.1 12.0 0.00083 0.89 4 4.000 1.00
CCDC50 -0.74 7.1 11.0 0.00120 0.95 5 5.300 1.10
CLK3 -0.87 6.8 11.0 0.00130 0.95 6 5.700 0.95
ID3 1.20 8.1 9.7 0.00210 1.00 7 9.000 1.30
FANCL 1.10 6.8 9.7 0.00210 1.00 8 9.000 1.10
ZDHHC12 1.10 6.8 9.3 0.00260 1.00 9 11.000 1.30
TRMT61A -0.82 6.7 9.0 0.00300 1.00 10 13.000 1.30
1e-04 NA NA NA NA NA 0 0.970 Inf
1e-05 NA NA NA NA NA 0 0.230 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "GALNT10_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
FZD3 -0.54 7.7 11.0 0.0010 1 1 4.800 4.8
SYPL1 0.91 7.1 11.0 0.0011 1 2 5.000 2.5
PUS3 1.10 6.7 11.0 0.0013 1 3 6.400 2.1
CMBL 1.00 6.8 9.6 0.0022 1 4 9.600 2.4
TGIF2 0.93 6.9 9.4 0.0025 1 5 11.000 2.1
ZNF787 0.98 6.7 9.3 0.0027 1 6 12.000 1.9
TP53RK -0.71 7.0 9.3 0.0027 1 7 12.000 1.7
MIS12 -0.78 6.8 8.9 0.0032 1 8 14.000 1.7
PRR11 -0.85 6.7 8.4 0.0042 1 9 17.000 1.9
CRABP1 1.20 10.0 7.8 0.0058 1 10 24.000 2.4
1e-04 NA NA NA NA NA 0 0.900 Inf
1e-05 NA NA NA NA NA 0 0.230 Inf
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "GALNT10_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NEAT1 -1.30 8.8 20.0 1.2e-05 0.051 1 0.23 0.23
ZNF512 -0.88 6.8 14.0 2.2e-04 0.470 2 1.80 0.92
SPOCK1 -1.00 6.7 13.0 3.8e-04 0.530 3 2.40 0.81
GAP43 -0.92 8.2 12.0 8.1e-04 0.860 4 4.30 1.10
PKIB 0.97 7.0 11.0 1.1e-03 0.960 5 5.80 1.20
NEU1 -0.78 7.2 9.6 2.3e-03 1.000 6 10.00 1.70
LYPD1 -0.77 7.7 9.4 2.4e-03 1.000 7 11.00 1.60
SPARC -0.51 8.7 9.3 2.6e-03 1.000 8 12.00 1.50
RAB13 -0.48 8.0 9.1 2.8e-03 1.000 9 13.00 1.50
PHLDA1 -0.94 7.1 9.1 3.0e-03 1.000 10 14.00 1.40
1e-04 NA NA NA NA NA 1 1.10 1.10
1e-05 NA NA NA NA NA 0 0.23 Inf
1e-06 NA NA NA NA NA 0 0.00 NaN
1e-07 NA NA NA NA NA 0 0.00 NaN
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "KCTD13_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CWC25 -0.99 6.8 13.0 0.00047 0.95 1 2.600 2.6
GNG5 0.43 9.2 12.0 0.00082 0.95 2 4.300 2.1
HES6 -1.10 9.2 11.0 0.00092 0.95 3 4.600 1.5
SLC25A39 0.80 7.6 10.0 0.00180 0.95 4 8.900 2.2
CPNE1 -0.69 7.4 10.0 0.00180 0.95 5 8.900 1.8
CDO1 -0.92 6.8 9.9 0.00200 0.95 6 9.600 1.6
USMG5 0.43 8.8 9.7 0.00210 0.95 7 10.000 1.4
NLRP1 0.97 7.5 9.7 0.00210 0.95 8 10.000 1.3
MRPL23 0.71 7.5 8.9 0.00330 0.95 9 15.000 1.7
RABAC1 0.56 7.9 8.8 0.00340 0.95 10 16.000 1.6
1e-04 NA NA NA NA NA 0 0.700 Inf
1e-05 NA NA NA NA NA 0 0.270 Inf
1e-06 NA NA NA NA NA 0 0.100 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "KCTD13_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NINJ1 1.30 7.0 14.0 0.00029 1 1 2.400 2.4
RDX 0.54 8.4 11.0 0.00120 1 2 6.300 3.2
PIGBOS1 1.10 6.8 10.0 0.00170 1 3 7.800 2.6
SEC14L1 1.20 6.8 10.0 0.00170 1 4 7.800 2.0
ELOC 0.47 8.4 10.0 0.00180 1 5 8.100 1.6
PTPN1 1.10 6.9 9.8 0.00210 1 6 9.000 1.5
ZNF787 1.10 6.8 9.6 0.00230 1 7 9.600 1.4
PDLIM1 0.98 7.3 9.6 0.00230 1 8 9.800 1.2
RP11-14N7.2 1.10 7.5 9.3 0.00260 1 9 11.000 1.2
KLHDC8B 1.20 7.1 9.2 0.00270 1 10 11.000 1.1
1e-04 NA NA NA NA NA 0 1.000 Inf
1e-05 NA NA NA NA NA 0 0.200 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "KCTD13_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TLE4 -1.4 7.0 16.0 0.00010 0.40 1 1.200 1.20
GEMIN2 -1.3 6.9 15.0 0.00018 0.40 2 1.500 0.73
IPO9 -1.1 7.2 12.0 0.00065 0.92 3 3.500 1.20
SLC20A1 -1.1 6.8 10.0 0.00170 0.92 4 7.200 1.80
HSPA14 -1.1 6.9 10.0 0.00190 0.92 5 7.600 1.50
GOLGB1 -1.2 6.8 9.8 0.00200 0.92 6 8.100 1.40
MYL9 2.2 7.6 9.6 0.00230 0.92 7 9.200 1.30
STMN3 1.0 7.7 9.6 0.00230 0.92 8 9.200 1.20
HNRNPL -1.0 7.1 9.5 0.00240 0.92 9 9.800 1.10
RAB32 2.1 6.8 9.3 0.00280 0.92 10 11.000 1.10
1e-04 NA NA NA NA NA 0 1.200 Inf
1e-05 NA NA NA NA NA 0 0.470 Inf
1e-06 NA NA NA NA NA 0 0.170 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "KMT2E_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
FTH1 -0.99 12.0 12.0 0.00063 1 1 4.900 4.9
FAM161A 2.40 6.9 12.0 0.00079 1 2 5.600 2.8
CNRIP1 -1.20 6.9 9.6 0.00230 1 3 14.000 4.7
NCSTN 2.30 6.8 9.6 0.00230 1 4 14.000 3.6
BIN1 -1.30 6.8 9.5 0.00240 1 5 15.000 3.0
FANCL 2.20 6.8 9.4 0.00250 1 6 16.000 2.6
ZBTB8OS 1.20 7.5 9.4 0.00260 1 7 16.000 2.3
NR2F2 -0.92 7.5 8.7 0.00380 1 8 21.000 2.7
DEF8 1.10 7.5 8.6 0.00390 1 9 22.000 2.5
DIO3 2.20 7.2 8.5 0.00410 1 10 23.000 2.3
1e-04 NA NA NA NA NA 0 1.700 Inf
1e-05 NA NA NA NA NA 0 0.670 Inf
1e-06 NA NA NA NA NA 0 0.400 Inf
1e-07 NA NA NA NA NA 0 0.200 Inf
1e-08 NA NA NA NA NA 0 0.100 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "KMT2E_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
EZR -1.2 7.6 19.0 2.0e-05 0.086 1 0.430 0.43
QPRT 2.7 6.9 17.0 6.9e-05 0.150 2 0.770 0.38
RNF168 2.2 6.7 15.0 1.7e-04 0.250 3 1.500 0.50
RAB8A 1.5 7.1 12.0 7.2e-04 0.750 4 4.800 1.20
CCDC28B 1.8 6.7 12.0 8.5e-04 0.750 5 5.800 1.20
CSNK1D 1.3 7.2 10.0 1.7e-03 0.990 6 10.000 1.70
CCDC107 1.4 6.9 9.8 2.1e-03 0.990 7 12.000 1.80
ID3 1.8 8.2 9.6 2.3e-03 0.990 8 13.000 1.70
NKTR 1.2 7.2 9.5 2.5e-03 0.990 9 14.000 1.60
CMBL 1.5 6.9 9.2 2.8e-03 0.990 10 16.000 1.60
1e-04 NA NA NA NA NA 2 0.870 0.43
1e-05 NA NA NA NA NA 0 0.270 Inf
1e-06 NA NA NA NA NA 0 0.170 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "KMT2E_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TP53I3 -1.40 7.0 19.0 2.7e-05 0.11 1 0.530 0.53
GPT2 1.80 6.9 14.0 2.3e-04 0.50 2 2.000 0.98
FDXR -1.20 7.1 12.0 7.0e-04 1.00 3 4.300 1.40
NCSTN 1.70 6.8 11.0 1.3e-03 1.00 4 6.700 1.70
HSP90AA1 0.49 10.0 9.7 2.1e-03 1.00 5 11.000 2.20
C11orf73 0.70 7.9 9.2 2.8e-03 1.00 6 14.000 2.30
KIN 1.40 6.8 8.7 3.6e-03 1.00 7 17.000 2.40
ZNF830 1.30 6.8 8.3 4.6e-03 1.00 8 21.000 2.60
GOT2 0.87 7.4 8.3 4.6e-03 1.00 9 21.000 2.30
CEBPB 1.80 6.9 8.1 5.0e-03 1.00 10 23.000 2.30
1e-04 NA NA NA NA NA 1 1.100 1.10
1e-05 NA NA NA NA NA 0 0.230 Inf
1e-06 NA NA NA NA NA 0 0.100 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "LINC00637_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
HSP90AA1 -0.93 11.0 33.0 3.5e-08 0.00015 1 0.000 0.000
MALAT1 -0.64 14.0 19.0 2.5e-05 0.04100 2 0.500 0.250
PKMYT1 1.50 6.7 18.0 2.9e-05 0.04100 3 0.600 0.200
FKBP1B 1.30 6.8 15.0 1.5e-04 0.16000 4 1.700 0.420
DERL1 0.92 6.9 12.0 8.4e-04 0.72000 5 5.700 1.100
HSPH1 -0.82 7.6 11.0 1.1e-03 0.77000 6 6.900 1.100
SEP15 -0.50 8.0 10.0 1.8e-03 0.99000 7 9.900 1.400
JAG1 -1.00 7.0 9.9 1.9e-03 0.99000 8 10.000 1.300
NEFM -1.10 7.8 9.2 2.8e-03 0.99000 9 14.000 1.500
ZDHHC3 0.82 6.9 9.1 2.9e-03 0.99000 10 14.000 1.400
1e-04 NA NA NA NA NA 3 1.300 0.430
1e-05 NA NA NA NA NA 1 0.400 0.400
1e-06 NA NA NA NA NA 1 0.130 0.130
1e-07 NA NA NA NA NA 1 0.067 0.067
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "LINC00637_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TP53I3 -1.20 7.1 17.0 5.1e-05 0.22 1 0.830 0.83
SPOCK1 -1.00 6.7 11.0 9.2e-04 1.00 2 6.200 3.10
COASY 1.20 6.8 11.0 1.2e-03 1.00 3 7.300 2.40
BRCA1 -0.96 6.8 9.9 1.9e-03 1.00 4 11.000 2.70
BAALC 1.40 6.8 9.8 2.0e-03 1.00 5 11.000 2.20
DAP3 0.68 7.4 8.8 3.5e-03 1.00 6 16.000 2.70
SOX21 -0.84 6.8 8.0 5.3e-03 1.00 7 24.000 3.40
PIGH 0.93 6.9 7.9 5.6e-03 1.00 8 26.000 3.20
C9orf3 1.00 6.7 7.8 5.7e-03 1.00 9 26.000 2.90
STT3B 0.88 6.9 7.7 6.1e-03 1.00 10 28.000 2.80
1e-04 NA NA NA NA NA 1 1.200 1.20
1e-05 NA NA NA NA NA 0 0.400 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "LINC00637_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MIAT 1.80 6.9 18 0.00004 0.17 1 0.630 0.63
TNFRSF12A -1.10 8.0 14 0.00029 0.42 2 2.500 1.20
DIO3 1.20 7.1 14 0.00029 0.42 3 2.500 0.82
TPM1 -0.73 8.5 12 0.00059 0.61 4 4.100 1.00
ZNHIT6 -0.83 6.7 12 0.00070 0.61 5 4.600 0.91
TAGLN3 1.30 7.1 11 0.00088 0.63 6 5.200 0.87
SMOC1 1.10 7.0 11 0.00120 0.65 7 6.400 0.91
MTPN -0.62 7.2 11 0.00120 0.65 8 6.400 0.80
PIM3 -0.81 6.8 11 0.00130 0.65 9 6.900 0.77
MCM5 0.84 7.1 10 0.00170 0.68 10 8.600 0.86
1e-04 NA NA NA NA NA 1 1.200 1.20
1e-05 NA NA NA NA NA 0 0.200 Inf
1e-06 NA NA NA NA NA 0 0.100 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "LOC100507431_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CCND2 -1.60 7.2 17.0 5.4e-05 0.23 1 0.770 0.77
SNHG1 -0.86 8.2 10.0 1.5e-03 1.00 2 6.300 3.20
TPM1 -0.88 8.4 9.7 2.2e-03 1.00 3 8.600 2.90
TBL1XR1 1.70 6.8 9.7 2.2e-03 1.00 4 8.600 2.20
TCEAL7 -1.30 6.8 9.4 2.5e-03 1.00 5 9.800 2.00
C4orf48 0.87 7.9 9.1 3.0e-03 1.00 6 11.000 1.90
DOHH 1.30 7.1 9.0 3.1e-03 1.00 7 12.000 1.70
MTERF4 -0.98 6.9 9.0 3.2e-03 1.00 8 12.000 1.50
MTA1 1.20 7.1 8.8 3.5e-03 1.00 9 13.000 1.40
PPP1CB -0.89 7.4 8.7 3.6e-03 1.00 10 13.000 1.30
1e-04 NA NA NA NA NA 1 0.900 0.90
1e-05 NA NA NA NA NA 0 0.430 Inf
1e-06 NA NA NA NA NA 0 0.230 Inf
1e-07 NA NA NA NA NA 0 0.130 Inf
1e-08 NA NA NA NA NA 0 0.100 Inf
1e-09 NA NA NA NA NA 0 0.100 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "LOC100507431_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
S100A13 -1.40 7.2 20 1.2e-05 0.036 1 0.430 0.43
DHRS7 -1.30 6.8 20 1.6e-05 0.036 2 0.470 0.23
SPOCK1 -1.30 6.7 17 5.9e-05 0.073 3 1.000 0.33
LAPTM4A -0.99 7.2 17 6.7e-05 0.073 4 1.100 0.28
GPM6B -0.69 8.5 16 9.2e-05 0.080 5 1.500 0.29
GAP43 -1.20 8.2 15 1.4e-04 0.099 6 1.900 0.31
SPARC -0.69 8.7 14 3.2e-04 0.200 7 3.200 0.46
KCTD1 -1.10 6.8 13 3.7e-04 0.200 8 3.400 0.42
SDC2 -0.81 7.8 13 5.2e-04 0.250 9 4.200 0.47
CRABP1 1.80 9.9 12 5.7e-04 0.250 10 4.500 0.45
1e-04 NA NA NA NA NA 5 1.500 0.31
1e-05 NA NA NA NA NA 0 0.430 Inf
1e-06 NA NA NA NA NA 0 0.200 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "LOC100507431_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
DDIT4 -1.30 8.2 23 3.3e-06 0.014 1 0.033 0.033
EEF2 -0.41 11.0 13 3.4e-04 0.560 2 1.500 0.770
TRIB3 -1.10 7.4 12 7.2e-04 0.560 3 3.000 1.000
TAF6 -0.65 7.3 12 7.8e-04 0.560 4 3.100 0.780
SHMT2 -0.72 7.7 11 9.1e-04 0.560 5 3.500 0.710
MPHOSPH6 0.67 7.2 11 1.0e-03 0.560 6 3.800 0.630
WARS -0.79 7.5 11 1.2e-03 0.560 7 4.600 0.660
HERPUD1 -0.86 7.4 11 1.2e-03 0.560 8 4.600 0.580
EIF3L -0.35 9.6 11 1.3e-03 0.560 9 4.900 0.540
ING4 0.86 6.8 10 1.5e-03 0.560 10 5.900 0.590
1e-04 NA NA NA NA NA 1 0.630 0.630
1e-05 NA NA NA NA NA 1 0.100 0.100
1e-06 NA NA NA NA NA 0 0.000 NaN
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "LOC105376975_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NEFM -1.70 7.9 17.0 6.6e-05 0.29 1 0.670 0.67
NEFL -0.87 8.6 10.0 1.8e-03 0.98 2 7.700 3.80
DIO3 1.20 7.1 10.0 1.8e-03 0.98 3 8.000 2.70
ISY1 -0.88 6.8 9.9 1.9e-03 0.98 4 8.400 2.10
ATAD2 1.30 6.8 9.6 2.3e-03 0.98 5 10.000 2.00
ENTPD6 -0.73 7.0 9.5 2.4e-03 0.98 6 10.000 1.70
SMCHD1 1.00 6.9 9.5 2.4e-03 0.98 7 10.000 1.50
MGST1 -0.70 8.0 9.4 2.5e-03 0.98 8 11.000 1.40
SLC9A3R1 -0.85 6.8 9.2 2.8e-03 0.98 9 12.000 1.30
DHCR24 -0.65 7.3 9.0 3.1e-03 0.98 10 13.000 1.30
1e-04 NA NA NA NA NA 1 0.830 0.83
1e-05 NA NA NA NA NA 0 0.300 Inf
1e-06 NA NA NA NA NA 0 0.200 Inf
1e-07 NA NA NA NA NA 0 0.100 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "LOC105376975_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MCM5 0.98 7.1 13.0 0.00036 0.52 1 2.200 2.20
PSAT1 0.76 8.4 13.0 0.00044 0.52 2 2.800 1.40
PHGDH 0.75 8.6 13.0 0.00050 0.52 3 3.100 1.00
NAT9 0.91 6.8 12.0 0.00057 0.52 4 3.400 0.84
MTHFD2 0.89 7.4 12.0 0.00066 0.52 5 3.800 0.77
TCAF1 1.00 6.8 12.0 0.00077 0.52 6 4.400 0.74
CEBPB 1.30 6.9 11.0 0.00095 0.52 7 5.200 0.74
MRPS34 -0.42 8.6 11.0 0.00096 0.52 8 5.200 0.65
CENPA -0.92 7.1 11.0 0.00110 0.54 9 5.800 0.64
ZNF24 -0.64 7.1 9.9 0.00190 0.68 10 9.100 0.91
1e-04 NA NA NA NA NA 0 0.970 Inf
1e-05 NA NA NA NA NA 0 0.300 Inf
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "LOC105376975_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ACBD3 -1.70 6.9 14.0 0.00021 0.59 1 1.800 1.8
SPOCK1 -1.90 6.7 14.0 0.00031 0.59 2 2.500 1.2
SDC2 -1.40 7.7 13.0 0.00041 0.59 3 3.100 1.0
KIF5C 2.40 7.3 11.0 0.00100 0.73 4 5.400 1.3
HES4 2.30 7.7 11.0 0.00150 0.73 5 7.100 1.4
FNBP4 3.10 6.8 10.0 0.00150 0.73 6 7.100 1.2
OSBPL1A 3.00 6.8 10.0 0.00180 0.73 7 8.200 1.2
RIF1 3.30 6.9 9.8 0.00210 0.73 8 9.900 1.2
ELOB -0.66 9.5 9.8 0.00210 0.73 9 9.900 1.1
