metaseqR report

Summary

Analysis summary

Summary: The raw bam files, one for each RNA-Seq sample, were summarized to a gene read counts table, using the Bioconductor package GenomicRanges. In the final read counts table, each row represented one gene, each column one RNA-Seq sample and each cell, the corresponding read counts associated with each row and column.The gene counts table was normalized for inherent systematic or experimental biases (e.g. sequencing depth, gene length, GC content bias etc.) using the Bioconductor package edgeR after removing genes that had zero counts over all the RNA-Seq samples (3496 genes). The output of the normalization algorithm was a table with normalized counts, which can be used for differential expression analysis with statistical algorithms developed specifically for count data. Prior to the statistical testing procedure, the gene read counts were filtered for possible artifacts that could affect the subsequent statistical testing procedures. Genes presenting any of the following were excluded from further analysis: i) genes with length less than 500 (62 genes), ii) genes whose average reads per 100 bp was less than the 25^th quantile of the total normalized distribution of average reads per 100bp (0 genes with cutoff value 0.02668 average reads per 100 bp), iii) genes with read counts below the median read counts of the total normalized count distribution (7023 genes with cutoff value 40 normalized read counts). The total number of genes excluded due to the application of gene filters was 2152. The total (unified) number of genes excluded due to the application of all filters was 10732. The resulting gene counts table was subjected to differential expression analysis for the contrasts Prol versus D2plus, Prol versus D4plus, Prol versus D8minus, Prol versus D8plus using the Bioconductor package edgeR. The final numbers of differentially expressed genes were (per contrast): for the contrast Prol versus D2plus, 911 (64) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 543 (59) were up-regulated, 368 (5) were down-regulated and 0 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast Prol versus D4plus, 402 (36) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 203 (27) were up-regulated, 199 (9) were down-regulated and 0 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast Prol versus D8minus, 571 (12) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 254 (5) were up-regulated, 316 (7) were down-regulated and 1 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast Prol versus D8plus, 655 (57) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 428 (43) were up-regulated, 227 (14) were down-regulated and 0 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale. Literature references for all the algorithms used can be found at the end of this report.

Input options

Read counts file: imported sam/bam/bed files
Conditions: Prol, D4plus, D8minus, D8plus, D2plus
Samples included: IT3R59_24_Prol, IT3R63_28_Prol, IT3R60_25_D4plus, IT3R65_30_D4plus, IT3R61_26_D8minus, IT3R66_31_D8minus, IT3R62_27_D8plus, IT3R67_32_D8plus, IT3R64_29_D2plus
Samples excluded: none
Requested contrasts: Prol_vs_D2plus, Prol_vs_D4plus, Prol_vs_D8minus, Prol_vs_D8plus
Library sizes:

IT3R59_24_Prol: 11455909
IT3R63_28_Prol: 5608661
IT3R60_25_D4plus: 5561737
IT3R65_30_D4plus: 4739938
IT3R61_26_D8minus: 4528946
IT3R66_31_D8minus: 3620228
IT3R62_27_D8plus: 4734068
IT3R67_32_D8plus: 5750761
IT3R64_29_D2plus: 4549451

Annotation: download
Organism: human (Homo sapiens), genome version alias hg19
Annotation source: RefSeq database
Count type: gene
Exon filters: none applied
Gene filters: length, avg.reads, expression, biotype

length
- length: 500

avg.reads
- average.per.bp: 100
- quantile: 0.25

expression
- median: TRUE
- mean: FALSE
- quantile: NA
- known: NA
- custom: NA

biotype
- pseudogene: FALSE
- lincRNA: FALSE
- protein_coding: FALSE
- antisense: FALSE
- processed_transcript: FALSE
- snRNA: FALSE
- sense_intronic: FALSE
- miRNA: FALSE
- misc_RNA: FALSE
- snoRNA: FALSE
- rRNA: TRUE
- polymorphic_pseudogene: FALSE
- sense_overlapping: FALSE
- three_prime_overlapping_ncrna: FALSE
- TR_V_gene: FALSE
- TR_V_pseudogene: TRUE
- TR_D_gene: FALSE
- TR_J_gene: FALSE
- TR_C_gene: FALSE
- TR_J_pseudogene: TRUE
- IG_C_gene: FALSE
- IG_C_pseudogene: TRUE
- IG_J_gene: FALSE
- IG_J_pseudogene: TRUE
- IG_D_gene: FALSE
- IG_V_gene: FALSE
- IG_V_pseudogene: TRUE