HACD1 3.20 6.9 9.7 0.00230 0.73 10 10.000 1.0
1e-04 NA NA NA NA NA 0 0.930 Inf
1e-05 NA NA NA NA NA 0 0.470 Inf
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "miR137_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
PKMYT1 1.40 6.8 16 0.00011 0.47 1 0.870 0.87
APMAP 0.66 7.5 12 0.00061 0.58 2 3.100 1.60
CDC6 1.30 7.0 12 0.00065 0.58 3 3.200 1.10
ARMCX6 -0.81 7.1 12 0.00071 0.58 4 3.500 0.88
NDC80 -1.00 6.8 12 0.00085 0.58 5 4.000 0.80
SOX21 -0.87 6.8 11 0.00092 0.58 6 4.400 0.73
THG1L -0.77 7.0 11 0.00093 0.58 7 4.400 0.63
EIF4A3 0.64 7.7 11 0.00110 0.60 8 5.300 0.66
ATAD2 1.20 6.8 11 0.00140 0.68 9 6.600 0.73
PPIF 0.76 7.4 10 0.00160 0.68 10 7.200 0.72
1e-04 NA NA NA NA NA 0 0.770 Inf
1e-05 NA NA NA NA NA 0 0.200 Inf
1e-06 NA NA NA NA NA 0 0.100 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "miR137_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MTX2 1.10 7.0 13.0 0.00051 0.99 1 2.700 2.7
FRZB 1.70 7.0 12.0 0.00053 0.99 2 2.800 1.4
ASRGL1 1.00 7.0 11.0 0.00130 0.99 3 5.900 2.0
NDUFA9 0.74 7.6 10.0 0.00180 0.99 4 7.600 1.9
COMMD6 -0.37 8.7 9.7 0.00210 0.99 5 8.900 1.8
PHYHIPL 1.20 6.8 9.5 0.00240 0.99 6 10.000 1.7
RND3 -0.83 7.0 9.5 0.00240 0.99 7 10.000 1.5
ELAVL3 1.30 6.9 9.1 0.00300 0.99 8 13.000 1.6
CCNG1 -0.49 8.2 8.9 0.00330 0.99 9 14.000 1.5
SSBP1 -0.34 9.0 8.8 0.00350 0.99 10 14.000 1.4
1e-04 NA NA NA NA NA 0 0.970 Inf
1e-05 NA NA NA NA NA 0 0.270 Inf
1e-06 NA NA NA NA NA 0 0.100 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "miR137_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
DST -1.10 6.8 19 1.7e-05 0.074 1 0.17 0.17
NQO1 -1.10 7.5 16 1.1e-04 0.230 2 0.57 0.28
PDLIM7 -0.57 8.5 13 3.2e-04 0.330 3 1.60 0.52
GPN1 -0.67 7.4 13 3.5e-04 0.330 4 1.60 0.40
ARMCX6 -0.80 7.0 13 3.9e-04 0.330 5 1.80 0.36
ACTG1 -0.24 13.0 12 5.4e-04 0.380 6 2.40 0.39
TPM1 -0.66 8.4 11 9.7e-04 0.590 7 3.40 0.49
CALM2 -0.37 10.0 11 1.3e-03 0.680 8 4.30 0.54
PRR11 -0.87 6.7 10 1.4e-03 0.680 9 4.90 0.54
PTX3 -0.77 6.8 10 1.8e-03 0.780 10 5.90 0.59
1e-04 NA NA NA NA NA 1 0.57 0.57
1e-05 NA NA NA NA NA 0 0.10 Inf
1e-06 NA NA NA NA NA 0 0.00 NaN
1e-07 NA NA NA NA NA 0 0.00 NaN
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "NAB2_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ISY1 -0.94 6.8 12.0 0.00053 1 1 4.100 4.1
PSMA5 0.57 7.9 11.0 0.00087 1 2 6.000 3.0
WDR18 0.70 7.5 10.0 0.00160 1 3 9.400 3.1
PIM3 -0.89 6.9 9.8 0.00200 1 4 11.000 2.7
EIF2B2 0.90 7.0 9.7 0.00210 1 5 11.000 2.3
SOX21 -0.89 6.8 9.7 0.00220 1 6 12.000 1.9
SFSWAP -0.75 6.9 9.4 0.00250 1 7 13.000 1.9
ROMO1 0.51 7.9 9.0 0.00300 1 8 15.000 1.9
TMEM38B 1.00 6.7 8.3 0.00450 1 9 21.000 2.4
ERP29 0.40 8.6 8.0 0.00530 1 10 25.000 2.5
1e-04 NA NA NA NA NA 0 1.400 Inf
1e-05 NA NA NA NA NA 0 0.370 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "NAB2_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
CLU -1.90 7.8 44 4.7e-10 2.0e-06 1 0.033
NQO1 -1.90 7.6 32 6.5e-08 1.4e-04 2 0.067
GAP43 -1.70 8.3 28 4.6e-07 6.6e-04 3 0.170
FTH1 -1.10 12.0 24 2.6e-06 2.7e-03 4 0.330
CTD-2006C1.2 -1.20 7.0 19 2.5e-05 2.1e-02 5 0.670
IFI27L1 -1.20 6.8 18 3.1e-05 2.2e-02 6 0.700
EIF4A2 -0.73 8.1 14 2.3e-04 1.4e-01 7 2.500
SQSTM1 -1.30 8.3 14 3.0e-04 1.6e-01 8 3.000
CRABP2 1.40 7.6 13 4.8e-04 2.3e-01 9 3.900
ARMCX6 -0.95 7.0 12 5.6e-04 2.4e-01 10 4.200
1e-04 NA NA NA NA NA 6 1.500
1e-05 NA NA NA NA NA 4 0.530
1e-06 NA NA NA NA NA 3 0.200
1e-07 NA NA NA NA NA 2 0.067
1e-08 NA NA NA NA NA 1 0.067
1e-09 NA NA NA NA NA 1 0.033
1e-10 NA NA NA NA NA 0 0.033
EmpiricalFDR
CLU 0.033
NQO1 0.033
GAP43 0.056
FTH1 0.083
CTD-2006C1.2 0.130
IFI27L1 0.120
EIF4A2 0.350
SQSTM1 0.380
CRABP2 0.430
ARMCX6 0.420
1e-04 0.240
1e-05 0.130
1e-06 0.067
1e-07 0.033
1e-08 0.067
1e-09 0.033
1e-10 Inf
[1] "NAB2_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MT-ATP6 -0.64 11.0 13.0 0.00042 0.91 1 1.500 1.50
PKMYT1 1.60 6.8 13.0 0.00043 0.91 2 1.500 0.77
TP53 1.10 7.1 12.0 0.00066 0.93 3 2.600 0.86
ASCL1 -1.30 7.2 11.0 0.00130 1.00 4 4.800 1.20
HCCS -0.92 6.8 9.9 0.00200 1.00 5 6.700 1.30
CAPZA1 -0.58 7.8 9.9 0.00200 1.00 6 6.800 1.10
PEX2 1.10 6.8 9.3 0.00270 1.00 7 9.000 1.30
TMEM106C 0.88 7.4 9.0 0.00310 1.00 8 10.000 1.30
ID1 -1.20 6.9 8.9 0.00330 1.00 9 11.000 1.20
UCHL5 1.10 6.8 8.9 0.00330 1.00 10 11.000 1.10
1e-04 NA NA NA NA NA 0 0.330 Inf
1e-05 NA NA NA NA NA 0 0.100 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "NGEF_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NQO1 -1.70 7.4 14 0.00025 0.53 1 2.000 2.00
SKP1 0.73 9.0 14 0.00025 0.53 2 2.000 1.00
CTTN -1.40 7.0 13 0.00041 0.58 3 2.500 0.82
CMBL 2.50 6.9 12 0.00054 0.58 4 2.900 0.73
APRT 0.99 8.4 12 0.00083 0.63 5 4.200 0.84
DEF8 1.30 7.5 11 0.00096 0.63 6 4.600 0.76
TPX2 -1.40 7.1 11 0.00110 0.63 7 5.300 0.76
PHLDA3 1.90 7.8 11 0.00130 0.63 8 6.400 0.80
ARFGAP2 1.40 7.3 11 0.00150 0.63 9 6.900 0.76
PCDH17 -1.30 7.2 10 0.00150 0.63 10 7.200 0.72
1e-04 NA NA NA NA NA 0 1.100 Inf
1e-05 NA NA NA NA NA 0 0.330 Inf
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.100 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "NGEF_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
EMG1 -1.8 7.7 13.0 0.00044 0.98 1 2.600 2.6
SGO2 -2.4 6.9 12.0 0.00062 0.98 2 3.300 1.7
TROAP -2.5 6.7 12.0 0.00081 0.98 3 4.200 1.4
CDCA3 -2.5 6.9 11.0 0.00120 0.98 4 5.400 1.4
AURKB -2.3 7.3 9.9 0.00200 0.98 5 8.700 1.7
KPNA2 -1.8 8.7 9.8 0.00210 0.98 6 8.900 1.5
REEP4 -2.1 6.8 9.5 0.00240 0.98 7 10.000 1.4
PSRC1 -2.2 7.7 9.5 0.00250 0.98 8 10.000 1.3
MIS18BP1 -2.2 6.7 9.0 0.00320 0.98 9 13.000 1.4
TMCO1 2.9 7.8 9.0 0.00320 0.98 10 13.000 1.3
1e-04 NA NA NA NA NA 0 0.870 Inf
1e-05 NA NA NA NA NA 0 0.470 Inf
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "PBRM1_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
PLK1 -2.7 7.5 22 5.8e-06 0.025 1 0.500
RP11-339B21.12 -2.3 7.0 17 7.2e-05 0.097 2 1.200
JUN -1.9 7.9 16 8.8e-05 0.097 3 1.200
CDC25B -2.5 7.2 16 8.9e-05 0.097 4 1.200
TPX2 -2.2 7.1 15 2.0e-04 0.180 5 2.100
PTTG1 -2.0 8.5 13 3.5e-04 0.230 6 2.700
PSRC1 -2.0 7.7 13 3.6e-04 0.230 7 2.800
CCDC167 -1.1 8.1 11 1.0e-03 0.570 8 5.600
NUDCD2 -1.4 7.5 11 1.3e-03 0.590 9 6.700
NUF2 -2.0 6.8 10 1.5e-03 0.590 10 7.300
1e-04 NA NA NA NA NA 4 1.400
1e-05 NA NA NA NA NA 1 0.600
1e-06 NA NA NA NA NA 0 0.400
1e-07 NA NA NA NA NA 0 0.170
1e-08 NA NA NA NA NA 0 0.067
1e-09 NA NA NA NA NA 0 0.067
1e-10 NA NA NA NA NA 0 0.033
EmpiricalFDR
PLK1 0.50
RP11-339B21.12 0.62
JUN 0.41
CDC25B 0.31
TPX2 0.42
PTTG1 0.46
PSRC1 0.40
CCDC167 0.70
NUDCD2 0.74
NUF2 0.73
1e-04 0.35
1e-05 0.60
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
INTU -1.50 6.9 17.0 7.5e-05 0.32 1 1.300 1.30
IFITM3 -1.60 8.8 15.0 1.5e-04 0.32 2 1.800 0.92
TFPT 2.10 6.9 11.0 9.3e-04 1.00 3 7.200 2.40
MKI67 -1.30 7.3 11.0 1.2e-03 1.00 4 8.500 2.10
ILKAP 1.60 6.9 9.9 2.0e-03 1.00 5 13.000 2.60
PRSS23 -0.94 8.2 9.4 2.6e-03 1.00 6 16.000 2.60
BCAT2 1.60 6.9 9.3 2.8e-03 1.00 7 16.000 2.30
NUDT14 1.60 7.0 8.9 3.2e-03 1.00 8 19.000 2.30
TLE4 -1.20 6.9 8.7 3.7e-03 1.00 9 20.000 2.30
UBE2C -1.40 8.2 8.6 3.8e-03 1.00 10 21.000 2.10
1e-04 NA NA NA NA NA 1 1.500 1.50
1e-05 NA NA NA NA NA 0 0.570 Inf
1e-06 NA NA NA NA NA 0 0.200 Inf
1e-07 NA NA NA NA NA 0 0.130 Inf
1e-08 NA NA NA NA NA 0 0.100 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "PBRM1_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SPARC -1.6 8.6 20 1.7e-05 0.074 1 1.300 1.30
HDAC2 2.0 8.6 16 9.3e-05 0.180 2 2.400 1.20
HEBP1 -2.0 7.0 15 1.3e-04 0.180 3 2.700 0.89
CCND2 -2.3 7.1 15 1.7e-04 0.190 4 3.100 0.77
SCD -1.7 7.6 14 2.6e-04 0.210 5 3.800 0.75
NDN -1.7 7.5 14 3.0e-04 0.210 6 3.900 0.65
PCSK1N -2.0 7.1 13 4.8e-04 0.260 7 4.900 0.70
ID1 -2.4 6.9 13 4.8e-04 0.260 8 5.000 0.62
CMBL -1.9 7.0 12 7.7e-04 0.310 9 6.700 0.75
COPS3 2.3 7.9 12 7.7e-04 0.310 10 6.700 0.67
1e-04 NA NA NA NA NA 2 2.500 1.30
1e-05 NA NA NA NA NA 0 1.000 Inf
1e-06 NA NA NA NA NA 0 0.530 Inf
1e-07 NA NA NA NA NA 0 0.330 Inf
1e-08 NA NA NA NA NA 0 0.200 Inf
1e-09 NA NA NA NA NA 0 0.100 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "PCDHA123_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ARMCX6 -0.86 7.0 16 9.6e-05 0.41 1 1.0 1.0
PDLIM2 -0.75 7.5 12 5.5e-04 0.75 2 3.7 1.8
PHLDA1 -1.00 7.1 12 6.3e-04 0.75 3 4.2 1.4
GAP43 -0.85 8.2 11 9.2e-04 0.75 4 5.5 1.4
SSR3 -0.48 8.1 11 9.2e-04 0.75 5 5.5 1.1
SUMO2 0.27 10.0 11 1.1e-03 0.75 6 6.8 1.1
GOSR1 -0.64 7.1 11 1.2e-03 0.75 7 7.1 1.0
PPP2R2B -0.81 6.8 10 1.6e-03 0.76 8 8.9 1.1
CDC6 1.00 6.9 10 1.7e-03 0.76 9 9.5 1.1
MAT2A 0.68 7.3 10 1.9e-03 0.76 10 10.0 1.0
1e-04 NA NA NA NA NA 1 1.0 1.0
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 0.0 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] "PCDHA123_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CTGF -0.84 8.6 13 0.00040 0.66 1 1.900 1.90
LASP1 -0.82 6.8 12 0.00065 0.66 2 2.400 1.20
IMPA2 0.91 6.8 12 0.00084 0.66 3 2.800 0.92
MCM5 0.79 7.1 11 0.00088 0.66 4 2.900 0.72
CYR61 -0.63 8.0 11 0.00100 0.66 5 3.200 0.65
GRSF1 -0.47 7.7 11 0.00110 0.66 6 3.300 0.55
NINJ1 0.77 7.0 11 0.00130 0.66 7 4.500 0.64
SEPT2 -0.36 8.2 11 0.00140 0.66 8 4.600 0.58
DDIT4 -0.86 8.1 10 0.00140 0.66 9 4.600 0.51
PDE6D -0.70 6.7 10 0.00170 0.71 10 5.500 0.55
1e-04 NA NA NA NA NA 0 0.370 Inf
1e-05 NA NA NA NA NA 0 0.130 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "PCDHA123_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NRDC 0.83 7.0 14.0 0.00020 0.65 1 0.93 0.93
GPM6B -0.45 8.5 13.0 0.00031 0.65 2 1.30 0.63
SOX4 0.74 8.4 10.0 0.00170 1.00 3 5.50 1.80
RBM22 -0.54 7.2 9.9 0.00190 1.00 4 6.10 1.50
IGF2BP1 0.51 7.5 9.1 0.00290 1.00 5 9.00 1.80
BNIP3 0.61 7.2 8.1 0.00480 1.00 6 15.00 2.40
DPYSL3 0.75 6.8 8.1 0.00500 1.00 7 15.00 2.20
TMEM101 -0.59 6.9 8.0 0.00510 1.00 8 16.00 2.00
FYN 0.60 7.1 8.0 0.00510 1.00 9 16.00 1.70
RNF220 -0.69 6.7 8.0 0.00520 1.00 10 16.00 1.60
1e-04 NA NA NA NA NA 0 0.50 Inf
1e-05 NA NA NA NA NA 0 0.17 Inf
1e-06 NA NA NA NA NA 0 0.00 NaN
1e-07 NA NA NA NA NA 0 0.00 NaN
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "pos_SNAP91_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TDG 4.1 7.3 8.7 0.0038 1 1 16.000 16.0
MGME1 -1.8 6.9 8.1 0.0050 1 2 21.000 10.0
USP16 4.0 7.2 7.8 0.0059 1 3 24.000 8.1
FOXB1 -1.8 7.0 7.7 0.0064 1 4 26.000 6.5
LLPH 4.0 7.2 7.5 0.0068 1 5 27.000 5.4
RP11-329L6.2 4.3 7.4 7.5 0.0068 1 6 27.000 4.5
MT-CO2 -1.2 12.0 7.4 0.0074 1 7 30.000 4.2
SPAG16 4.3 7.4 7.3 0.0079 1 8 32.000 3.9
RBCK1 3.8 7.2 7.1 0.0084 1 9 34.000 3.7
MT-CYB -1.1 11.0 7.1 0.0086 1 10 34.000 3.4
1e-04 NA NA NA NA NA 0 1.700 Inf
1e-05 NA NA NA NA NA 0 0.600 Inf
1e-06 NA NA NA NA NA 0 0.330 Inf
1e-07 NA NA NA NA NA 0 0.270 Inf
1e-08 NA NA NA NA NA 0 0.100 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "pos_SNAP91_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
THG1L -1.10 7.0 16.0 8.9e-05 0.38 1 0.700 0.70
PRSS23 -0.77 8.3 11.0 1.4e-03 1.00 2 6.300 3.20
CD3EAP 1.30 6.7 10.0 1.5e-03 1.00 3 6.500 2.20
SF3B4 0.68 7.7 10.0 1.5e-03 1.00 4 6.600 1.60
CAV1 -1.20 7.3 10.0 1.8e-03 1.00 5 7.700 1.50
PPP2R2B -1.00 6.8 9.8 2.0e-03 1.00 6 8.500 1.40
TMEM259 0.94 7.1 9.4 2.6e-03 1.00 7 10.000 1.50
LONP1 1.10 7.1 8.7 3.6e-03 1.00 8 14.000 1.80
TP53I3 -0.93 7.0 8.7 3.7e-03 1.00 9 15.000 1.60
DPH3 -0.69 7.3 8.5 4.0e-03 1.00 10 16.000 1.60
1e-04 NA NA NA NA NA 1 0.730 0.73
1e-05 NA NA NA NA NA 0 0.270 Inf
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.100 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "PPP1R16B_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CAV1 -1.30 7.4 15.0 0.00014 0.58 1 1.300 1.3
SRPK2 -0.64 7.4 12.0 0.00073 0.87 2 4.300 2.2
NEFM -1.30 7.9 10.0 0.00160 0.87 3 7.900 2.6
CMTM3 -0.51 7.7 10.0 0.00170 0.87 4 8.100 2.0
TCTN1 0.90 6.8 9.6 0.00230 0.87 5 11.000 2.2
RPS19 -0.24 13.0 9.4 0.00250 0.87 6 12.000 2.0
YIF1B 0.79 6.8 9.1 0.00290 0.87 7 13.000 1.9
GCAT 0.81 7.0 9.0 0.00300 0.87 8 14.000 1.7
NQO1 -0.95 7.4 8.9 0.00320 0.87 9 15.000 1.6
TFDP1 0.72 7.2 8.9 0.00330 0.87 10 15.000 1.5
1e-04 NA NA NA NA NA 0 0.970 Inf
1e-05 NA NA NA NA NA 0 0.170 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "PPP1R16B_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
EZR -0.83 7.5 12.0 0.00058 1 1 3.000 3.0
ZNF512 -0.95 6.7 11.0 0.00090 1 2 4.600 2.3
TLE4 -0.91 7.0 10.0 0.00170 1 3 7.100 2.4
TET1 -0.87 6.8 10.0 0.00190 1 4 8.000 2.0
RPN1 1.10 6.7 9.3 0.00260 1 5 10.000 2.1
USP7 -0.84 6.8 8.9 0.00340 1 6 13.000 2.1
WASF1 -0.80 6.9 8.8 0.00340 1 7 13.000 1.8
NSG1 1.10 7.0 8.2 0.00470 1 8 18.000 2.2
CDC42 -0.45 8.0 8.2 0.00480 1 9 18.000 2.0
LAPTM4A -0.65 7.1 7.8 0.00580 1 10 22.000 2.2
1e-04 NA NA NA NA NA 0 0.670 Inf
1e-05 NA NA NA NA NA 0 0.130 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "PPP1R16B_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ASCL1 -1.30 7.3 14.0 0.00028 0.77 1 1.800 1.8
GTF2F2 -0.64 7.5 12.0 0.00066 0.77 2 3.700 1.8
IRX5 -0.98 6.9 12.0 0.00071 0.77 3 4.000 1.3
SNAPC2 -0.86 7.1 12.0 0.00076 0.77 4 4.200 1.0
DBI 0.46 8.9 11.0 0.00130 0.77 5 6.600 1.3
HES6 -1.00 9.2 11.0 0.00130 0.77 6 6.600 1.1
MBOAT7 1.00 6.8 10.0 0.00150 0.77 7 7.200 1.0
THG1L -0.77 7.0 9.6 0.00220 0.77 8 11.000 1.4
TWF2 -0.83 6.9 9.6 0.00230 0.77 9 11.000 1.2
SOX11 -0.75 8.0 9.6 0.00230 0.77 10 11.000 1.1
1e-04 NA NA NA NA NA 0 0.870 Inf
1e-05 NA NA NA NA NA 0 0.170 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "RERE_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SNX27 -0.85 6.8 12.0 0.00053 0.92 1 3.10 3.1
TPX2 -0.95 7.2 12.0 0.00067 0.92 2 3.90 2.0
NDC80 -0.97 6.8 12.0 0.00078 0.92 3 4.50 1.5
ISG20L2 0.92 7.0 11.0 0.00086 0.92 4 4.80 1.2
NINJ1 0.86 7.0 9.1 0.00290 0.99 5 13.00 2.5
ARF4 0.60 8.4 8.9 0.00330 0.99 6 14.00 2.4
IMPDH1 0.84 6.9 8.7 0.00370 0.99 7 16.00 2.2
KNSTRN -0.79 7.1 8.4 0.00420 0.99 8 18.00 2.2
TROVE2 0.48 7.7 8.4 0.00420 0.99 9 18.00 2.0
MKI67 -0.77 7.4 8.2 0.00460 0.99 10 19.00 1.9
1e-04 NA NA NA NA NA 0 0.73 Inf
1e-05 NA NA NA NA NA 0 0.10 Inf
1e-06 NA NA NA NA NA 0 0.00 NaN
1e-07 NA NA NA NA NA 0 0.00 NaN
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "RERE_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
USMG5 0.46 8.8 16.0 0.00011 0.45 1 1.300 1.30
KDELR2 0.62 8.0 14.0 0.00021 0.45 2 1.900 0.95
FBXO5 1.20 7.0 12.0 0.00054 0.62 3 3.900 1.30
MRPL23 0.69 7.5 12.0 0.00058 0.62 4 4.000 1.00
TAGLN3 -1.20 7.5 11.0 0.00100 0.90 5 6.100 1.20
BTG1 -0.61 8.6 10.0 0.00160 1.00 6 8.500 1.40
P3H4 0.85 6.9 9.9 0.00190 1.00 7 9.700 1.40
CIAPIN1 -0.52 7.6 9.7 0.00220 1.00 8 11.000 1.40
DDX6 0.81 7.0 9.5 0.00240 1.00 9 12.000 1.30
DCAF15 -0.79 6.9 9.2 0.00280 1.00 10 14.000 1.40
1e-04 NA NA NA NA NA 0 1.300 Inf
1e-05 NA NA NA NA NA 0 0.230 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "RERE_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
BRCA1 -1.10 6.8 13.0 0.00052 1 1 3.90 3.9
HIPK2 -0.92 7.1 11.0 0.00097 1 2 5.80 2.9
CADM1 -0.99 7.0 11.0 0.00140 1 3 7.70 2.6
HMGCS1 -0.69 8.2 10.0 0.00190 1 4 9.50 2.4
EZR -0.77 7.5 8.8 0.00350 1 5 17.00 3.3
AKAP12 -0.83 7.4 8.5 0.00390 1 6 19.00 3.1
ACBD6 -0.65 7.3 8.3 0.00460 1 7 22.00 3.1
C11orf58 0.39 9.0 8.2 0.00480 1 8 22.00 2.8
GLA 1.20 6.8 8.1 0.00490 1 9 23.00 2.6
SURF1 0.93 7.1 7.9 0.00550 1 10 25.00 2.5
1e-04 NA NA NA NA NA 0 1.20 Inf
1e-05 NA NA NA NA NA 0 0.30 Inf
1e-06 NA NA NA NA NA 0 0.13 Inf
1e-07 NA NA NA NA NA 0 0.10 Inf
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "SETD1A_1st_exon_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SNAPC3 -1.10 6.9 11.0 0.00093 1 1 7.100 7.1
NUP50 -1.00 6.9 11.0 0.00120 1 2 8.400 4.2
ACTA2 -1.10 7.4 9.5 0.00250 1 3 14.000 4.6
HES6 1.30 8.8 9.4 0.00260 1 4 14.000 3.6
LRIF1 1.30 6.9 9.3 0.00260 1 5 15.000 2.9
UCP2 1.40 6.8 9.3 0.00270 1 6 15.000 2.5
CARD19 1.30 6.9 9.0 0.00310 1 7 17.000 2.4
MAP1A 1.30 7.0 8.9 0.00320 1 8 17.000 2.2
ITGAE 0.66 7.7 8.6 0.00380 1 9 20.000 2.2
CCND3 1.20 7.1 8.3 0.00450 1 10 23.000 2.3
1e-04 NA NA NA NA NA 0 1.800 Inf
1e-05 NA NA NA NA NA 0 0.600 Inf
1e-06 NA NA NA NA NA 0 0.270 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "SETD1A_1st_exon_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
RAB13 -0.80 8.0 19 2.2e-05 0.055 1 0.670 0.67
ASRGL1 1.50 7.0 19 2.6e-05 0.055 2 0.700 0.35
CALD1 -0.99 8.1 17 4.7e-05 0.066 3 0.870 0.29
RIT1 -1.10 6.9 14 2.0e-04 0.180 4 2.100 0.52
MPZL1 -0.93 6.8 14 2.1e-04 0.180 5 2.200 0.44
MYL9 -1.20 7.9 13 3.2e-04 0.200 6 2.900 0.48
TAGLN -1.20 9.3 13 3.7e-04 0.200 7 3.100 0.44
EMP3 -1.20 6.9 13 3.7e-04 0.200 8 3.100 0.38
TYMS 0.87 8.4 13 5.0e-04 0.240 9 4.000 0.44
PRSS23 -0.85 8.3 12 6.2e-04 0.260 10 4.500 0.45
1e-04 NA NA NA NA NA 3 1.500 0.50
1e-05 NA NA NA NA NA 0 0.500 Inf
1e-06 NA NA NA NA NA 0 0.200 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "SETD1A_1st_exon_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
UBB 4.0 9.5 16 0.00012 0.49 1 0.830 0.83
FXYD6 3.5 8.1 13 0.00037 0.49 2 1.500 0.77
BEX2 -2.4 6.9 13 0.00041 0.49 3 1.700 0.57
PTN -2.1 8.1 13 0.00045 0.49 4 1.800 0.44
TMSB10 -1.1 12.0 12 0.00060 0.52 5 2.200 0.45
FTH1 -1.3 12.0 11 0.00120 0.66 6 3.800 0.63
SEPHS2 -2.0 7.0 11 0.00130 0.66 7 4.000 0.58
MKNK2 -1.9 6.9 11 0.00140 0.66 8 4.200 0.52
COX11 4.1 7.3 11 0.00140 0.66 9 4.200 0.46
CST3 2.1 8.2 10 0.00160 0.69 10 4.600 0.46
1e-04 NA NA NA NA NA 0 0.770 Inf
1e-05 NA NA NA NA NA 0 0.067 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "STAT6_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SOX21 -0.99 6.8 10.0 0.0017 1 1 8.800 8.8
EIF2D 1.10 6.8 10.0 0.0018 1 2 9.700 4.8
ITM2C 1.00 7.1 9.6 0.0023 1 3 11.000 3.7
RAB28 -0.89 6.9 9.4 0.0025 1 4 12.000 3.1
NBEAL1 0.59 8.1 8.9 0.0033 1 5 15.000 3.0
CCNDBP1 1.20 6.7 8.0 0.0051 1 6 22.000 3.7
TMEM170A -0.76 7.0 7.7 0.0062 1 7 26.000 3.8
TAF6 -0.65 7.2 7.2 0.0081 1 8 33.000 4.1
ZMAT3 -0.86 7.0 7.1 0.0083 1 9 33.000 3.7
CACUL1 -0.62 7.2 6.8 0.0099 1 10 38.000 3.8
1e-04 NA NA NA NA NA 0 1.300 Inf
1e-05 NA NA NA NA NA 0 0.400 Inf
1e-06 NA NA NA NA NA 0 0.100 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "STAT6_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TP53I3 -1.20 7.1 17 6.3e-05 0.19 1 0.470 0.47
IMPA2 1.40 6.8 16 8.8e-05 0.19 2 0.570 0.28
DHFR 0.95 7.8 14 2.1e-04 0.25 3 1.100 0.36
CYFIP2 -0.95 6.9 14 2.3e-04 0.25 4 1.200 0.31
ENHO 1.20 6.7 12 5.7e-04 0.49 5 2.500 0.49
CCNH -0.88 6.8 12 6.7e-04 0.49 6 3.000 0.49
ATAD5 1.20 6.8 11 1.0e-03 0.59 7 4.400 0.63
LAMTOR5 -0.46 8.4 11 1.1e-03 0.59 8 4.800 0.60
TP53TG1 -0.90 6.9 10 1.4e-03 0.63 9 5.900 0.65
NSMCE1 -0.88 6.9 10 1.4e-03 0.63 10 5.900 0.59
1e-04 NA NA NA NA NA 2 0.570 0.28
1e-05 NA NA NA NA NA 0 0.067 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "STAT6_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MPZL1 -0.81 6.9 14.0 0.00026 0.88 1 1.600 1.60
TACC3 1.10 6.9 13.0 0.00041 0.88 2 1.900 0.97
PLK1 1.20 7.2 11.0 0.00110 1.00 3 4.900 1.60
ZNF787 0.91 6.7 11.0 0.00130 1.00 4 5.900 1.50
U2SURP 0.54 7.7 9.7 0.00210 1.00 5 9.200 1.80
DST -0.84 6.8 9.6 0.00230 1.00 6 9.900 1.60
FZD3 -0.45 7.7 8.6 0.00380 1.00 7 16.000 2.20
CCNB1 0.85 7.3 8.1 0.00480 1.00 8 20.000 2.50
MAP1LC3B 0.55 7.9 8.1 0.00480 1.00 9 20.000 2.20
HMGCS1 -0.47 8.3 8.0 0.00510 1.00 10 21.000 2.10
1e-04 NA NA NA NA NA 0 0.570 Inf
1e-05 NA NA NA NA NA 0 0.033 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "TCF4-ITF2_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
IDI1 0.62 8.2 13.0 0.00032 0.96 1 2.700 2.7
CLK3 -0.88 6.9 13.0 0.00043 0.96 2 3.400 1.7
HMBS 0.73 7.2 12.0 0.00069 0.97 3 4.800 1.6
GPI 0.78 7.1 11.0 0.00087 0.97 4 6.000 1.5
TRMT61A -0.80 6.8 11.0 0.00130 0.97 5 7.800 1.6
IFITM3 0.96 8.4 10.0 0.00170 0.97 6 9.300 1.6
MOCS2 0.87 6.8 10.0 0.00180 0.97 7 10.000 1.4
SEC11C 0.61 7.6 9.9 0.00190 0.97 8 10.000 1.3
TGIF2 0.87 7.0 9.7 0.00220 0.97 9 12.000 1.3
C7orf73 0.41 8.1 9.6 0.00230 0.97 10 12.000 1.2
1e-04 NA NA NA NA NA 0 1.000 Inf
1e-05 NA NA NA NA NA 0 0.300 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "TCF4-ITF2_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ATPIF1 -0.53 8.3 15.0 0.00013 0.58 1 1.500 1.5
FOS -1.00 6.9 12.0 0.00076 1.00 2 5.400 2.7
MCM5 0.86 7.2 9.6 0.00220 1.00 3 13.000 4.4
TRIM2 -0.71 7.2 9.6 0.00230 1.00 4 13.000 3.3
USP34 -0.80 6.7 9.3 0.00270 1.00 5 15.000 3.0
SALL2 -0.77 6.8 9.2 0.00270 1.00 6 15.000 2.5
TDP2 -0.69 6.9 8.9 0.00330 1.00 7 18.000 2.6
VGLL4 0.77 6.9 8.6 0.00390 1.00 8 21.000 2.6
TMEM129 -0.78 6.8 8.5 0.00410 1.00 9 22.000 2.4
GLIPR2 0.83 6.9 8.4 0.00410 1.00 10 22.000 2.2
1e-04 NA NA NA NA NA 0 1.300 Inf
1e-05 NA NA NA NA NA 0 0.230 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "TCF4-ITF2_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CLN8 2.80 6.7 13.0 0.00036 1 1 2.800 2.8
MRPS28 2.40 6.9 12.0 0.00067 1 2 4.300 2.2
DIO3 -1.50 7.3 11.0 0.00096 1 3 5.300 1.8
LMO4 2.00 7.1 11.0 0.00110 1 4 6.100 1.5
PRPF38B -0.97 7.5 11.0 0.00120 1 5 6.300 1.3
PLK2 -1.30 7.5 9.4 0.00260 1 6 11.000 1.9
UBN1 1.80 7.0 9.1 0.00300 1 7 13.000 1.9
STARD3 2.00 6.7 8.8 0.00340 1 8 14.000 1.8
PCBP1 0.71 8.6 8.8 0.00350 1 9 15.000 1.6
TOP1 -0.69 7.8 8.7 0.00370 1 10 15.000 1.5
1e-04 NA NA NA NA NA 0 1.500 Inf
1e-05 NA NA NA NA NA 0 0.470 Inf
1e-06 NA NA NA NA NA 0 0.170 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "TRANK1_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
HMGCS1 -1.6 8.2 12.0 0.00075 1 1 4.300 4.3
SDF2L1 -2.0 7.4 11.0 0.00120 1 2 6.200 3.1
INIP -1.9 7.0 11.0 0.00120 1 3 6.200 2.1
PYCR1 -2.3 7.0 9.9 0.00200 1 4 8.500 2.1
MRPS34 1.9 8.5 9.7 0.00220 1 5 9.300 1.9
HSPB11 4.4 7.5 8.7 0.00380 1 6 15.000 2.4
EEF2KMT -1.9 6.9 8.6 0.00390 1 7 15.000 2.2
SEC11C -1.4 7.7 8.5 0.00410 1 8 16.000 2.0
TP53 3.9 7.2 8.0 0.00530 1 9 21.000 2.3
OTUB1 1.8 7.9 7.9 0.00550 1 10 21.000 2.1
1e-04 NA NA NA NA NA 0 1.300 Inf
1e-05 NA NA NA NA NA 0 0.400 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "TRANK1_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
UGP2 1.20 7.2 10.0 0.0015 1 1 8.200 8.2
FZD3 -0.68 7.6 9.8 0.0021 1 2 10.000 5.2
SNRNP200 1.00 7.1 9.2 0.0029 1 3 14.000 4.6
GNAQ 1.40 6.7 8.9 0.0033 1 4 16.000 4.0
HERPUD1 1.40 7.2 8.7 0.0036 1 5 17.000 3.4
CCNK -0.90 7.0 8.7 0.0037 1 6 18.000 3.0
TMEM230 0.62 8.0 8.7 0.0038 1 7 18.000 2.5
XBP1 1.00 7.7 8.2 0.0048 1 8 22.000 2.8
SLC20A1 -0.92 6.7 8.0 0.0052 1 9 24.000 2.7
MLLT10 -0.86 6.9 8.0 0.0052 1 10 24.000 2.4
1e-04 NA NA NA NA NA 0 1.100 Inf
1e-05 NA NA NA NA NA 0 0.270 Inf
1e-06 NA NA NA NA NA 0 0.170 Inf
1e-07 NA NA NA NA NA 0 0.100 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "TRANK1_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CLK3 -0.75 6.8 12.0 0.00068 1 1 3.00 3.0
RPUSD1 0.79 6.8 12.0 0.00068 1 2 3.00 1.5
PKMYT1 0.88 6.7 10.0 0.00180 1 3 7.30 2.4
RPRD1A -0.63 7.0 9.9 0.00190 1 4 7.30 1.8
RND3 -0.75 7.0 9.9 0.00190 1 5 7.40 1.5
STX18 0.67 6.9 9.8 0.00200 1 6 7.90 1.3
SOX21 -0.75 6.8 9.7 0.00210 1 7 7.90 1.1
THG1L -0.61 6.9 8.3 0.00440 1 8 17.00 2.1
TBPL1 0.57 7.1 8.2 0.00460 1 9 17.00 1.9
ZNF48 -0.65 6.7 8.1 0.00480 1 10 18.00 1.8
1e-04 NA NA NA NA NA 0 0.83 Inf
1e-05 NA NA NA NA NA 0 0.27 Inf
1e-06 NA NA NA NA NA 0 0.00 NaN
1e-07 NA NA NA NA NA 0 0.00 NaN
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "UBE2Q2P1_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
JAG1 -2.20 7.0 28 4.3e-07 0.0018 1 0.13 0.13
SERPINH1 -1.10 7.9 16 8.9e-05 0.1800 2 0.97 0.48
NQO1 -1.70 7.4 15 1.4e-04 0.1800 3 1.20 0.41
SGO1 2.60 6.9 14 2.1e-04 0.1800 4 1.50 0.37
RCN1 -0.94 8.8 14 2.8e-04 0.1800 5 1.70 0.34
HSP90AA1 -0.68 11.0 14 3.2e-04 0.1800 6 1.80 0.29
PPP1CB -1.20 7.4 14 3.3e-04 0.1800 7 1.80 0.25
COX7A2 -0.53 9.5 13 3.5e-04 0.1800 8 1.90 0.24
PRDX6 -0.60 9.3 13 4.4e-04 0.2100 9 2.40 0.26
DNAJB1 -1.30 6.9 13 5.2e-04 0.2200 10 2.90 0.29
1e-04 NA NA NA NA NA 2 1.00 0.50
1e-05 NA NA NA NA NA 1 0.27 0.27
1e-06 NA NA NA NA NA 1 0.13 0.13
1e-07 NA NA NA NA NA 0 0.10 Inf
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "UBE2Q2P1_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TERF2IP -1.60 7.5 17.0 6.2e-05 0.27 1 0.700 0.70