Filter application: after normalization
Normalization algorithm: edgeR
Normalization arguments: method, refColumn, logratioTrim, sumTrim, doWeighting, Acutoff, p

method: TMM
logratioTrim: 0.3
sumTrim: 0.05
doWeighting: TRUE
Acutoff: -1e+10
p: 0.75

Statistical algorithm(s): edgeR
Statistical arguments for edgeR: main.method, rowsum.filter, prior.df, trend, span, tag.method, grid.length, grid.range, offset, glm.method, subset, AveLogCPM, trend.method, dispersion, offset, weights, lib.size, prior.count, start, method, test, abundance.trend, robust, winsor.tail.p

main.method: classic
rowsum.filter: 5
prior.df: 10
trend: movingave
tag.method: grid
grid.length: 11
grid.range: -6, 6
glm.method: CoxReid
subset: 10000
trend.method: auto
prior.count: 0.125
method: auto
test: chisq
abundance.trend: TRUE
robust: FALSE
winsor.tail.p: 0.05, 0.1

Meta-analysis method: no meta-analysis, reported p-values from the first supplied statistical algorithm
Multiple testing correction: Benjamini-Hochberg FDR
p-value threshold: 0.05
Logarithmic tranformation offset: 1
Analysis preset: not available
Quality control plots: multidimensional scaling, biotype detection, biotype counts, sample and biotype saturation, filtered biotypes, correlation heatmap and correlogram, pairwise scatterplots between samples, boxplots, GC-content bias, transcript length bias, mean-difference plot, mean-variance plot, DEG biotype detection, volcano plot, DEG heatmap
Figure format: png, pdf
Output directory: /data/images/proton2/run391/www/metaseqr_run391
Output data: Annotation, p-value, Adjusted p-value (FDR), Fold change, Statistics, Read counts
Output scale(s): log2 scale, Reads per Gene Model
Output values: Normalized values
Output statistics: Mean, Median, Standard deviation, Median Absolute Deviation (MAD), Coefficient of Variation, Robust Coefficient of Variation
Total run time: 12 minutes 19 seconds

Filtered genes

Number of filtered genes: 10732 which is the union of

Filtered because of zero reads: 3496
Filtered because of exon filters: 0
Filtered because of gene filters: 7236 which is the union of
- length: 62 genes with filter cutoff value 500
- avg.reads: 2088 genes with filter cutoff value 0.0266798
- expression: 7023 genes further decomposed to (filter name, filtered genes, filter cutoff):
- - median: 7023 genes with filter cutoff value 40
- biotype: 1 genes with filter cutoff value rRNA, TR_V_pseudogene, TR_J_pseudogene, IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene

Differentially expressed genes

Number of differentially expressed genes per contrast:

Prol_vs_D2plus: 911 (64) statistically significant genes of which 543 (59) up regulated, 368 (5) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
Prol_vs_D4plus: 402 (36) statistically significant genes of which 203 (27) up regulated, 199 (9) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
Prol_vs_D8minus: 571 (12) statistically significant genes of which 254 (5) up regulated, 316 (7) down regulated and 1 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.
Prol_vs_D8plus: 655 (57) statistically significant genes of which 428 (43) up regulated, 227 (14) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log₂ scale.