MALAT1 -0.96 14.0 13.0 3.8e-04 0.53 2 2.100 1.00
ATP5B -0.78 9.6 13.0 4.0e-04 0.53 3 2.100 0.71
UFSP2 2.50 7.0 12.0 6.0e-04 0.53 4 3.100 0.78
PPP1R2 -1.40 6.9 12.0 6.1e-04 0.53 5 3.200 0.64
C1orf21 2.50 7.0 11.0 1.1e-03 0.72 6 5.400 0.89
SFRP1 3.80 7.1 11.0 1.2e-03 0.72 7 5.600 0.80
DRAXIN 2.90 6.8 10.0 1.8e-03 0.78 8 8.600 1.10
NEFL -1.40 8.5 10.0 1.9e-03 0.78 9 9.000 1.00
PABPC1 0.70 10.0 9.8 2.1e-03 0.78 10 10.000 1.00
1e-04 NA NA NA NA NA 1 0.900 0.90
1e-05 NA NA NA NA NA 0 0.300 Inf
1e-06 NA NA NA NA NA 0 0.170 Inf
1e-07 NA NA NA NA NA 0 0.130 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "UBE2Q2P1_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NAV1 -1.5 6.9 17.0 0.00006 0.26 1 1.10 1.1
CCNH -1.3 6.7 11.0 0.00094 1.00 2 6.10 3.1
REEP2 2.2 7.0 10.0 0.00170 1.00 3 10.00 3.3
CDKN1B 2.0 6.9 10.0 0.00190 1.00 4 11.00 2.8
WNK1 -1.1 7.0 9.7 0.00230 1.00 5 12.00 2.5
DDR1 -1.1 7.2 9.6 0.00230 1.00 6 12.00 2.1
RNF168 2.0 6.7 8.1 0.00500 1.00 7 24.00 3.4
TMEM132A -1.2 6.8 7.8 0.00580 1.00 8 27.00 3.4
FBXW5 1.6 6.9 7.7 0.00610 1.00 9 29.00 3.2
CAMLG 1.0 7.6 7.6 0.00650 1.00 10 30.00 3.0
1e-04 NA NA NA NA NA 1 1.50 1.5
1e-05 NA NA NA NA NA 0 0.67 Inf
1e-06 NA NA NA NA NA 0 0.30 Inf
1e-07 NA NA NA NA NA 0 0.23 Inf
1e-08 NA NA NA NA NA 0 0.13 Inf
1e-09 NA NA NA NA NA 0 0.13 Inf
1e-10 NA NA NA NA NA 0 0.10 Inf
[1] "VPS45_1_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
IFITM3 -2.10 8.9 36 1.2e-08 5.2e-05 1 0.17 0.170
GPM6B -1.20 8.5 28 4.1e-07 8.9e-04 2 0.23 0.120
PTN -1.90 8.2 27 6.3e-07 9.1e-04 3 0.23 0.078
CLU -1.80 7.6 26 1.0e-06 1.1e-03 4 0.23 0.058
WLS -1.40 7.2 17 5.6e-05 4.0e-02 5 1.30 0.270
CTSC -1.60 6.9 17 5.6e-05 4.0e-02 6 1.30 0.220
RCN1 -0.93 8.8 16 8.3e-05 5.2e-02 7 1.40 0.200
ORC6 2.40 7.4 15 1.3e-04 6.6e-02 8 1.80 0.230
GAP43 -1.50 8.1 15 1.4e-04 6.6e-02 9 1.90 0.210
PHLDA1 -1.70 7.1 15 1.7e-04 7.3e-02 10 2.20 0.220
1e-04 NA NA NA NA NA 7 1.60 0.230
1e-05 NA NA NA NA NA 4 0.57 0.140
1e-06 NA NA NA NA NA 3 0.23 0.078
1e-07 NA NA NA NA NA 1 0.23 0.230
1e-08 NA NA NA NA NA 0 0.17 Inf
1e-09 NA NA NA NA NA 0 0.10 Inf
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "VPS45_2_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NINJ1 0.97 7.0 17.0 4.3e-05 0.19 1 0.90 0.9
SUMO3 0.48 8.0 13.0 3.2e-04 0.68 2 2.80 1.4
GAP43 -0.86 8.2 12.0 5.3e-04 0.76 3 4.20 1.4
SNAPC3 -0.72 6.9 11.0 8.5e-04 0.92 4 6.10 1.5
U2SURP 0.47 7.7 9.8 2.0e-03 1.00 5 12.00 2.5
PAQR4 0.78 6.9 9.5 2.3e-03 1.00 6 14.00 2.3
MLLT11 -0.50 8.8 9.2 2.7e-03 1.00 7 15.00 2.1
TRMT112 0.28 8.9 9.0 3.0e-03 1.00 8 16.00 2.0
PPP5C 0.58 7.0 8.8 3.4e-03 1.00 9 18.00 2.0
PPP2R2B -0.71 6.8 8.7 3.6e-03 1.00 10 19.00 1.9
1e-04 NA NA NA NA NA 1 1.40 1.4
1e-05 NA NA NA NA NA 0 0.33 Inf
1e-06 NA NA NA NA NA 0 0.13 Inf
1e-07 NA NA NA NA NA 0 0.00 NaN
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "VPS45_3_gene_edgeR-qlf_Neg1.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NKAIN4 -2.1 7.1 17.0 5.2e-05 0.22 1 0.70 0.70
PCGF2 3.5 7.0 16.0 1.1e-04 0.23 2 0.97 0.48
GNPDA1 -1.7 6.9 13.0 4.0e-04 0.44 3 2.30 0.78
UCK2 2.9 6.8 13.0 4.5e-04 0.44 4 2.60 0.64
TXNRD1 -1.6 7.3 13.0 5.1e-04 0.44 5 2.90 0.58
CTDSP2 2.9 6.8 11.0 1.2e-03 0.65 6 5.60 0.93
ARG2 -1.5 6.8 11.0 1.4e-03 0.65 7 6.30 0.90
CHTF8 1.8 7.3 10.0 1.7e-03 0.65 8 7.80 0.98
SF3B4 1.3 7.7 9.9 2.0e-03 0.65 9 8.80 0.98
COA1 1.1 7.9 9.9 2.0e-03 0.65 10 9.00 0.90
1e-04 NA NA NA NA NA 1 0.97 0.97
1e-05 NA NA NA NA NA 0 0.30 Inf
1e-06 NA NA NA NA NA 0 0.20 Inf
1e-07 NA NA NA NA NA 0 0.10 Inf
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaNsource("code/empiricalFDR.R")
pbins <- 10** (-4:-10)
for (gRNAfile in list.files("data/gRNA_edgeR-QLF/", "*edgeR-qlf_Neg2.Rd")){
print(gRNAfile)
load(paste0("data/gRNA_edgeR-QLF/", 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
LARP1 0.84 7.3 13.0 0.00028 0.44 1 1.400 1.40
CCND1 0.91 8.2 13.0 0.00030 0.44 2 1.500 0.75
ARPC3 0.44 8.5 13.0 0.00032 0.44 3 1.600 0.52
CNOT11 1.10 6.7 12.0 0.00060 0.63 4 2.500 0.62
PCF11 1.20 6.6 11.0 0.00081 0.67 5 2.900 0.59
RMDN1 1.00 6.7 10.0 0.00120 0.87 6 4.300 0.71
UFM1 0.84 7.1 9.9 0.00160 0.87 7 5.400 0.77
TPM2 1.90 7.2 9.7 0.00180 0.87 8 6.300 0.78
CAMLG 0.56 7.6 9.6 0.00200 0.87 9 6.900 0.76
ATP2B1 0.85 7.0 9.5 0.00210 0.87 10 7.200 0.72
1e-04 NA NA NA NA NA 0 0.770 Inf
1e-05 NA NA NA NA NA 0 0.400 Inf
1e-06 NA NA NA NA NA 0 0.200 Inf
1e-07 NA NA NA NA NA 0 0.170 Inf
1e-08 NA NA NA NA NA 0 0.130 Inf
1e-09 NA NA NA NA NA 0 0.100 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "BAG5_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MIAT -1.20 7.1 13.0 0.00034 0.63 1 2.500 2.50
NIN -0.89 6.8 13.0 0.00036 0.63 2 2.500 1.20
RAB32 1.60 6.7 12.0 0.00045 0.63 3 2.800 0.92
RPL14 0.26 11.0 12.0 0.00066 0.69 4 3.900 0.97
RPS23 0.28 13.0 11.0 0.00110 0.81 5 5.700 1.10
BAG1 -0.48 7.7 10.0 0.00130 0.81 6 6.400 1.10
OS9 -0.67 7.2 10.0 0.00150 0.81 7 7.000 1.00
TSN -0.51 7.3 9.6 0.00200 0.81 8 9.500 1.20
ECHDC1 -0.60 7.4 9.4 0.00210 0.81 9 10.000 1.10
RPL35A 0.22 12.0 9.3 0.00230 0.81 10 10.000 1.00
1e-04 NA NA NA NA NA 0 1.100 Inf
1e-05 NA NA NA NA NA 0 0.570 Inf
1e-06 NA NA NA NA NA 0 0.230 Inf
1e-07 NA NA NA NA NA 0 0.200 Inf
1e-08 NA NA NA NA NA 0 0.130 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "BAG5_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
DFFA -0.83 7.0 18.0 2.7e-05 0.11 1 0.330 0.33
ASCL1 2.20 7.1 13.0 2.9e-04 0.61 2 1.100 0.53
CDKN1A 1.60 8.1 11.0 7.8e-04 0.72 3 2.900 0.96
MED4 0.67 7.4 11.0 1.0e-03 0.72 4 3.700 0.93
LAMTOR5 0.48 8.3 11.0 1.1e-03 0.72 5 4.100 0.81
DLL1 2.10 6.9 11.0 1.2e-03 0.72 6 4.300 0.71
TIGAR 1.20 6.8 10.0 1.2e-03 0.72 7 4.300 0.62
BIN3 1.00 6.7 10.0 1.4e-03 0.72 8 4.900 0.61
C7orf73 -0.42 8.0 9.6 1.9e-03 0.81 9 6.300 0.70
METTL12 -0.72 6.8 9.3 2.4e-03 0.81 10 7.600 0.76
1e-04 NA NA NA NA NA 1 0.630 0.63
1e-05 NA NA NA NA NA 0 0.170 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "BCL11B_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ARL3 0.71 8.2 9.9 0.0017 1 1 9.10 9.1
LIMCH1 1.50 7.4 8.8 0.0030 1 2 14.00 7.2
NEFM -1.40 7.5 8.8 0.0030 1 3 15.00 4.9
SMCO4 1.90 6.7 8.7 0.0032 1 4 15.00 3.8
UXS1 1.70 6.6 8.6 0.0035 1 5 16.00 3.3
CCDC124 0.84 7.7 8.5 0.0036 1 6 17.00 2.9
ADI1 1.40 7.1 8.4 0.0037 1 7 18.00 2.5
ATF5 2.60 7.0 8.1 0.0044 1 8 20.00 2.5
UNG 2.00 6.8 8.0 0.0047 1 9 21.00 2.3
AKIRIN1 -0.63 7.8 7.9 0.0050 1 10 22.00 2.2
1e-04 NA NA NA NA NA 0 1.60 Inf
1e-05 NA NA NA NA NA 0 0.57 Inf
1e-06 NA NA NA NA NA 0 0.27 Inf
1e-07 NA NA NA NA NA 0 0.20 Inf
1e-08 NA NA NA NA NA 0 0.17 Inf
1e-09 NA NA NA NA NA 0 0.13 Inf
1e-10 NA NA NA NA NA 0 0.10 Inf
[1] "BCL11B_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
JAG1 -1.10 6.8 18 2.7e-05 0.071 1 1.30 1.30
PHLDA1 -1.20 7.0 17 3.4e-05 0.071 2 1.50 0.75
RPRML 1.50 6.7 14 2.3e-04 0.300 3 3.30 1.10
CACYBP 0.60 8.1 13 3.8e-04 0.300 4 4.50 1.10
APLP1 0.86 7.4 12 4.1e-04 0.300 5 4.80 0.95
DDX6 1.00 6.9 12 4.4e-04 0.300 6 5.00 0.83
GCSH 0.46 8.6 12 6.0e-04 0.360 7 6.30 0.90
RMI2 1.30 6.6 11 7.6e-04 0.380 8 7.20 0.90
ATF3 -0.95 7.1 11 8.8e-04 0.380 9 7.90 0.87
C9orf116 0.88 7.2 11 9.1e-04 0.380 10 8.10 0.81
1e-04 NA NA NA NA NA 2 2.30 1.20
1e-05 NA NA NA NA NA 0 0.97 Inf
1e-06 NA NA NA NA NA 0 0.43 Inf
1e-07 NA NA NA NA NA 0 0.30 Inf
1e-08 NA NA NA NA NA 0 0.17 Inf
1e-09 NA NA NA NA NA 0 0.17 Inf
1e-10 NA NA NA NA NA 0 0.17 Inf
[1] "BCL11B_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
DKK3 -1.30 6.6 13.0 0.0004 1 1 3.000 3.0
EIF5 0.78 9.0 11.0 0.0010 1 2 5.700 2.9
FASTK 1.50 7.0 10.0 0.0013 1 3 6.800 2.3
DUSP1 2.50 6.7 9.8 0.0018 1 4 8.600 2.1
FAAP20 1.20 7.4 9.2 0.0025 1 5 11.000 2.1
GOLGA7 0.94 7.4 7.9 0.0049 1 6 19.000 3.1
GTF2H2 1.80 6.7 7.8 0.0054 1 7 20.000 2.9
FNBP1L 1.70 6.6 7.7 0.0056 1 8 21.000 2.6
ACP1 0.53 8.7 7.6 0.0058 1 9 22.000 2.4
MED24 1.40 6.7 7.5 0.0062 1 10 23.000 2.3
1e-04 NA NA NA NA NA 0 1.600 Inf
1e-05 NA NA NA NA NA 0 0.730 Inf
1e-06 NA NA NA NA NA 0 0.370 Inf
1e-07 NA NA NA NA NA 0 0.230 Inf
1e-08 NA NA NA NA NA 0 0.170 Inf
1e-09 NA NA NA NA NA 0 0.130 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "CHRNA3_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ISG15 -1.80 6.8 8.9 0.0028 0.93 1 11.000 11.0
PHAX 2.80 7.4 8.6 0.0034 0.93 2 13.000 6.4
C8orf59 -1.20 7.5 8.1 0.0044 0.93 3 16.000 5.5
MIIP -1.70 6.8 8.0 0.0046 0.93 4 17.000 4.3
NUDCD2 -1.40 7.4 8.0 0.0047 0.93 5 17.000 3.4
ERH -0.73 9.5 8.0 0.0048 0.93 6 18.000 2.9
MTHFD1L 3.80 7.0 7.9 0.0049 0.93 7 18.000 2.6
HMG20B 3.60 6.9 7.9 0.0050 0.93 8 18.000 2.3
SCAMP3 3.60 6.9 7.9 0.0051 0.93 9 19.000 2.1
ADD1 3.60 6.9 7.8 0.0052 0.93 10 19.000 1.9
1e-04 NA NA NA NA NA 0 1.200 Inf
1e-05 NA NA NA NA NA 0 0.430 Inf
1e-06 NA NA NA NA NA 0 0.170 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "CHRNA3_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SLC25A26 1.50 6.7 14.0 0.00022 0.81 1 2.10 2.10
BNIP3 -0.76 7.1 11.0 0.00096 0.81 2 5.20 2.60
ZNF503 -0.99 6.8 11.0 0.00097 0.81 3 5.30 1.80
PRDX1 -0.42 9.5 10.0 0.00130 0.81 4 6.70 1.70
MRPL37 0.61 8.0 10.0 0.00150 0.81 5 7.20 1.40
PWP1 0.93 7.1 10.0 0.00150 0.81 6 7.20 1.20
DDX41 0.94 7.0 9.9 0.00170 0.81 7 7.70 1.10
SUCLG1 0.72 7.6 9.9 0.00170 0.81 8 7.70 0.96
OIP5 1.40 6.6 9.8 0.00180 0.81 9 8.00 0.89
HADHB -0.69 7.1 9.1 0.00250 0.96 10 10.00 1.00
1e-04 NA NA NA NA NA 0 1.50 Inf
1e-05 NA NA NA NA NA 0 0.60 Inf
1e-06 NA NA NA NA NA 0 0.50 Inf
1e-07 NA NA NA NA NA 0 0.33 Inf
1e-08 NA NA NA NA NA 0 0.23 Inf
1e-09 NA NA NA NA NA 0 0.13 Inf
1e-10 NA NA NA NA NA 0 0.10 Inf
[1] "CHRNA3_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ARF4 -1.00 8.3 22 3.6e-06 0.0055 1 0.470 0.47
CDC42EP3 -1.50 6.7 21 3.8e-06 0.0055 2 0.500 0.25
NANS -1.30 6.9 21 4.0e-06 0.0055 3 0.500 0.17
ALG3 -1.00 7.1 15 1.4e-04 0.1200 4 1.600 0.41
TUBB2A -0.99 8.9 15 1.4e-04 0.1200 5 1.600 0.33
RRP9 -1.00 7.0 13 2.7e-04 0.1900 6 2.200 0.37
CIB1 -0.91 7.2 13 3.9e-04 0.2300 7 2.700 0.39
AKAP12 -1.00 7.4 11 7.8e-04 0.3900 8 4.200 0.53
NIFK -0.69 7.8 11 9.2e-04 0.3900 9 4.600 0.51
HNRNPC 0.46 9.9 11 1.1e-03 0.3900 10 5.400 0.54
1e-04 NA NA NA NA NA 3 1.300 0.42
1e-05 NA NA NA NA NA 3 0.530 0.18
1e-06 NA NA NA NA NA 0 0.330 Inf
1e-07 NA NA NA NA NA 0 0.230 Inf
1e-08 NA NA NA NA NA 0 0.130 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "DPYD_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
CTD-2006C1.2 -1.70 6.9 120 1.7e-27 7.3e-24 1 0.033
DUSP4 -1.20 6.6 31 3.5e-08 7.4e-05 2 0.170
NTRK2 1.30 7.3 18 2.1e-05 2.1e-02 3 0.600
RP11-14N7.2 -0.83 7.3 18 2.7e-05 2.1e-02 4 0.630
UROD -0.70 7.1 17 3.1e-05 2.1e-02 5 0.700
CTSD -0.79 7.3 17 3.6e-05 2.1e-02 6 0.770
DLGAP5 1.60 6.7 17 3.7e-05 2.1e-02 7 0.800
FASN 1.10 7.1 17 4.1e-05 2.1e-02 8 0.870
SIRT7 -0.79 6.7 17 4.5e-05 2.1e-02 9 0.900
PITHD1 -0.59 7.4 16 5.3e-05 2.2e-02 10 0.970
1e-04 NA NA NA NA NA 17 1.200
1e-05 NA NA NA NA NA 2 0.600
1e-06 NA NA NA NA NA 2 0.400
1e-07 NA NA NA NA NA 2 0.200
1e-08 NA NA NA NA NA 1 0.170
1e-09 NA NA NA NA NA 1 0.067
1e-10 NA NA NA NA NA 1 0.067
EmpiricalFDR
CTD-2006C1.2 0.033
DUSP4 0.083
NTRK2 0.200
RP11-14N7.2 0.160
UROD 0.140
CTSD 0.130
DLGAP5 0.110
FASN 0.110
SIRT7 0.100
PITHD1 0.097
1e-04 0.073
1e-05 0.300
1e-06 0.200
1e-07 0.100
1e-08 0.170
1e-09 0.067
1e-10 0.067
[1] "DPYD_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MEG3 -0.86 7.5 28 1.2e-07 0.00051 1 0.33 0.33
CSRP1 -0.92 7.1 23 1.4e-06 0.00280 2 0.40 0.20
SMPD4 0.84 6.7 17 4.3e-05 0.06100 3 0.83 0.28
NUDT3 0.76 6.9 15 9.0e-05 0.09400 4 1.00 0.25
CRNDE 0.47 8.4 14 1.5e-04 0.12000 5 1.20 0.24
MYL9 -0.75 7.6 13 3.3e-04 0.23000 6 2.00 0.34
MRFAP1 0.24 8.9 13 3.9e-04 0.24000 7 2.30 0.32
ANKRD11 0.48 7.6 12 5.6e-04 0.29000 8 2.70 0.34
VTA1 0.65 6.7 12 6.3e-04 0.29000 9 2.90 0.32
DPYSL5 0.52 7.2 11 8.5e-04 0.35000 10 3.90 0.39
1e-04 NA NA NA NA NA 4 1.00 0.25
1e-05 NA NA NA NA NA 2 0.57 0.28
1e-06 NA NA NA NA NA 1 0.40 0.40
1e-07 NA NA NA NA NA 0 0.33 Inf