Run log

[ 2018-04-10 18:34:34 ] INFO 2018-04-10 18:34:34: Data processing started...
[ 2018-04-10 18:34:34 ] INFO Read counts file: imported sam/bam/bed files
[ 2018-04-10 18:34:34 ] INFO Conditions: Prol, D4plus, D8minus, D8plus, D2plus
[ 2018-04-10 18:34:34 ] INFO Samples to include: IT3R59_24_Prol, IT3R63_28_Prol, IT3R60_25_D4plus, IT3R65_30_D4plus, IT3R61_26_D8minus, IT3R66_31_D8minus, IT3R62_27_D8plus, IT3R67_32_D8plus, IT3R64_29_D2plus
[ 2018-04-10 18:34:34 ] INFO Samples to exclude: none
[ 2018-04-10 18:34:34 ] INFO Requested contrasts: Prol_vs_D2plus, Prol_vs_D4plus, Prol_vs_D8minus, Prol_vs_D8plus
[ 2018-04-10 18:34:34 ] INFO Annotation: download
[ 2018-04-10 18:34:34 ] INFO Organism: hg19
[ 2018-04-10 18:34:34 ] INFO Reference source: refseq
[ 2018-04-10 18:34:34 ] INFO Count type: gene
[ 2018-04-10 18:34:34 ] INFO Exon filters: none applied
[ 2018-04-10 18:34:34 ] INFO Gene filters: length, avg.reads, expression, biotype
[ 2018-04-10 18:34:34 ] INFO length:
[ 2018-04-10 18:34:34 ] INFO length: 500
[ 2018-04-10 18:34:34 ] INFO avg.reads:
[ 2018-04-10 18:34:34 ] INFO average.per.bp: 100
[ 2018-04-10 18:34:34 ] INFO quantile: 0.25
[ 2018-04-10 18:34:34 ] INFO expression:
[ 2018-04-10 18:34:34 ] INFO median: TRUE
[ 2018-04-10 18:34:34 ] INFO mean: FALSE
[ 2018-04-10 18:34:34 ] INFO quantile: NA
[ 2018-04-10 18:34:34 ] INFO known: NA
[ 2018-04-10 18:34:34 ] INFO custom: NA
[ 2018-04-10 18:34:34 ] INFO biotype:
[ 2018-04-10 18:34:34 ] INFO pseudogene: FALSE
[ 2018-04-10 18:34:34 ] INFO lincRNA: FALSE
[ 2018-04-10 18:34:34 ] INFO protein_coding: FALSE
[ 2018-04-10 18:34:34 ] INFO antisense: FALSE
[ 2018-04-10 18:34:34 ] INFO processed_transcript: FALSE
[ 2018-04-10 18:34:34 ] INFO snRNA: FALSE
[ 2018-04-10 18:34:34 ] INFO sense_intronic: FALSE
[ 2018-04-10 18:34:34 ] INFO miRNA: FALSE
[ 2018-04-10 18:34:34 ] INFO misc_RNA: FALSE
[ 2018-04-10 18:34:34 ] INFO snoRNA: FALSE
[ 2018-04-10 18:34:34 ] INFO rRNA: TRUE
[ 2018-04-10 18:34:34 ] INFO polymorphic_pseudogene: FALSE
[ 2018-04-10 18:34:34 ] INFO sense_overlapping: FALSE
[ 2018-04-10 18:34:34 ] INFO three_prime_overlapping_ncrna: FALSE
[ 2018-04-10 18:34:34 ] INFO TR_V_gene: FALSE
[ 2018-04-10 18:34:34 ] INFO TR_V_pseudogene: TRUE
[ 2018-04-10 18:34:34 ] INFO TR_D_gene: FALSE
[ 2018-04-10 18:34:34 ] INFO TR_J_gene: FALSE
[ 2018-04-10 18:34:34 ] INFO TR_C_gene: FALSE
[ 2018-04-10 18:34:34 ] INFO TR_J_pseudogene: TRUE
[ 2018-04-10 18:34:34 ] INFO IG_C_gene: FALSE
[ 2018-04-10 18:34:34 ] INFO IG_C_pseudogene: TRUE
[ 2018-04-10 18:34:34 ] INFO IG_J_gene: FALSE
[ 2018-04-10 18:34:34 ] INFO IG_J_pseudogene: TRUE
[ 2018-04-10 18:34:34 ] INFO IG_D_gene: FALSE
[ 2018-04-10 18:34:34 ] INFO IG_V_gene: FALSE
[ 2018-04-10 18:34:34 ] INFO IG_V_pseudogene: TRUE
[ 2018-04-10 18:34:34 ] INFO Filter application: postnorm
[ 2018-04-10 18:34:34 ] INFO Normalization algorithm: edger
[ 2018-04-10 18:34:34 ] INFO Normalization arguments:
[ 2018-04-10 18:34:34 ] INFO method: TMM
[ 2018-04-10 18:34:34 ] INFO logratioTrim: 0.3
[ 2018-04-10 18:34:34 ] INFO sumTrim: 0.05
[ 2018-04-10 18:34:34 ] INFO doWeighting: TRUE
[ 2018-04-10 18:34:34 ] INFO Acutoff: -1e+10
[ 2018-04-10 18:34:34 ] INFO p: 0.75
[ 2018-04-10 18:34:34 ] INFO Statistical algorithm: edger
[ 2018-04-10 18:34:34 ] INFO Statistical arguments:
[ 2018-04-10 18:34:34 ] INFO edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