1e-08 NA NA NA NA NA 0 0.30 Inf
1e-09 NA NA NA NA NA 0 0.23 Inf
1e-10 NA NA NA NA NA 0 0.20 Inf
[1] "DPYD_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NEAT1 2.00 8.6 17.0 3.8e-05 0.16 1 0.500 0.5
C4orf48 0.62 8.0 11.0 8.6e-04 1.00 2 3.500 1.8
REXO2 0.86 7.2 9.9 1.7e-03 1.00 3 6.500 2.2
APEX1 -0.37 9.0 9.7 1.8e-03 1.00 4 6.700 1.7
SERINC2 1.20 6.8 9.4 2.1e-03 1.00 5 7.800 1.6
SNX3 0.52 8.0 9.4 2.2e-03 1.00 6 7.900 1.3
GAP43 1.20 8.2 9.3 2.3e-03 1.00 7 8.600 1.2
B2M 0.74 8.9 8.9 2.9e-03 1.00 8 10.000 1.3
HNRNPC -0.26 9.9 8.8 3.0e-03 1.00 9 11.000 1.2
COPS3 -0.44 7.9 8.7 3.2e-03 1.00 10 11.000 1.1
1e-04 NA NA NA NA NA 1 0.800 0.8
1e-05 NA NA NA NA NA 0 0.300 Inf
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "GALNT10_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
FAM104B 1.00 6.9 15.0 0.00014 0.58 1 1.600 1.6
MAT2B -0.70 6.9 12.0 0.00050 0.80 2 3.200 1.6
WSB1 0.64 7.6 11.0 0.00073 0.80 3 4.400 1.5
DCAF15 1.00 6.7 11.0 0.00076 0.80 4 4.400 1.1
FZD3 0.56 7.7 9.8 0.00180 1.00 5 9.300 1.9
DECR1 0.98 6.8 9.2 0.00240 1.00 6 12.000 2.0
ZNF462 0.77 7.0 9.0 0.00270 1.00 7 14.000 1.9
MLLT4 0.74 7.1 8.8 0.00310 1.00 8 15.000 1.8
AHSA1 -0.50 7.2 8.6 0.00340 1.00 9 16.000 1.8
TAGLN3 -0.90 7.1 8.5 0.00360 1.00 10 17.000 1.7
1e-04 NA NA NA NA NA 0 1.400 Inf
1e-05 NA NA NA NA NA 0 0.430 Inf
1e-06 NA NA NA NA NA 0 0.270 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "GALNT10_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SYPL1 0.79 7.0 9.8 0.0017 1 1 5.600 5.6
C14orf2 0.27 9.2 9.7 0.0019 1 2 6.100 3.1
PYURF 0.43 7.9 9.1 0.0026 1 3 8.200 2.7
TUBB2B -0.38 11.0 8.7 0.0032 1 4 9.600 2.4
TP53RK -0.59 6.9 8.2 0.0042 1 5 13.000 2.5
TYW3 0.65 7.1 7.8 0.0052 1 6 16.000 2.7
CCNH 0.82 6.6 7.6 0.0060 1 7 19.000 2.7
RBBP4 -0.37 7.8 7.5 0.0062 1 8 20.000 2.4
CMBL 0.94 6.8 7.5 0.0062 1 9 20.000 2.2
UBR4 0.76 6.8 7.2 0.0072 1 10 23.000 2.3
1e-04 NA NA NA NA NA 0 0.900 Inf
1e-05 NA NA NA NA NA 0 0.130 Inf
1e-06 NA NA NA NA NA 0 0.100 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "GALNT10_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NEAT1 -1.10 8.6 22.0 2.4e-06 0.0099 1 0.067 0.067
SPARC -0.41 8.6 11.0 8.8e-04 1.0000 2 4.700 2.300
NAV1 0.90 6.7 11.0 1.0e-03 1.0000 3 5.300 1.800
UPP1 -0.63 7.8 9.8 1.7e-03 1.0000 4 8.600 2.200
CDC25B 0.98 7.0 9.7 1.8e-03 1.0000 5 9.100 1.800
TUBB2A -0.47 8.9 9.7 1.9e-03 1.0000 6 9.500 1.600
HMGA1 -0.34 11.0 9.2 2.4e-03 1.0000 7 12.000 1.700
SPOP 0.54 7.1 9.2 2.5e-03 1.0000 8 12.000 1.500
C9orf114 0.73 6.7 9.0 2.7e-03 1.0000 9 13.000 1.400
RCN1 -0.35 8.7 8.8 3.1e-03 1.0000 10 15.000 1.500
1e-04 NA NA NA NA NA 1 0.800 0.800
1e-05 NA NA NA NA NA 1 0.230 0.230
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "KCTD13_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TUBA1C 3.10 6.8 20 7.0e-06 0.029 1 0.170 0.17
SLC25A39 0.84 7.6 16 6.4e-05 0.130 2 0.470 0.23
NDUFB2 0.48 8.8 14 2.0e-04 0.200 3 1.100 0.36
GNG5 0.41 9.2 13 2.6e-04 0.200 4 1.500 0.38
TMSB10 0.66 12.0 13 2.6e-04 0.200 5 1.500 0.31
CYTOR 1.30 7.7 13 3.1e-04 0.200 6 1.800 0.31
SRGAP1 1.10 7.1 13 3.4e-04 0.200 7 2.000 0.28
PHLDA1 1.70 7.0 12 6.2e-04 0.300 8 2.900 0.36
MAGEF1 -0.58 7.4 12 6.9e-04 0.300 9 3.200 0.35
TPM2 2.20 7.2 11 7.7e-04 0.300 10 3.500 0.35
1e-04 NA NA NA NA NA 2 0.570 0.28
1e-05 NA NA NA NA NA 1 0.170 0.17
1e-06 NA NA NA NA NA 0 0.100 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "KCTD13_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
LPP 1.40 6.8 14.0 0.00018 0.71 1 1.70
FAM63B 0.98 7.0 11.0 0.00110 0.71 2 6.40
PTPN1 1.00 6.8 11.0 0.00120 0.71 3 6.70
ACOT13 -0.67 7.1 10.0 0.00140 0.71 4 7.60
SEC14L1 1.10 6.7 10.0 0.00150 0.71 5 7.80
NDUFB8 0.35 8.8 10.0 0.00160 0.71 6 8.10
RP3-395M20.12 -0.93 6.8 9.4 0.00220 0.71 7 10.00
CYTOR 0.98 7.7 9.2 0.00250 0.71 8 11.00
PJA2 1.10 6.6 9.1 0.00260 0.71 9 11.00
EHMT1 0.98 6.7 9.0 0.00270 0.71 10 12.00
1e-04 NA NA NA NA NA 0 1.30
1e-05 NA NA NA NA NA 0 0.43
1e-06 NA NA NA NA NA 0 0.30
1e-07 NA NA NA NA NA 0 0.20
1e-08 NA NA NA NA NA 0 0.20
1e-09 NA NA NA NA NA 0 0.20
1e-10 NA NA NA NA NA 0 0.17
EmpiricalFDR
LPP 1.7
FAM63B 3.2
PTPN1 2.2
ACOT13 1.9
SEC14L1 1.6
NDUFB8 1.3
RP3-395M20.12 1.5
CYTOR 1.4
PJA2 1.3
EHMT1 1.2
1e-04 Inf
1e-05 Inf
1e-06 Inf
1e-07 Inf
1e-08 Inf
1e-09 Inf
1e-10 Inf
[1] "KCTD13_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
GEMIN2 -1.10 6.8 13.0 0.00025 0.96 1 2.20 2.2
IPO9 -0.93 7.0 12.0 0.00069 0.96 2 4.20 2.1
HSPA14 -1.10 6.7 11.0 0.00091 0.96 3 5.00 1.7
HNRNPL -0.94 7.0 11.0 0.00100 0.96 4 5.50 1.4
KMT2A -0.87 7.1 10.0 0.00140 0.96 5 6.80 1.4
TLE4 -0.99 6.9 9.8 0.00180 0.96 6 8.20 1.4
USP39 -0.84 7.1 9.4 0.00210 0.96 7 9.90 1.4
AEN -1.00 7.4 9.3 0.00230 0.96 8 11.00 1.3
PSMA3 0.59 8.2 8.2 0.00420 0.96 9 17.00 1.9
TMEM101 1.30 6.9 8.1 0.00440 0.96 10 17.00 1.7
1e-04 NA NA NA NA NA 0 1.30 Inf
1e-05 NA NA NA NA NA 0 0.60 Inf
1e-06 NA NA NA NA NA 0 0.40 Inf
1e-07 NA NA NA NA NA 0 0.30 Inf
1e-08 NA NA NA NA NA 0 0.20 Inf
1e-09 NA NA NA NA NA 0 0.13 Inf
1e-10 NA NA NA NA NA 0 0.13 Inf
[1] "KMT2E_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NCSTN 2.30 6.7 11.0 0.00098 1 1 3.300 3.3
FAM161A 2.40 6.7 11.0 0.00110 1 2 3.700 1.9
BET1 1.80 6.9 9.7 0.00190 1 3 5.900 2.0
USP47 1.60 6.8 7.8 0.00520 1 4 14.000 3.6
ZBTB8OS 1.10 7.4 7.7 0.00560 1 5 16.000 3.2
SNX6 0.98 7.5 7.4 0.00640 1 6 18.000 3.0
MRPL19 1.20 7.2 7.1 0.00760 1 7 21.000 3.0
DEF8 1.10 7.4 7.1 0.00760 1 8 21.000 2.7
SLC25A11 1.00 7.3 6.9 0.00850 1 9 24.000 2.6
CADM1 1.60 6.9 6.8 0.00920 1 10 26.000 2.6
1e-04 NA NA NA NA NA 0 0.630 Inf
1e-05 NA NA NA NA NA 0 0.230 Inf
1e-06 NA NA NA NA NA 0 0.100 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "KMT2E_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CCDC107 1.60 6.9 15 8.6e-05 0.27 1 1.500 1.50
CCDC28B 2.10 6.7 14 1.8e-04 0.27 2 2.100 1.00
RAB8A 1.50 7.0 14 1.9e-04 0.27 3 2.100 0.70
CSNK1D 1.30 7.1 13 2.7e-04 0.28 4 2.500 0.62
QPRT 2.70 6.8 13 3.6e-04 0.30 5 2.700 0.55
NKTR 1.20 7.1 11 7.5e-04 0.50 6 5.000 0.84
EZR -0.87 7.5 11 8.3e-04 0.50 7 5.400 0.77
FOS 2.20 6.7 11 1.2e-03 0.60 8 6.900 0.86
TIGAR 1.60 6.8 10 1.4e-03 0.60 9 7.700 0.85
PSMD11 -0.58 7.9 10 1.5e-03 0.60 10 7.800 0.78
1e-04 NA NA NA NA NA 1 1.600 1.60
1e-05 NA NA NA NA NA 0 0.900 Inf
1e-06 NA NA NA NA NA 0 0.570 Inf
1e-07 NA NA NA NA NA 0 0.300 Inf
1e-08 NA NA NA NA NA 0 0.200 Inf
1e-09 NA NA NA NA NA 0 0.130 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "KMT2E_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TP53I3 -1.30 6.9 15.0 0.00010 0.43 1 1.90 1.9
GPT2 1.70 6.8 12.0 0.00044 0.67 2 3.50 1.7
NCSTN 1.70 6.7 12.0 0.00048 0.67 3 3.70 1.2
FDXR -1.00 7.0 11.0 0.00120 1.00 4 6.10 1.5
KCTD1 -1.00 6.6 9.4 0.00210 1.00 5 9.40 1.9
KIN 1.40 6.7 9.3 0.00230 1.00 6 10.00 1.7
COX7A2 0.38 9.5 9.1 0.00250 1.00 7 11.00 1.5
C11orf73 0.66 7.8 8.9 0.00290 1.00 8 12.00 1.5
CMC1 1.10 6.9 8.6 0.00340 1.00 9 14.00 1.5
HSP90AA1 0.51 10.0 8.3 0.00400 1.00 10 16.00 1.6
1e-04 NA NA NA NA NA 0 1.90 Inf
1e-05 NA NA NA NA NA 0 0.87 Inf
1e-06 NA NA NA NA NA 0 0.40 Inf
1e-07 NA NA NA NA NA 0 0.27 Inf
1e-08 NA NA NA NA NA 0 0.20 Inf
1e-09 NA NA NA NA NA 0 0.17 Inf
1e-10 NA NA NA NA NA 0 0.13 Inf
[1] "LINC00637_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
HSP90AA1 -0.86 10.0 76.0 3.5e-18 1.5e-14 1 0.033 0.033
HSPH1 -0.84 7.3 28.0 1.2e-07 2.4e-04 2 0.100 0.050
HSPD1 -0.39 9.6 18.0 1.9e-05 2.7e-02 3 0.500 0.170
NEFM -1.00 7.5 15.0 1.4e-04 1.5e-01 4 1.300 0.320
DERL1 0.86 6.8 12.0 5.9e-04 4.9e-01 5 3.600 0.730
COX14 0.71 7.2 11.0 7.6e-04 5.3e-01 6 4.100 0.690
SEP15 -0.42 7.9 11.0 1.2e-03 6.9e-01 7 5.800 0.820
DIO3 -0.83 7.1 10.0 1.3e-03 6.9e-01 8 6.500 0.810
CINP -0.58 6.8 9.3 2.3e-03 8.8e-01 9 9.800 1.100
ESF1 -0.47 7.3 9.2 2.5e-03 8.8e-01 10 10.000 1.000
1e-04 NA NA NA NA NA 3 1.000 0.340
1e-05 NA NA NA NA NA 2 0.370 0.180
1e-06 NA NA NA NA NA 2 0.130 0.067
1e-07 NA NA NA NA NA 1 0.100 0.100
1e-08 NA NA NA NA NA 1 0.067 0.067
1e-09 NA NA NA NA NA 1 0.033 0.033
1e-10 NA NA NA NA NA 1 0.033 0.033
[1] "LINC00637_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TP53I3 -1.00 6.9 17.0 4.7e-05 0.20 1 0.90 0.90
COASY 1.20 6.7 13.0 3.3e-04 0.69 2 2.30 1.10
YWHAB 0.43 8.8 12.0 5.1e-04 0.72 3 2.90 0.96
PIR 1.40 6.7 11.0 7.3e-04 0.77 4 3.60 0.91
C15orf40 0.97 6.7 9.5 2.1e-03 1.00 5 8.80 1.80
SDHAF1 0.96 6.7 9.3 2.3e-03 1.00 6 9.60 1.60
RABGGTB 0.78 7.2 9.3 2.3e-03 1.00 7 9.60 1.40
PPIL4 0.80 7.0 8.7 3.1e-03 1.00 8 12.00 1.60
RBBP6 0.76 7.0 8.7 3.2e-03 1.00 9 13.00 1.40
ARHGDIA 0.46 8.3 8.6 3.3e-03 1.00 10 13.00 1.30
1e-04 NA NA NA NA NA 1 1.20 1.20
1e-05 NA NA NA NA NA 0 0.50 Inf
1e-06 NA NA NA NA NA 0 0.30 Inf
1e-07 NA NA NA NA NA 0 0.17 Inf
1e-08 NA NA NA NA NA 0 0.13 Inf
1e-09 NA NA NA NA NA 0 0.10 Inf
1e-10 NA NA NA NA NA 0 0.10 Inf
[1] "LINC00637_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
MIAT 1.90 7.1 19 1.5e-05 0.063 1 0.67 0.67
TPM2 -1.00 7.2 15 1.4e-04 0.260 2 1.70 0.87
SMOC1 1.10 7.0 14 1.9e-04 0.260 3 1.90 0.62
DIO3 1.20 7.1 13 3.2e-04 0.310 4 2.40 0.61
HES6 1.10 9.0 13 4.0e-04 0.310 5 3.00 0.59
TNFRSF12A -0.82 7.8 12 4.4e-04 0.310 6 3.20 0.53
DLL1 1.50 6.9 12 5.5e-04 0.330 7 3.60 0.52
CDC25B 0.98 7.0 11 1.2e-03 0.550 8 6.20 0.78
SAR1A -0.46 7.2 10 1.3e-03 0.550 9 6.60 0.73
TAGLN3 1.20 7.1 10 1.3e-03 0.550 10 6.70 0.67
1e-04 NA NA NA NA NA 1 1.50 1.50
1e-05 NA NA NA NA NA 0 0.47 Inf
1e-06 NA NA NA NA NA 0 0.30 Inf
1e-07 NA NA NA NA NA 0 0.17 Inf
1e-08 NA NA NA NA NA 0 0.13 Inf
1e-09 NA NA NA NA NA 0 0.10 Inf
1e-10 NA NA NA NA NA 0 0.10 Inf
[1] "LOC100507431_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CCND2 -1.40 7.0 18.0 2.3e-05 0.096 1 0.730 0.73
TPM2 -1.70 7.2 15.0 8.7e-05 0.180 2 1.100 0.55
C4orf48 0.96 8.0 13.0 3.2e-04 0.380 3 2.400 0.80
LMCD1 -1.30 6.7 13.0 3.6e-04 0.380 4 2.600 0.64
TAGLN3 -1.50 7.1 12.0 6.7e-04 0.560 5 4.400 0.87
CRLS1 1.40 6.9 11.0 1.1e-03 0.650 6 5.800 0.96
MTA1 1.30 7.0 11.0 1.1e-03 0.650 7 5.900 0.85
VGLL4 -1.00 6.7 10.0 1.2e-03 0.650 8 6.400 0.80
TBL1XR1 1.70 6.7 10.0 1.6e-03 0.740 9 7.600 0.84
MED11 1.50 6.7 8.8 3.0e-03 1.000 10 13.000 1.30
1e-04 NA NA NA NA NA 2 1.200 0.62
1e-05 NA NA NA NA NA 0 0.470 Inf
1e-06 NA NA NA NA NA 0 0.270 Inf
1e-07 NA NA NA NA NA 0 0.170 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "LOC100507431_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
S100A13 -1.20 7.0 24 1.2e-06 0.0049 1 0.230 0.23
GLUL -0.66 8.0 13 4.1e-04 0.4500 2 2.400 1.20
DUSP1 -0.96 6.7 12 5.3e-04 0.4500 3 2.900 0.97
KLF6 -0.82 7.1 12 5.9e-04 0.4500 4 3.000 0.76
SPARC -0.55 8.6 12 6.0e-04 0.4500 5 3.100 0.61
MZT2B 0.45 9.1 11 7.3e-04 0.4500 6 3.400 0.57
RANGRF 1.00 6.9 11 7.5e-04 0.4500 7 3.500 0.50
CRK -0.56 7.4 11 1.1e-03 0.4500 8 4.200 0.53
ASAH1 -0.72 7.0 11 1.1e-03 0.4500 9 4.400 0.49
DHRS7 -0.85 6.7 11 1.1e-03 0.4500 10 4.500 0.45
1e-04 NA NA NA NA NA 1 1.200 1.20
1e-05 NA NA NA NA NA 1 0.400 0.40
1e-06 NA NA NA NA NA 0 0.200 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "LOC100507431_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
HERPUD1 -0.97 7.1 22 3.2e-06 0.0074 1 0.330 0.33
DDIT4 -1.00 8.0 22 3.5e-06 0.0074 2 0.400 0.20
ATF5 -0.99 7.0 18 2.3e-05 0.0320 3 0.670 0.22
TRIB3 -1.00 7.1 15 1.2e-04 0.1300 4 1.400 0.35
WARS -0.67 7.3 13 2.8e-04 0.2300 5 1.800 0.37
CEBPB -0.88 6.9 13 3.7e-04 0.2600 6 2.200 0.37
PSAT1 -0.55 8.4 11 7.2e-04 0.4100 7 3.400 0.48
TCEA1 -0.40 8.0 11 8.8e-04 0.4100 8 3.900 0.49
HAX1 -0.42 7.8 11 8.8e-04 0.4100 9 3.900 0.44
SHMT2 -0.60 7.5 11 1.0e-03 0.4200 10 4.500 0.45
1e-04 NA NA NA NA NA 3 1.200 0.41
1e-05 NA NA NA NA NA 2 0.500 0.25
1e-06 NA NA NA NA NA 0 0.200 Inf
1e-07 NA NA NA NA NA 0 0.130 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "LOC105376975_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NEFM -1.70 7.5 35 4.5e-09 1.9e-05 1 0.20 0.20
FNDC3A 1.30 6.6 14 1.5e-04 2.6e-01 2 1.20 0.62
PSMB7 0.42 9.2 14 2.3e-04 2.6e-01 3 1.40 0.47
NEFL -0.78 8.4 13 2.8e-04 2.6e-01 4 1.50 0.38
CRABP2 -0.92 7.5 13 4.0e-04 2.6e-01 5 2.00 0.40
CTNNA1 0.77 7.2 12 4.3e-04 2.6e-01 6 2.20 0.37
MGST1 -0.72 7.8 12 5.1e-04 2.6e-01 7 2.50 0.35
UQCRFS1 0.46 8.5 12 5.3e-04 2.6e-01 8 2.50 0.32
RSL1D1 0.44 9.0 12 5.6e-04 2.6e-01 9 2.60 0.29
MRPS30 0.86 7.2 12 6.4e-04 2.7e-01 10 3.10 0.31
1e-04 NA NA NA NA NA 1 1.10 1.10
1e-05 NA NA NA NA NA 1 0.53 0.53
1e-06 NA NA NA NA NA 1 0.27 0.27
1e-07 NA NA NA NA NA 1 0.23 0.23
1e-08 NA NA NA NA NA 1 0.23 0.23
1e-09 NA NA NA NA NA 0 0.13 Inf
1e-10 NA NA NA NA NA 0 0.13 Inf
[1] "LOC105376975_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NQO1 1.60 7.5 16 5.4e-05 0.11 1 1.100 1.10
MRPS34 -0.41 8.4 16 6.5e-05 0.11 2 1.300 0.63
NAT9 0.97 6.8 16 7.7e-05 0.11 3 1.400 0.46
ATF5 1.40 7.0 14 1.9e-04 0.17 4 1.700 0.42
FHL1 -0.61 7.2 14 2.0e-04 0.17 5 1.700 0.35
CEBPB 1.40 6.9 12 4.2e-04 0.29 6 2.600 0.43
WARS 0.83 7.3 11 8.8e-04 0.46 7 4.900 0.70
TCAF1 0.87 6.7 11 9.0e-04 0.46 8 5.000 0.62
TXNRD1 0.96 7.1 10 1.3e-03 0.46 9 6.800 0.76
CTSD 0.75 7.3 10 1.3e-03 0.46 10 6.800 0.68
1e-04 NA NA NA NA NA 3 1.400 0.48
1e-05 NA NA NA NA NA 0 0.570 Inf
1e-06 NA NA NA NA NA 0 0.330 Inf
1e-07 NA NA NA NA NA 0 0.200 Inf
1e-08 NA NA NA NA NA 0 0.170 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "LOC105376975_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ACBD3 -1.70 6.7 14.0 0.00021 0.78 1 1.700 1.70
FNBP4 3.40 6.8 12.0 0.00048 0.78 2 3.000 1.50
PLGRKT 3.40 6.8 11.0 0.00076 0.78 3 4.200 1.40
KIF5C 2.40 7.3 10.0 0.00140 0.78 4 7.000 1.80
RIF1 3.30 6.7 10.0 0.00150 0.78 5 7.100 1.40
NOP16 -1.30 7.0 9.8 0.00180 0.78 6 8.300 1.40
PPP2R1B 3.10 6.7 9.7 0.00190 0.78 7 8.600 1.20
DAD1 -0.87 8.3 9.6 0.00190 0.78 8 8.900 1.10
RQCD1 3.10 6.7 9.6 0.00200 0.78 9 9.200 1.00
OSBPL1A 3.10 6.7 9.5 0.00200 0.78 10 9.400 0.94
1e-04 NA NA NA NA NA 0 1.200 Inf
1e-05 NA NA NA NA NA 0 0.470 Inf
1e-06 NA NA NA NA NA 0 0.200 Inf
1e-07 NA NA NA NA NA 0 0.200 Inf
1e-08 NA NA NA NA NA 0 0.130 Inf
1e-09 NA NA NA NA NA 0 0.130 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "miR137_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
YWHAZ 0.48 8.3 13.0 0.00027 0.98 1 1.400 1.4
DPH2 0.85 6.9 11.0 0.00072 0.98 2 3.200 1.6
APMAP 0.58 7.4 11.0 0.00110 0.98 3 4.000 1.3
CORO1C 0.90 6.7 11.0 0.00110 0.98 4 4.100 1.0
PTBP1 0.43 8.0 10.0 0.00160 0.98 5 5.400 1.1
PSMB6 0.32 9.0 9.2 0.00250 0.98 6 8.700 1.4
NEAT1 0.99 8.6 8.7 0.00320 0.98 7 11.000 1.6
ID3 -0.79 8.0 8.6 0.00340 0.98 8 12.000 1.5
ATP5B 0.28 9.5 8.4 0.00370 0.98 9 13.000 1.4
NRM 0.82 6.7 8.3 0.00390 0.98 10 13.000 1.3
1e-04 NA NA NA NA NA 0 0.900 Inf
1e-05 NA NA NA NA NA 0 0.400 Inf
1e-06 NA NA NA NA NA 0 0.200 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "miR137_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SLC4A1AP 1.60 6.6 17.0 3.2e-05 0.14 1 0.600 0.6
PRKAB1 1.10 6.8 11.0 7.3e-04 0.99 2 4.000 2.0
CDC23 1.10 6.7 11.0 9.5e-04 0.99 3 4.800 1.6
ARID1B 1.10 6.6 10.0 1.5e-03 0.99 4 7.000 1.8
RNF130 -0.51 7.5 9.5 2.0e-03 0.99 5 8.900 1.8
HIRIP3 0.92 7.0 9.4 2.2e-03 0.99 6 9.400 1.6
MTX2 0.85 6.9 9.2 2.5e-03 0.99 7 10.000 1.4
TRIM69 -0.80 6.6 9.2 2.5e-03 0.99 8 10.000 1.3
NDUFA9 0.66 7.6 9.1 2.6e-03 0.99 9 11.000 1.2
DYNC1LI2 0.60 7.5 8.7 3.2e-03 0.99 10 13.000 1.3
1e-04 NA NA NA NA NA 1 1.100 1.1
1e-05 NA NA NA NA NA 0 0.430 Inf
1e-06 NA NA NA NA NA 0 0.300 Inf
1e-07 NA NA NA NA NA 0 0.170 Inf
1e-08 NA NA NA NA NA 0 0.130 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "miR137_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NDUFB11 0.28 9.2 14.0 0.00021 0.48 1 1.800 1.80
TUBB2A -0.51 8.9 14.0 0.00023 0.48 2 1.800 0.90
DST -0.67 6.7 12.0 0.00046 0.64 3 2.500 0.84
PDLIM7 -0.40 8.4 11.0 0.00110 1.00 4 5.300 1.30
PTX3 -0.62 6.7 10.0 0.00120 1.00 5 5.500 1.10
PRPF6 0.53 7.2 9.5 0.00210 1.00 6 9.200 1.50
PFKP -0.60 6.8 9.4 0.00220 1.00 7 9.600 1.40
CAST -0.58 6.7 8.7 0.00310 1.00 8 12.000 1.50
BRD2 0.40 7.7 8.5 0.00360 1.00 9 14.000 1.50
ING2 0.64 6.7 8.3 0.00410 1.00 10 16.000 1.60
1e-04 NA NA NA NA NA 0 1.000 Inf
1e-05 NA NA NA NA NA 0 0.400 Inf
1e-06 NA NA NA NA NA 0 0.230 Inf
1e-07 NA NA NA NA NA 0 0.130 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "NAB2_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
RP11-143E21.7 -0.82 6.8 13.0 0.00028 0.58 1 2.000
PRKAB1 1.20 6.8 13.0 0.00028 0.58 2 2.000
EIF2B2 0.90 7.0 12.0 0.00055 0.77 3 2.800
EEF2KMT 0.97 6.8 11.0 0.00083 0.87 4 3.500
WDR18 0.65 7.4 11.0 0.00120 0.95 5 4.400
NSRP1 0.69 7.3 9.3 0.00230 0.95 6 8.300
CCT2 0.32 9.1 9.0 0.00280 0.95 7 9.500
AHSA1 0.64 7.2 8.8 0.00300 0.95 8 10.000
DOLPP1 0.90 6.7 8.7 0.00320 0.95 9 11.000
ACTA2 1.00 7.4 8.6 0.00340 0.95 10 12.000
1e-04 NA NA NA NA NA 0 1.200
1e-05 NA NA NA NA NA 0 0.400
1e-06 NA NA NA NA NA 0 0.270
1e-07 NA NA NA NA NA 0 0.130
1e-08 NA NA NA NA NA 0 0.067
1e-09 NA NA NA NA NA 0 0.067
1e-10 NA NA NA NA NA 0 0.067
EmpiricalFDR
RP11-143E21.7 2.00
PRKAB1 1.00
EIF2B2 0.93
EEF2KMT 0.88
WDR18 0.89
NSRP1 1.40
CCT2 1.40
AHSA1 1.30
DOLPP1 1.20
ACTA2 1.20
1e-04 Inf
1e-05 Inf
1e-06 Inf
1e-07 Inf
1e-08 Inf
1e-09 Inf
1e-10 Inf
[1] "NAB2_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
CLU -1.80 7.4 67 4.3e-16 1.8e-12 1 0.10
NQO1 -1.40 7.5 21 4.1e-06 8.5e-03 2 0.83
FTH1 -0.93 12.0 19 1.3e-05 1.6e-02 3 1.00
RP11-14N7.2 -1.00 7.3 19 1.5e-05 1.6e-02 4 1.00
IFI27L1 -1.00 6.6 18 2.7e-05 1.8e-02 5 1.30
GAP43 -1.20 8.2 18 2.8e-05 1.8e-02 6 1.30
CTD-2006C1.2 -1.10 6.9 17 3.0e-05 1.8e-02 7 1.40
TUBB2B -0.61 11.0 17 4.6e-05 2.4e-02 8 1.50
SQSTM1 -1.10 8.0 16 6.2e-05 2.9e-02 9 1.50
PTN -1.10 7.9 15 1.2e-04 5.2e-02 10 1.90
1e-04 NA NA NA NA NA 9 1.70
1e-05 NA NA NA NA NA 2 0.93
1e-06 NA NA NA NA NA 1 0.57
1e-07 NA NA NA NA NA 1 0.37
1e-08 NA NA NA NA NA 1 0.30
1e-09 NA NA NA NA NA 1 0.23
1e-10 NA NA NA NA NA 1 0.20
EmpiricalFDR
CLU 0.10
NQO1 0.42
FTH1 0.33
RP11-14N7.2 0.26
IFI27L1 0.25
GAP43 0.22
CTD-2006C1.2 0.20
TUBB2B 0.19
SQSTM1 0.17
PTN 0.19
1e-04 0.19
1e-05 0.47
1e-06 0.57
1e-07 0.37
1e-08 0.30
1e-09 0.23
1e-10 0.20
[1] "NAB2_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TP53 1.00 7.0 11.0 0.00081 1 1 3.500 3.5
STRA13 0.64 8.2 11.0 0.00100 1 2 4.000 2.0
GLUL -0.65 8.0 11.0 0.00110 1 3 4.300 1.4
NIPSNAP1 -0.65 7.3 10.0 0.00150 1 4 5.500 1.4
NUP93 1.00 6.8 8.9 0.00290 1 5 9.600 1.9
FAM120AOS 1.00 6.8 8.7 0.00320 1 6 11.000 1.8
PEX2 1.00 6.7 8.3 0.00400 1 7 13.000 1.9
HCCS -0.71 6.7 7.5 0.00620 1 8 20.000 2.4
SRSF11 0.41 8.3 7.4 0.00660 1 9 21.000 2.3
C7orf49 0.92 6.8 7.3 0.00680 1 10 21.000 2.1
1e-04 NA NA NA NA NA 0 1.100 Inf
1e-05 NA NA NA NA NA 0 0.700 Inf
1e-06 NA NA NA NA NA 0 0.330 Inf
1e-07 NA NA NA NA NA 0 0.200 Inf
1e-08 NA NA NA NA NA 0 0.130 Inf
1e-09 NA NA NA NA NA 0 0.100 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "neg_CTRL_00018_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
FTL 2.00 13.0 14 0.00016 0.43 1 2.200 2.20
BRI3 0.97 8.5 13 0.00039 0.43 2 3.300 1.60
GAP43 2.20 8.2 12 0.00047 0.43 3 3.600 1.20
MSH2 -1.10 6.7 12 0.00057 0.43 4 3.900 0.98
YWHAG 1.10 7.3 12 0.00062 0.43 5 4.200 0.83
TXN2 0.65 8.1 11 0.00094 0.43 6 5.800 0.97
BIN3 -0.97 6.7 11 0.00098 0.43 7 6.100 0.87
MBD3 1.40 6.9 11 0.00120 0.43 8 6.800 0.85
FTH1 1.00 12.0 10 0.00120 0.43 9 6.900 0.77
LMCD1 -1.20 6.7 10 0.00130 0.43 10 7.100 0.71
1e-04 NA NA NA NA NA 0 1.700 Inf
1e-05 NA NA NA NA NA 0 0.700 Inf
1e-06 NA NA NA NA NA 0 0.430 Inf
1e-07 NA NA NA NA NA 0 0.270 Inf
1e-08 NA NA NA NA NA 0 0.170 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "neg_CTRL_00022_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NEFM -1.30 7.5 15.0 0.00014 0.43 1 1.70 1.70
PDLIM2 1.10 7.5 14.0 0.00021 0.43 2 1.90 0.97
GDI1 -0.68 7.4 11.0 0.00073 0.79 3 4.40 1.50
CHCHD6 -0.71 6.9 10.0 0.00130 0.79 4 6.70 1.70
USP11 -0.66 7.3 10.0 0.00140 0.79 5 7.10 1.40
OLA1 -0.39 8.4 10.0 0.00140 0.79 6 7.10 1.20
LSM10 0.76 7.4 10.0 0.00150 0.79 7 7.10 1.00
MPZL1 1.10 6.8 10.0 0.00150 0.79 8 7.50 0.93
OSER1 -0.73 6.9 8.6 0.00340 0.99 9 14.00 1.60
NINJ1 -0.73 6.8 8.4 0.00370 0.99 10 16.00 1.60
1e-04 NA NA NA NA NA 0 1.40 Inf
1e-05 NA NA NA NA NA 0 0.63 Inf
1e-06 NA NA NA NA NA 0 0.33 Inf
1e-07 NA NA NA NA NA 0 0.20 Inf
1e-08 NA NA NA NA NA 0 0.13 Inf
1e-09 NA NA NA NA NA 0 0.10 Inf
1e-10 NA NA NA NA NA 0 0.10 Inf
[1] "neg_EGFP_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CHCHD10 -1.4 7.8 15.0 0.00013 0.54 1 0.630 0.63
ROCK1 3.4 6.8 11.0 0.00082 0.65 2 2.700 1.40
ID3 -2.1 8.0 11.0 0.00095 0.65 3 3.000 1.00
PPP1R1A 3.9 7.0 9.9 0.00170 0.65 4 5.500 1.40
IRX5 3.4 6.8 9.7 0.00190 0.65 5 6.100 1.20
SRP72 1.3 8.1 9.6 0.00200 0.65 6 6.300 1.00
COQ4 -1.1 7.3 9.5 0.00210 0.65 7 7.000 1.00
ITSN1 2.7 7.1 9.3 0.00230 0.65 8 7.900 0.98
MYEF2 3.2 6.7 9.2 0.00250 0.65 9 8.400 0.94
RUFY1 3.1 6.7 9.2 0.00250 0.65 10 8.600 0.86
1e-04 NA NA NA NA NA 0 0.570 Inf
1e-05 NA NA NA NA NA 0 0.170 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "neg_EGFP_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
UBE2E2 1.50 6.6 15 0.00013 0.29 1 0.970 0.97
TAX1BP1 0.95 7.4 14 0.00020 0.29 2 1.300 0.67
SYMPK 1.40 6.7 14 0.00021 0.29 3 1.400 0.48
NEFM 2.00 7.5 12 0.00049 0.42 4 2.500 0.62
C19orf10 0.66 8.5 12 0.00051 0.42 5 2.500 0.50
RPS19BP1 0.52 8.5 11 0.00072 0.43 6 3.100 0.52
RNF181 0.72 7.8 11 0.00086 0.43 7 3.800 0.54
APOPT1 0.80 7.3 11 0.00096 0.43 8 4.100 0.51
SNAPC2 1.00 7.0 11 0.00110 0.43 9 4.900 0.54
CLTA 0.45 9.0 10 0.00120 0.43 10 5.200 0.52
1e-04 NA NA NA NA NA 0 0.870 Inf
1e-05 NA NA NA NA NA 0 0.430 Inf
1e-06 NA NA NA NA NA 0 0.270 Inf
1e-07 NA NA NA NA NA 0 0.200 Inf
1e-08 NA NA NA NA NA 0 0.100 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "neg_EGFP_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ARF4 -0.68 8.3 20.0 6.6e-06 0.028 1 0.330 0.33
NDC80 1.30 6.7 11.0 9.2e-04 1.000 2 3.800 1.90
PRPF38B 0.64 7.4 11.0 1.2e-03 1.000 3 5.000 1.70
ATP6AP2 -0.65 6.9 10.0 1.3e-03 1.000 4 5.300 1.30
RP11-14N7.2 -0.71 7.3 10.0 1.6e-03 1.000 5 6.200 1.20
THG1L 0.80 6.9 9.8 1.8e-03 1.000 6 7.200 1.20
MVK -0.68 7.0 9.5 2.1e-03 1.000 7 8.400 1.20
ZNF706 0.44 8.1 9.5 2.1e-03 1.000 8 8.400 1.00
ZNF512 0.93 6.7 8.9 2.8e-03 1.000 9 11.000 1.20
CCND3 -0.71 6.9 8.7 3.1e-03 1.000 10 11.000 1.10
1e-04 NA NA NA NA NA 1 1.000 1.00
1e-05 NA NA NA NA NA 1 0.370 0.37
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "NGEF_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SKP1 0.73 9.0 15.0 0.00014 0.58 1 2.100 2.10
HSD17B10 0.94 8.0 12.0 0.00055 0.60 2 4.100 2.00
KIFC1 -1.30 6.7 11.0 0.00110 0.60 3 6.600 2.20
PHLDA3 2.00 7.9 11.0 0.00110 0.60 4 6.700 1.70
MRPL49 1.50 7.4 11.0 0.00120 0.60 5 6.800 1.40
POMP 0.59 9.3 10.0 0.00140 0.60 6 7.600 1.30
TMEM167A 1.00 7.6 10.0 0.00140 0.60 7 7.700 1.10
CCDC14 -1.10 6.8 10.0 0.00150 0.60 8 7.900 0.99
DEF8 1.30 7.4 9.9 0.00170 0.60 9 8.600 0.96
APRT 0.87 8.3 9.7 0.00190 0.60 10 9.300 0.93
1e-04 NA NA NA NA NA 0 1.900 Inf
1e-05 NA NA NA NA NA 0 1.100 Inf
1e-06 NA NA NA NA NA 0 0.570 Inf
1e-07 NA NA NA NA NA 0 0.330 Inf
1e-08 NA NA NA NA NA 0 0.300 Inf
1e-09 NA NA NA NA NA 0 0.100 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "NGEF_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
EMG1 -1.8 7.6 11.0 0.00088 1 1 4.70 4.7
GLOD4 -1.5 7.4 9.7 0.00190 1 2 7.60 3.8
TMCO1 2.9 7.8 9.6 0.00200 1 3 7.80 2.6
KDELR1 2.2 8.2 8.8 0.00300 1 4 11.00 2.7
UBA1 4.3 7.2 8.6 0.00350 1 5 12.00 2.4
AURKB -2.2 7.3 8.4 0.00380 1 6 13.00 2.2
SGO2 -2.3 6.8 8.2 0.00410 1 7 14.00 2.0
REEP4 -2.0 6.7 8.0 0.00480 1 8 15.00 1.9
AKR7A2 4.3 7.2 7.8 0.00540 1 9 17.00 1.9
CDCA3 -2.3 6.8 7.5 0.00620 1 10 20.00 2.0
1e-04 NA NA NA NA NA 0 2.00 Inf
1e-05 NA NA NA NA NA 0 1.10 Inf
1e-06 NA NA NA NA NA 0 0.67 Inf
1e-07 NA NA NA NA NA 0 0.47 Inf
1e-08 NA NA NA NA NA 0 0.27 Inf
1e-09 NA NA NA NA NA 0 0.20 Inf
1e-10 NA NA NA NA NA 0 0.13 Inf
[1] "PBRM1_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm
CDC25B -2.5 7.0 20.0 6.7e-06 0.028 1 0.270
RP11-339B21.12 -2.4 6.8 18.0 1.8e-05 0.037 2 0.400
NDC80 -2.2 6.7 14.0 1.6e-04 0.230 3 1.400
DLL1 -2.6 6.9 13.0 2.6e-04 0.230 4 1.700
PLK1 -2.3 7.5 13.0 2.8e-04 0.230 5 1.800
YWHAB 1.5 8.8 13.0 3.3e-04 0.230 6 2.000
JUN -1.7 7.9 12.0 6.3e-04 0.380 7 3.100
ELAVL1 1.5 8.1 10.0 1.4e-03 0.730 8 5.600
PTTG1 -1.8 8.5 9.9 1.6e-03 0.730 9 6.300
DLGAP5 -1.9 6.7 9.3 2.2e-03 0.730 10 9.200
1e-04 NA NA NA NA NA 2 1.000
1e-05 NA NA NA NA NA 1 0.330
1e-06 NA NA NA NA NA 0 0.130
1e-07 NA NA NA NA NA 0 0.033
1e-08 NA NA NA NA NA 0 0.000
1e-09 NA NA NA NA NA 0 0.000
1e-10 NA NA NA NA NA 0 0.000
EmpiricalFDR
CDC25B 0.27
RP11-339B21.12 0.20
NDC80 0.47
DLL1 0.43
PLK1 0.36
YWHAB 0.34
JUN 0.44
ELAVL1 0.70
PTTG1 0.70
DLGAP5 0.92
1e-04 0.52
1e-05 0.33
1e-06 Inf
1e-07 Inf
1e-08 NaN
1e-09 NaN
1e-10 NaN
[1] "PBRM1_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
RP4-758J18.2 2.4 6.7 14.0 0.00019 0.68 1 1.100 1.10
TFPT 2.1 6.8 12.0 0.00049 0.68 2 2.000 1.00
AZI2 1.8 6.8 11.0 0.00078 0.68 3 3.100 1.00
IFITM3 -1.4 8.6 11.0 0.00079 0.68 4 3.100 0.77
TMEM14A -1.1 6.8 11.0 0.00093 0.68 5 3.800 0.76
INTU -1.2 6.8 11.0 0.00098 0.68 6 4.000 0.66
ILKAP 1.6 6.8 10.0 0.00150 0.85 7 5.700 0.82
FAM195A 2.1 6.7 9.8 0.00180 0.85 8 6.300 0.79
C19orf24 1.4 7.1 9.6 0.00200 0.85 9 7.500 0.83
TPM2 -1.5 7.2 9.5 0.00200 0.85 10 7.500 0.75
1e-04 NA NA NA NA NA 0 0.870 Inf
1e-05 NA NA NA NA NA 0 0.370 Inf
1e-06 NA NA NA NA NA 0 0.200 Inf
1e-07 NA NA NA NA NA 0 0.130 Inf
1e-08 NA NA NA NA NA 0 0.100 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "PBRM1_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TPM2 -3.5 7.2 33 9.4e-09 3.9e-05 1 0.17 0.17
SPARC -1.5 8.5 18 1.8e-05 3.8e-02 2 1.20 0.60
HDAC2 2.1 8.6 17 3.2e-05 4.5e-02 3 1.40 0.47
HEBP1 -2.0 6.8 16 6.7e-05 6.9e-02 4 1.60 0.41
CCND2 -2.2 7.0 14 2.4e-04 2.0e-01 5 2.20 0.45
LRRC47 4.4 7.3 13 3.1e-04 2.1e-01 6 2.40 0.41
COPS3 2.3 7.9 12 4.1e-04 2.5e-01 7 2.80 0.40
SBNO1 4.1 7.1 12 5.7e-04 2.6e-01 8 3.50 0.43
BCCIP 2.9 7.5 11 7.6e-04 2.6e-01 9 4.00 0.45
CSE1L 4.2 7.2 11 7.8e-04 2.6e-01 10 4.10 0.41
1e-04 NA NA NA NA NA 4 1.80 0.44
1e-05 NA NA NA NA NA 1 1.00 1.00
1e-06 NA NA NA NA NA 1 0.47 0.47
1e-07 NA NA NA NA NA 1 0.33 0.33
1e-08 NA NA NA NA NA 1 0.17 0.17
1e-09 NA NA NA NA NA 0 0.10 Inf
1e-10 NA NA NA NA NA 0 0.10 Inf
[1] "PCDHA123_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
PFDN4 -0.41 8.2 15.0 0.00011 0.45 1 1.400 1.4
SIAH1 0.82 6.7 12.0 0.00060 0.99 2 3.600 1.8
MAT2A 0.57 7.3 11.0 0.00120 0.99 3 5.600 1.9
MAGOH 0.42 7.7 9.8 0.00170 0.99 4 7.700 1.9
RP11-14N7.2 -0.58 7.3 9.5 0.00200 0.99 5 8.700 1.7
PLIN3 -0.52 7.1 9.4 0.00220 0.99 6 9.300 1.6
TFPT -0.53 6.8 8.9 0.00290 0.99 7 12.000 1.7
MELK 0.77 6.6 8.4 0.00380 0.99 8 15.000 1.8
ATP5C1 -0.24 8.4 8.4 0.00390 0.99 9 15.000 1.7
SUMO2 0.21 10.0 8.3 0.00390 0.99 10 15.000 1.5
1e-04 NA NA NA NA NA 0 1.300 Inf
1e-05 NA NA NA NA NA 0 0.370 Inf
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.100 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "PCDHA123_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CTGF -0.84 8.2 20.0 8.2e-06 0.035 1 0.40 0.40
CYR61 -0.66 7.7 15.0 8.5e-05 0.180 2 1.00 0.52
NIFK -0.36 7.8 11.0 7.7e-04 1.000 3 3.50 1.20
HIC2 0.72 6.7 10.0 1.3e-03 1.000 4 6.10 1.50
SEPT2 -0.27 8.1 10.0 1.5e-03 1.000 5 6.80 1.40
PDAP1 0.26 8.5 9.8 1.8e-03 1.000 6 8.20 1.40
CCNK 0.57 6.9 9.5 2.1e-03 1.000 7 9.50 1.40
SYAP1 -0.42 7.1 9.0 2.7e-03 1.000 8 12.00 1.40
MRGBP -0.50 6.7 8.7 3.1e-03 1.000 9 13.00 1.50
MED21 0.54 6.9 8.4 3.8e-03 1.000 10 16.00 1.60
1e-04 NA NA NA NA NA 2 1.00 0.52
1e-05 NA NA NA NA NA 1 0.47 0.47
1e-06 NA NA NA NA NA 0 0.27 Inf
1e-07 NA NA NA NA NA 0 0.17 Inf
1e-08 NA NA NA NA NA 0 0.17 Inf
1e-09 NA NA NA NA NA 0 0.13 Inf
1e-10 NA NA NA NA NA 0 0.13 Inf
[1] "PCDHA123_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SOX4 0.86 8.7 15.0 0.00014 0.57 1 0.530 0.53
SERPINH1 -0.45 7.7 12.0 0.00058 1.00 2 2.000 0.98
HIC2 0.75 6.7 11.0 0.00093 1.00 3 2.800 0.93
NRDC 0.60 6.9 11.0 0.00098 1.00 4 2.900 0.72
LRRFIP2 0.66 6.8 9.9 0.00170 1.00 5 4.800 0.95
TIMM9 0.47 7.3 9.8 0.00180 1.00 6 5.000 0.84
IGF2BP1 0.45 7.5 9.5 0.00210 1.00 7 5.800 0.83
FYN 0.51 7.1 8.6 0.00350 1.00 8 10.000 1.30
RBM22 -0.40 7.1 8.3 0.00400 1.00 9 12.000 1.30
BNIP3 0.50 7.1 7.8 0.00520 1.00 10 16.000 1.60
1e-04 NA NA NA NA NA 0 0.470 Inf
1e-05 NA NA NA NA NA 0 0.130 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "pos_SNAP91_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TDG 4.50 7.3 11.0 0.00081 0.94 1 3.900 3.9
LLPH 4.30 7.2 10.0 0.00140 0.94 2 5.700 2.8
FOXB1 -2.00 6.7 9.5 0.00210 0.94 3 8.100 2.7
USP16 4.20 7.2 9.1 0.00260 0.94 4 9.800 2.4
MCM5 -1.90 6.9 8.6 0.00340 0.94 5 12.000 2.5
CCAR1 2.70 7.6 8.6 0.00340 0.94 6 12.000 2.1
NACA 0.67 11.0 7.8 0.00510 0.94 7 19.000 2.7
RNF187 -1.40 7.5 7.7 0.00550 0.94 8 20.000 2.5
RBCK1 4.00 7.0 7.6 0.00580 0.94 9 22.000 2.4
PDLIM2 4.70 7.5 7.6 0.00580 0.94 10 22.000 2.2
1e-04 NA NA NA NA NA 0 1.200 Inf
1e-05 NA NA NA NA NA 0 0.530 Inf
1e-06 NA NA NA NA NA 0 0.230 Inf
1e-07 NA NA NA NA NA 0 0.130 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "pos_SNAP91_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ADI1 -0.85 7.1 15.0 0.00011 0.44 1 1.30 1.3
COMMD10 1.30 6.6 11.0 0.00084 1.00 2 4.40 2.2
LONP1 1.10 7.1 11.0 0.00100 1.00 3 5.20 1.7
SERP1 0.50 8.2 9.8 0.00180 1.00 4 8.10 2.0
TMEM259 0.87 7.0 8.9 0.00290 1.00 5 12.00 2.5
AGBL5 1.00 6.7 8.3 0.00400 1.00 6 17.00 2.9
DNAJA1 0.45 8.7 8.2 0.00420 1.00 7 18.00 2.6
INTS11 0.79 7.0 8.1 0.00430 1.00 8 18.00 2.3
THG1L -0.61 6.9 7.4 0.00660 1.00 9 27.00 3.0
CAV1 -0.93 7.2 7.3 0.00690 1.00 10 28.00 2.8
1e-04 NA NA NA NA NA 0 1.30 Inf
1e-05 NA NA NA NA NA 0 0.47 Inf
1e-06 NA NA NA NA NA 0 0.17 Inf
1e-07 NA NA NA NA NA 0 0.00 NaN
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "PPP1R16B_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NEFM -1.20 7.5 20.0 6.8e-06 0.028 1 0.53 0.53
SRPK2 -0.59 7.2 16.0 6.2e-05 0.098 2 1.10 0.57
CAV1 -1.00 7.2 16.0 7.0e-05 0.098 3 1.20 0.40
YIF1B 0.83 6.8 12.0 5.0e-04 0.520 4 2.90 0.73
PNKP -0.60 6.7 9.1 2.6e-03 1.000 5 11.00 2.20
COPS2 -0.48 7.1 9.0 2.8e-03 1.000 6 11.00 1.90
CYB5D2 0.85 6.7 8.8 3.0e-03 1.000 7 12.00 1.80
ANKRD10 0.66 6.9 8.5 3.5e-03 1.000 8 14.00 1.80
MFGE8 0.78 6.7 8.3 3.9e-03 1.000 9 15.00 1.70
C12orf57 0.32 8.6 8.3 3.9e-03 1.000 10 15.00 1.50
1e-04 NA NA NA NA NA 3 1.40 0.46
1e-05 NA NA NA NA NA 1 0.63 0.63
1e-06 NA NA NA NA NA 0 0.43 Inf
1e-07 NA NA NA NA NA 0 0.37 Inf
1e-08 NA NA NA NA NA 0 0.30 Inf
1e-09 NA NA NA NA NA 0 0.27 Inf
1e-10 NA NA NA NA NA 0 0.27 Inf
[1] "PPP1R16B_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TAOK1 1.10 6.7 11.0 0.00096 1 1 3.300 3.3
FABP7 -0.94 7.1 9.7 0.00190 1 2 6.400 3.2
CTD-2006C1.2 1.10 6.9 9.5 0.00210 1 3 6.800 2.3
MRPL36 0.60 7.5 9.1 0.00260 1 4 8.500 2.1
NEFM -0.98 7.5 9.1 0.00260 1 5 8.600 1.7
HDAC7 0.95 6.7 8.6 0.00340 1 6 11.000 1.8
CENPK -0.73 6.9 8.5 0.00350 1 7 11.000 1.6
MRPL30 0.75 6.8 7.3 0.00710 1 8 23.000 2.8
NSG1 0.96 6.9 7.1 0.00760 1 9 24.000 2.7
TET1 -0.65 6.7 7.1 0.00780 1 10 25.000 2.5
1e-04 NA NA NA NA NA 0 0.670 Inf
1e-05 NA NA NA NA NA 0 0.230 Inf
1e-06 NA NA NA NA NA 0 0.033 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "PPP1R16B_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NUTF2 0.63 7.6 12.0 0.00057 0.69 1 3.90 3.90
ID1 1.70 6.8 11.0 0.00098 0.69 2 5.50 2.80
ERCC1 0.56 7.6 11.0 0.00110 0.69 3 6.00 2.00
DPYSL2 0.80 7.3 11.0 0.00120 0.69 4 6.50 1.60
SNAPC2 -0.65 7.0 10.0 0.00130 0.69 5 6.70 1.30
CYR61 -0.72 7.7 10.0 0.00130 0.69 6 6.80 1.10
EIF2B5 -0.60 7.1 10.0 0.00130 0.69 7 7.00 1.00
GYG1 0.79 7.2 9.9 0.00170 0.69 8 8.00 1.00
PHC2 -0.69 6.8 9.9 0.00170 0.69 9 8.10 0.90
MBOAT7 0.99 6.7 9.9 0.00170 0.69 10 8.10 0.81
1e-04 NA NA NA NA NA 0 1.30 Inf
1e-05 NA NA NA NA NA 0 0.57 Inf
1e-06 NA NA NA NA NA 0 0.17 Inf
1e-07 NA NA NA NA NA 0 0.10 Inf
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "RERE_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
C6orf203 0.97 6.6 12.0 0.00061 0.78 1 5.00 5.0
FSTL1 1.10 6.7 12.0 0.00068 0.78 2 5.20 2.6
RSPRY1 0.77 6.9 10.0 0.00130 0.78 3 7.60 2.5
PSMB6 0.34 9.0 10.0 0.00130 0.78 4 7.80 2.0
HUWE1 0.84 6.7 10.0 0.00130 0.78 5 7.80 1.6
ISG20L2 0.74 6.8 9.6 0.00200 0.78 6 10.00 1.7
ATF5 -0.82 7.0 9.4 0.00220 0.78 7 11.00 1.6
ARPC4 0.44 7.7 9.4 0.00220 0.78 8 11.00 1.4
CECR5 0.62 7.2 9.2 0.00240 0.78 9 12.00 1.3
SPTAN1 0.84 6.7 8.9 0.00280 0.78 10 14.00 1.4
1e-04 NA NA NA NA NA 0 2.20 Inf
1e-05 NA NA NA NA NA 0 1.30 Inf
1e-06 NA NA NA NA NA 0 0.80 Inf
1e-07 NA NA NA NA NA 0 0.60 Inf
1e-08 NA NA NA NA NA 0 0.43 Inf
1e-09 NA NA NA NA NA 0 0.40 Inf
1e-10 NA NA NA NA NA 0 0.27 Inf
[1] "RERE_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TAGLN3 -1.40 7.1 26.0 3.7e-07 0.0016 1 0.067 0.067
FLNA 0.79 7.8 17.0 3.9e-05 0.0810 2 0.330 0.170
USMG5 0.44 8.8 16.0 6.4e-05 0.0890 3 0.500 0.170
KDELR2 0.53 8.0 14.0 1.4e-04 0.1500 4 0.900 0.220
CIAPIN1 -0.44 7.5 11.0 9.3e-04 0.6500 5 3.100 0.620
SEMA5B 0.93 6.7 11.0 1.1e-03 0.6500 6 3.400 0.570
DOK5 0.99 7.0 10.0 1.3e-03 0.6500 7 3.900 0.560
MRPL23 0.56 7.4 9.9 1.6e-03 0.6500 8 4.900 0.610
MSMO1 0.69 7.9 9.9 1.7e-03 0.6500 9 5.000 0.560
DDX6 0.74 6.9 9.8 1.8e-03 0.6500 10 5.300 0.530
1e-04 NA NA NA NA NA 3 0.630 0.210
1e-05 NA NA NA NA NA 1 0.200 0.200
1e-06 NA NA NA NA NA 1 0.067 0.067
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "RERE_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ID3 -1.00 8.0 8.8 0.0030 1 1 11.000 11.0
HIPK2 -0.73 6.9 8.6 0.0034 1 2 12.000 6.0
FKBP10 -0.66 7.2 8.5 0.0035 1 3 12.000 4.1
PFDN4 0.55 8.2 8.5 0.0036 1 4 13.000 3.2
RP11-620J15.3 1.00 6.8 8.4 0.0037 1 5 13.000 2.6
SURF1 0.86 7.0 8.1 0.0045 1 6 16.000 2.6
LSM1 0.59 7.5 7.7 0.0054 1 7 18.000 2.6
ETFA 0.63 7.4 7.7 0.0056 1 8 19.000 2.3
RP11-21N3.1 0.62 7.5 7.6 0.0057 1 9 19.000 2.2
COMMD9 0.63 7.5 7.5 0.0063 1 10 21.000 2.1
1e-04 NA NA NA NA NA 0 0.500 Inf
1e-05 NA NA NA NA NA 0 0.067 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "SETD1A_1st_exon_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
LRIF1 1.40 6.9 11.0 0.00071 1 1 2.800 2.8
ITGAE 0.69 7.7 10.0 0.00150 1 2 5.200 2.6
ACIN1 0.76 7.6 10.0 0.00160 1 3 5.500 1.8
SFRP2 -1.10 7.0 9.8 0.00180 1 4 6.400 1.6
MAP1A 1.40 7.0 9.6 0.00190 1 5 7.000 1.4
MSL3 1.30 6.6 9.6 0.00200 1 6 7.000 1.2
UBE2J2 0.68 7.4 9.0 0.00270 1 7 9.800 1.4
CCAR1 0.68 7.6 8.8 0.00310 1 8 11.000 1.4
HES6 1.50 9.0 8.8 0.00310 1 9 11.000 1.2
CARD19 1.20 6.7 8.6 0.00340 1 10 13.000 1.3
1e-04 NA NA NA NA NA 0 0.530 Inf
1e-05 NA NA NA NA NA 0 0.270 Inf
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.033 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "SETD1A_1st_exon_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CALD1 -1.00 7.9 28 1.2e-07 0.00051 1 0.00 0.000
MYL9 -1.30 7.6 22 2.9e-06 0.00600 2 0.23 0.120
CD59 -0.91 7.0 19 1.2e-05 0.01700 3 0.37 0.120
CSRP1 -1.10 7.1 18 2.7e-05 0.02800 4 0.43 0.110
RAB13 -0.67 7.9 17 4.0e-05 0.03300 5 0.47 0.093
TPM2 -1.30 7.2 16 5.3e-05 0.03700 6 0.53 0.089
PDLIM1 -0.89 7.2 15 9.8e-05 0.05800 7 0.70 0.100
G6PD -0.91 7.0 15 1.3e-04 0.06700 8 0.80 0.100
ARL6IP5 -0.72 7.2 13 2.5e-04 0.11000 9 1.20 0.140
TOR1A -0.82 6.7 13 2.9e-04 0.12000 10 1.40 0.140
1e-04 NA NA NA NA NA 7 0.70 0.100
1e-05 NA NA NA NA NA 2 0.37 0.180
1e-06 NA NA NA NA NA 1 0.13 0.130
1e-07 NA NA NA NA NA 0 0.00 NaN
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "SETD1A_1st_exon_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
UBB 4.2 9.7 23 1.6e-06 0.0068 1 0.330 0.33
COX11 4.3 7.2 11 8.4e-04 0.6000 2 5.400 2.70
CREB3 4.2 7.2 11 9.8e-04 0.6000 3 5.900 2.00
CST3 2.2 8.2 11 1.2e-03 0.6000 4 6.600 1.60
PPP1R12A 4.1 7.1 10 1.2e-03 0.6000 5 6.800 1.40
ATF5 -2.2 7.0 10 1.2e-03 0.6000 6 6.800 1.10
NPDC1 4.3 7.2 10 1.3e-03 0.6000 7 6.800 0.98
SEPHS2 -1.9 6.8 10 1.3e-03 0.6000 8 6.800 0.85
BFAR 4.0 7.1 10 1.3e-03 0.6000 9 7.100 0.79
FXYD6 3.3 7.9 10 1.4e-03 0.6000 10 7.700 0.77
1e-04 NA NA NA NA NA 1 1.400 1.40
1e-05 NA NA NA NA NA 1 0.670 0.67
1e-06 NA NA NA NA NA 0 0.270 Inf
1e-07 NA NA NA NA NA 0 0.230 Inf
1e-08 NA NA NA NA NA 0 0.170 Inf
1e-09 NA NA NA NA NA 0 0.100 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "STAT6_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
EIF2D 1.20 6.8 12.0 0.00059 1 1 3.000 3.0
KMT2E 0.85 7.3 9.3 0.00230 1 2 8.700 4.3
ARMCX3 0.91 7.1 8.6 0.00340 1 3 13.000 4.3
PDCD11 1.10 6.7 8.6 0.00340 1 4 13.000 3.2
MAP6 1.20 6.7 8.3 0.00400 1 5 15.000 3.0
RAB28 -0.69 6.8 7.9 0.00490 1 6 18.000 3.0
NAA35 0.99 6.7 7.9 0.00490 1 7 18.000 2.5
SLC25A13 -0.67 6.8 7.6 0.00570 1 8 21.000 2.6
MYH9 1.10 6.9 7.5 0.00620 1 9 23.000 2.6
HNRNPM -0.34 9.6 7.5 0.00630 1 10 24.000 2.4
1e-04 NA NA NA NA NA 0 1.500 Inf
1e-05 NA NA NA NA NA 0 0.430 Inf
1e-06 NA NA NA NA NA 0 0.300 Inf
1e-07 NA NA NA NA NA 0 0.200 Inf
1e-08 NA NA NA NA NA 0 0.100 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "STAT6_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TP53I3 -1.00 6.9 17 0.00003 0.13 1 0.870 0.87
NUDT14 -0.72 6.9 14 0.00021 0.45 2 2.100 1.10
TP53TG1 -0.84 6.7 12 0.00043 0.51 3 3.500 1.20
PLTP -0.66 7.1 12 0.00064 0.51 4 4.200 1.00
ERCC1 0.55 7.6 11 0.00073 0.51 5 4.900 0.97
GANAB 0.69 7.2 11 0.00120 0.51 6 7.000 1.20
GTF2H2 1.10 6.7 10 0.00120 0.51 7 7.100 1.00
ACSL3 -0.72 6.6 10 0.00120 0.51 8 7.100 0.88
FJX1 0.96 6.9 10 0.00120 0.51 9 7.100 0.79
YIPF5 0.86 6.8 10 0.00130 0.51 10 7.600 0.76
1e-04 NA NA NA NA NA 1 1.400 1.40
1e-05 NA NA NA NA NA 0 0.570 Inf
1e-06 NA NA NA NA NA 0 0.170 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "STAT6_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
PLK1 1.50 7.5 18 2.3e-05 0.094 1 0.300 0.30
ALPL -0.73 6.9 14 1.5e-04 0.310 2 0.900 0.45
CCNB1 1.10 7.5 14 2.2e-04 0.310 3 1.100 0.38
UBE2C 1.20 8.3 12 4.3e-04 0.360 4 2.000 0.49
UBE2S 0.70 8.9 12 4.3e-04 0.360 5 2.000 0.40
TACC3 1.00 6.9 12 5.5e-04 0.360 6 2.500 0.42
PTTG1 0.85 8.5 12 6.1e-04 0.360 7 2.900 0.41
HMMR 1.10 6.8 11 9.6e-04 0.500 8 4.400 0.55
CDC20 0.93 7.7 11 1.2e-03 0.530 9 5.300 0.59
CENPA 0.97 7.0 10 1.3e-03 0.530 10 5.500 0.55
1e-04 NA NA NA NA NA 1 0.700 0.70
1e-05 NA NA NA NA NA 0 0.200 Inf
1e-06 NA NA NA NA NA 0 0.170 Inf
1e-07 NA NA NA NA NA 0 0.067 Inf
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "TCF4-ITF2_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
RPL27A 0.29 12.0 15 9.5e-05 0.16 1 0.630 0.63
TAGLN 1.20 9.3 15 1.1e-04 0.16 2 0.670 0.33
RPL37A 0.24 12.0 15 1.2e-04 0.16 3 0.670 0.22
TMEM170A 0.83 6.9 13 2.5e-04 0.20 4 1.200 0.31
RPL30 0.24 12.0 13 2.7e-04 0.20 5 1.300 0.26
GPI 0.75 7.1 13 2.9e-04 0.20 6 1.400 0.23
RPL38 0.24 11.0 13 3.7e-04 0.22 7 1.800 0.25
RPL36AL 0.29 9.5 12 5.0e-04 0.26 8 2.200 0.27
PTTG1IP 0.47 8.1 12 6.0e-04 0.26 9 2.600 0.29
CNPY3 0.73 7.0 11 7.2e-04 0.26 10 3.000 0.30
1e-04 NA NA NA NA NA 1 0.670 0.67
1e-05 NA NA NA NA NA 0 0.170 Inf
1e-06 NA NA NA NA NA 0 0.067 Inf
1e-07 NA NA NA NA NA 0 0.000 NaN
1e-08 NA NA NA NA NA 0 0.000 NaN
1e-09 NA NA NA NA NA 0 0.000 NaN
1e-10 NA NA NA NA NA 0 0.000 NaN
[1] "TCF4-ITF2_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
FOS -0.86 6.7 12.0 0.00044 0.95 1 3.20 3.2
ZKSCAN1 0.77 7.1 12.0 0.00047 0.95 2 3.30 1.6
THAP4 0.92 6.7 11.0 0.00084 0.95 3 4.70 1.6
PHLDA1 1.30 7.0 11.0 0.00091 0.95 4 5.20 1.3
NEFM 1.30 7.5 10.0 0.00120 1.00 5 6.50 1.3
BCLAF1 0.47 7.7 8.8 0.00300 1.00 6 14.00 2.3
PTOV1 -0.33 8.1 8.8 0.00310 1.00 7 14.00 2.0
TUBG1 -0.48 7.2 8.6 0.00330 1.00 8 15.00 1.9
TRIM2 -0.53 7.0 8.5 0.00350 1.00 9 16.00 1.8
BRD4 0.52 7.3 8.2 0.00410 1.00 10 18.00 1.8
1e-04 NA NA NA NA NA 0 1.20 Inf
1e-05 NA NA NA NA NA 0 0.50 Inf
1e-06 NA NA NA NA NA 0 0.30 Inf
1e-07 NA NA NA NA NA 0 0.20 Inf
1e-08 NA NA NA NA NA 0 0.20 Inf
1e-09 NA NA NA NA NA 0 0.17 Inf
1e-10 NA NA NA NA NA 0 0.17 Inf
[1] "TCF4-ITF2_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
LMO4 2.10 7.0 12.0 0.00052 0.65 1 3.90 3.90
DIO3 -1.60 7.1 11.0 0.00087 0.65 2 5.50 2.80
MRPS28 2.30 6.7 11.0 0.00093 0.65 3 5.90 2.00
COA5 2.00 6.8 11.0 0.00096 0.65 4 6.00 1.50
USP9X 2.30 6.7 11.0 0.00100 0.65 5 6.20 1.20
PCBP1 0.69 8.6 11.0 0.00100 0.65 6 6.30 1.00
STARD3 2.20 6.7 10.0 0.00120 0.65 7 7.30 1.00
UBN1 1.90 6.9 10.0 0.00120 0.65 8 7.40 0.92
CSNK1A1 1.40 7.3 10.0 0.00150 0.67 9 8.40 0.94
WDR82 1.80 6.9 9.8 0.00170 0.67 10 9.40 0.94
1e-04 NA NA NA NA NA 0 1.90 Inf
1e-05 NA NA NA NA NA 0 0.93 Inf
1e-06 NA NA NA NA NA 0 0.60 Inf
1e-07 NA NA NA NA NA 0 0.47 Inf
1e-08 NA NA NA NA NA 0 0.27 Inf
1e-09 NA NA NA NA NA 0 0.13 Inf
1e-10 NA NA NA NA NA 0 0.10 Inf
[1] "TRANK1_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SDF2L1 -2.1 7.2 16.0 7.9e-05 0.33 1 1.900 1.9
INIP -2.0 6.8 12.0 4.8e-04 1.00 2 3.900 1.9
PYCR1 -2.3 6.8 11.0 1.1e-03 1.00 3 6.200 2.1
SEC11C -1.5 7.5 9.3 2.3e-03 1.00 4 11.000 2.7
MRPS34 1.8 8.4 8.9 2.9e-03 1.00 5 13.000 2.7
HSPB11 4.5 7.3 8.3 3.9e-03 1.00 6 17.000 2.8
FUNDC2 2.1 7.8 7.9 5.1e-03 1.00 7 20.000 2.9
OTUB1 1.9 7.9 7.7 5.7e-03 1.00 8 23.000 2.8
FXR1 2.6 7.5 7.6 5.9e-03 1.00 9 24.000 2.6
ACO2 4.1 7.1 7.5 6.0e-03 1.00 10 24.000 2.4
1e-04 NA NA NA NA NA 1 2.200 2.2
1e-05 NA NA NA NA NA 0 1.000 Inf
1e-06 NA NA NA NA NA 0 0.670 Inf
1e-07 NA NA NA NA NA 0 0.370 Inf
1e-08 NA NA NA NA NA 0 0.200 Inf
1e-09 NA NA NA NA NA 0 0.100 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "TRANK1_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
TMEM230 0.65 8.0 12.0 0.00067 1 1 4.50 4.5
UGP2 1.10 7.1 11.0 0.00097 1 2 5.60 2.8
FAM133B -0.67 7.4 10.0 0.00150 1 3 7.50 2.5
GNAQ 1.40 6.7 10.0 0.00160 1 4 7.90 2.0
SNRNP200 1.00 7.0 9.0 0.00270 1 5 12.00 2.4
CCNK -0.76 6.9 8.4 0.00380 1 6 16.00 2.7
MLLT10 -0.80 6.7 8.1 0.00440 1 7 18.00 2.6
CD63 0.57 9.3 7.9 0.00510 1 8 21.00 2.6
NQO1 1.80 7.5 7.6 0.00570 1 9 23.00 2.5
DLL1 -1.20 6.9 7.6 0.00590 1 10 23.00 2.3
1e-04 NA NA NA NA NA 0 1.70 Inf
1e-05 NA NA NA NA NA 0 0.73 Inf
1e-06 NA NA NA NA NA 0 0.37 Inf
1e-07 NA NA NA NA NA 0 0.20 Inf
1e-08 NA NA NA NA NA 0 0.13 Inf
1e-09 NA NA NA NA NA 0 0.10 Inf
1e-10 NA NA NA NA NA 0 0.10 Inf
[1] "TRANK1_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
CCT7 -0.26 8.8 12.0 0.00052 1 1 3.100 3.1
RPRD1A -0.50 6.9 11.0 0.00079 1 2 4.100 2.1
UBE2E3 0.33 8.9 11.0 0.00087 1 3 4.400 1.5
TIMM21 -0.52 6.8 9.9 0.00170 1 4 8.300 2.1
HMGCR 0.65 7.0 9.8 0.00180 1 5 8.500 1.7
PHF20L1 0.53 7.0 9.7 0.00190 1 6 9.200 1.5
ADSL -0.37 7.4 9.4 0.00210 1 7 10.000 1.4
RPUSD1 0.60 6.7 9.4 0.00210 1 8 10.000 1.3
CITED2 -0.46 7.4 9.3 0.00230 1 9 11.000 1.2
PYURF 0.31 7.9 9.0 0.00270 1 10 12.000 1.2
1e-04 NA NA NA NA NA 0 1.000 Inf
1e-05 NA NA NA NA NA 0 0.330 Inf
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.130 Inf
1e-08 NA NA NA NA NA 0 0.100 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "UBE2Q2P1_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
JAG1 -1.90 6.8 22 3.1e-06 0.013 1 0.200 0.20
SERPINH1 -1.10 7.7 19 1.4e-05 0.029 2 0.270 0.13
RCN1 -0.89 8.7 15 9.8e-05 0.140 3 0.800 0.27
MGST1 -1.10 7.8 12 5.3e-04 0.400 4 2.500 0.62
SGO1 2.80 6.8 12 5.9e-04 0.400 5 2.700 0.53
DNAJB1 -1.20 6.7 11 7.5e-04 0.400 6 3.100 0.52
PHB2 -0.58 8.6 11 7.8e-04 0.400 7 3.100 0.45
HSP90AA1 -0.65 10.0 11 8.3e-04 0.400 8 3.200 0.40
TRIM8 2.10 6.8 11 8.5e-04 0.400 9 3.200 0.36
CLIC1 -0.90 8.7 11 1.2e-03 0.460 10 4.100 0.41
1e-04 NA NA NA NA NA 3 0.800 0.27
1e-05 NA NA NA NA NA 1 0.200 0.20
1e-06 NA NA NA NA NA 0 0.130 Inf
1e-07 NA NA NA NA NA 0 0.130 Inf
1e-08 NA NA NA NA NA 0 0.033 Inf
1e-09 NA NA NA NA NA 0 0.033 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "UBE2Q2P1_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
ATP5B -0.77 9.5 15 9.3e-05 0.20 1 1.200 1.20
TERF2IP -1.50 7.4 15 9.6e-05 0.20 2 1.300 0.63
ARF4 -1.10 8.3 12 4.5e-04 0.42 3 2.900 0.98
UFSP2 2.60 6.9 12 4.5e-04 0.42 4 2.900 0.73
SFRP1 4.10 7.1 12 6.7e-04 0.42 5 4.000 0.81
CA2 -1.60 7.1 11 7.7e-04 0.42 6 4.500 0.76
PITHD1 -1.10 7.3 11 8.0e-04 0.42 7 4.600 0.66
PABPC1 0.74 10.0 11 8.1e-04 0.42 8 4.600 0.58
YKT6 -1.20 7.0 11 9.6e-04 0.42 9 5.200 0.57
PPP1R2 -1.30 6.7 11 1.0e-03 0.42 10 5.300 0.53
1e-04 NA NA NA NA NA 2 1.300 0.63
1e-05 NA NA NA NA NA 0 0.430 Inf
1e-06 NA NA NA NA NA 0 0.200 Inf
1e-07 NA NA NA NA NA 0 0.100 Inf
1e-08 NA NA NA NA NA 0 0.067 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
[1] "UBE2Q2P1_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
NAV1 -1.40 6.7 15.0 0.00012 0.5 1 1.30 1.3
CAMLG 1.10 7.6 11.0 0.00095 1.0 2 5.00 2.5
REEP2 2.20 6.9 10.0 0.00150 1.0 3 6.70 2.2
PRKAB1 1.90 6.8 8.8 0.00310 1.0 4 11.00 2.8
CDKN1B 1.90 6.7 8.4 0.00380 1.0 5 14.00 2.8
C1orf43 0.66 8.5 8.2 0.00420 1.0 6 15.00 2.5
FBXW5 1.70 6.8 8.0 0.00470 1.0 7 16.00 2.3
SF3B3 1.60 6.8 7.9 0.00500 1.0 8 17.00 2.2
MRPS12 0.86 7.7 7.8 0.00510 1.0 9 18.00 2.0
RGS20 1.40 7.1 7.8 0.00520 1.0 10 18.00 1.8
1e-04 NA NA NA NA NA 0 1.20 Inf
1e-05 NA NA NA NA NA 0 0.50 Inf
1e-06 NA NA NA NA NA 0 0.30 Inf
1e-07 NA NA NA NA NA 0 0.23 Inf
1e-08 NA NA NA NA NA 0 0.00 NaN
1e-09 NA NA NA NA NA 0 0.00 NaN
1e-10 NA NA NA NA NA 0 0.00 NaN
[1] "VPS45_1_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
PTN -1.90 7.9 34 5.7e-09 2.4e-05 1 0.100 0.100
IFITM3 -2.00 8.6 30 3.8e-08 7.9e-05 2 0.130 0.067
CLU -1.70 7.4 27 1.9e-07 2.6e-04 3 0.200 0.067
CTSC -1.70 6.7 27 2.5e-07 2.6e-04 4 0.200 0.050
GPM6B -1.00 8.5 23 1.7e-06 1.4e-03 5 0.300 0.060
CD47 -1.40 7.0 20 6.6e-06 4.6e-03 6 0.470 0.078
WLS -1.40 7.0 18 2.0e-05 1.1e-02 7 0.600 0.086
RCN1 -0.92 8.7 18 2.0e-05 1.1e-02 8 0.600 0.075
ORC6 2.20 7.3 14 1.9e-04 8.8e-02 9 1.600 0.180
FUCA2 -1.30 6.6 13 3.0e-04 1.3e-01 10 2.200 0.220
1e-04 NA NA NA NA NA 8 1.200 0.150
1e-05 NA NA NA NA NA 6 0.500 0.083
1e-06 NA NA NA NA NA 4 0.300 0.075
1e-07 NA NA NA NA NA 2 0.200 0.100
1e-08 NA NA NA NA NA 1 0.100 0.100
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.033 Inf
[1] "VPS45_2_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
SUMO3 0.43 8.0 16 5.7e-05 0.17 1 1.30 1.30
DLL1 -0.96 6.9 16 8.3e-05 0.17 2 1.40 0.68
MLLT11 -0.44 8.7 14 2.3e-04 0.26 3 2.50 0.84
NEFM -0.80 7.5 13 2.8e-04 0.26 4 2.70 0.68
CYC1 0.30 8.8 13 3.1e-04 0.26 5 2.90 0.59
ISCU 0.42 7.8 11 7.7e-04 0.38 6 5.10 0.84
RBP1 -0.71 7.2 11 8.1e-04 0.38 7 5.30 0.76
DRAXIN -0.63 6.7 11 8.2e-04 0.38 8 5.30 0.67
ANKRD11 0.45 7.6 11 8.2e-04 0.38 9 5.30 0.59
PCBP4 -0.45 8.1 11 1.0e-03 0.43 10 6.20 0.62
1e-04 NA NA NA NA NA 2 1.50 0.75
1e-05 NA NA NA NA NA 0 0.67 Inf
1e-06 NA NA NA NA NA 0 0.50 Inf
1e-07 NA NA NA NA NA 0 0.40 Inf
1e-08 NA NA NA NA NA 0 0.27 Inf
1e-09 NA NA NA NA NA 0 0.23 Inf
1e-10 NA NA NA NA NA 0 0.17 Inf
[1] "VPS45_3_gene_edgeR-qlf_Neg2.Rd"
logFC logCPM F PValue FDR #in_real #in_perm EmpiricalFDR
PCGF2 3.80 7.0 21 5.7e-06 0.024 1 0.430 0.43
NKAIN4 -2.00 6.9 18 1.9e-05 0.041 2 0.530 0.27
TXNRD1 -1.60 7.1 13 3.6e-04 0.470 3 2.900 0.96
GNPDA1 -1.60 6.8 12 4.5e-04 0.470 4 3.100 0.78
NELFE 1.30 7.7 12 6.6e-04 0.470 5 4.000 0.79
CHTF8 1.80 7.2 12 6.8e-04 0.470 6 4.000 0.67
CTDSP2 3.00 6.7 11 1.2e-03 0.620 7 5.900 0.84
CPE -1.50 6.7 10 1.4e-03 0.620 8 6.700 0.84
MRPL1 1.50 7.6 10 1.6e-03 0.620 9 7.500 0.83
PPIA 0.53 10.0 10 1.6e-03 0.620 10 7.500 0.75
1e-04 NA NA NA NA NA 2 1.500 0.73
1e-05 NA NA NA NA NA 1 0.530 0.53
1e-06 NA NA NA NA NA 0 0.330 Inf
1e-07 NA NA NA NA NA 0 0.200 Inf
1e-08 NA NA NA NA NA 0 0.170 Inf
1e-09 NA NA NA NA NA 0 0.067 Inf
1e-10 NA NA NA NA NA 0 0.067 Inf
sessionInfo()R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Scientific Linux 7.4 (Nitrogen)
Matrix products: default
BLAS/LAPACK: /software/openblas-0.2.19-el7-x86_64/lib/libopenblas_haswellp-r0.2.19.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] edgeR_3.24.3 limma_3.38.2
loaded via a namespace (and not attached):
[1] locfit_1.5-9.1 workflowr_1.2.0 Rcpp_1.0.0 lattice_0.20-38
[5] digest_0.6.18 rprojroot_1.3-2 grid_3.5.1 backports_1.1.2
[9] git2r_0.23.0 magrittr_1.5 evaluate_0.12 stringi_1.3.1
[13] fs_1.2.6 whisker_0.3-2 rmarkdown_1.10 tools_3.5.1
[17] stringr_1.4.0 glue_1.3.0 yaml_2.2.0 compiler_3.5.1
[21] htmltools_0.3.6 knitr_1.20