[ 2018-04-10 18:34:34 ] INFO Meta-analysis method: none
[ 2018-04-10 18:34:34 ] INFO Multiple testing correction: BH
[ 2018-04-10 18:34:34 ] INFO p-value threshold: 0.05
[ 2018-04-10 18:34:34 ] INFO Logarithmic transformation offset: 1
[ 2018-04-10 18:34:34 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap
[ 2018-04-10 18:34:34 ] INFO Figure format: png, pdf
[ 2018-04-10 18:34:34 ] INFO Output directory: /data/images/proton2/run391/www/metaseqr_run391
[ 2018-04-10 18:34:34 ] INFO Output data: flags, annotation, p.value, adj.p.value, fold.change, stats, counts, flags
[ 2018-04-10 18:34:34 ] INFO Output scale(s): log2, rpgm
[ 2018-04-10 18:34:34 ] INFO Output values: normalized
[ 2018-04-10 18:34:34 ] INFO Output statistics: mean, median, sd, mad, cv, rcv
[ 2018-04-10 18:34:34 ] INFO Downloading gene annotation for hg19...
[ 2018-04-10 18:34:53 ] INFO Converting annotation to GenomicRanges object...
[ 2018-04-11 12:41:08 ] INFO Getting DNA sequences...
[ 2018-04-11 12:43:46 ] INFO 2018-04-11 12:43:46: Data processing started...
[ 2018-04-11 12:43:46 ] INFO Read counts file: imported sam/bam/bed files
[ 2018-04-11 12:43:46 ] INFO Conditions: Prol, D4plus, D8minus, D8plus, D2plus
[ 2018-04-11 12:43:46 ] INFO Samples to include: IT3R59_24_Prol, IT3R63_28_Prol, IT3R60_25_D4plus, IT3R65_30_D4plus, IT3R61_26_D8minus, IT3R66_31_D8minus, IT3R62_27_D8plus, IT3R67_32_D8plus, IT3R64_29_D2plus
[ 2018-04-11 12:43:47 ] INFO Samples to exclude: none
[ 2018-04-11 12:43:47 ] INFO Requested contrasts: Prol_vs_D2plus, Prol_vs_D4plus, Prol_vs_D8minus, Prol_vs_D8plus
[ 2018-04-11 12:43:47 ] INFO Annotation: download
[ 2018-04-11 12:43:47 ] INFO Organism: hg19
[ 2018-04-11 12:43:47 ] INFO Reference source: refseq
[ 2018-04-11 12:43:47 ] INFO Count type: gene
[ 2018-04-11 12:43:47 ] INFO Exon filters: none applied
[ 2018-04-11 12:43:47 ] INFO Gene filters: length, avg.reads, expression, biotype
[ 2018-04-11 12:43:47 ] INFO length:
[ 2018-04-11 12:43:47 ] INFO length: 500
[ 2018-04-11 12:43:47 ] INFO avg.reads:
[ 2018-04-11 12:43:47 ] INFO average.per.bp: 100
[ 2018-04-11 12:43:47 ] INFO quantile: 0.25
[ 2018-04-11 12:43:47 ] INFO expression:
[ 2018-04-11 12:43:47 ] INFO median: TRUE
[ 2018-04-11 12:43:47 ] INFO mean: FALSE
[ 2018-04-11 12:43:47 ] INFO quantile: NA
[ 2018-04-11 12:43:47 ] INFO known: NA
[ 2018-04-11 12:43:47 ] INFO custom: NA
[ 2018-04-11 12:43:47 ] INFO biotype:
[ 2018-04-11 12:43:47 ] INFO pseudogene: FALSE
[ 2018-04-11 12:43:47 ] INFO lincRNA: FALSE
[ 2018-04-11 12:43:47 ] INFO protein_coding: FALSE
[ 2018-04-11 12:43:47 ] INFO antisense: FALSE
[ 2018-04-11 12:43:47 ] INFO processed_transcript: FALSE
[ 2018-04-11 12:43:47 ] INFO snRNA: FALSE
[ 2018-04-11 12:43:47 ] INFO sense_intronic: FALSE
[ 2018-04-11 12:43:47 ] INFO miRNA: FALSE
[ 2018-04-11 12:43:47 ] INFO misc_RNA: FALSE
[ 2018-04-11 12:43:47 ] INFO snoRNA: FALSE
[ 2018-04-11 12:43:47 ] INFO rRNA: TRUE
[ 2018-04-11 12:43:47 ] INFO polymorphic_pseudogene: FALSE
[ 2018-04-11 12:43:47 ] INFO sense_overlapping: FALSE
[ 2018-04-11 12:43:47 ] INFO three_prime_overlapping_ncrna: FALSE
[ 2018-04-11 12:43:47 ] INFO TR_V_gene: FALSE
[ 2018-04-11 12:43:47 ] INFO TR_V_pseudogene: TRUE
[ 2018-04-11 12:43:47 ] INFO TR_D_gene: FALSE
[ 2018-04-11 12:43:47 ] INFO TR_J_gene: FALSE
[ 2018-04-11 12:43:47 ] INFO TR_C_gene: FALSE
[ 2018-04-11 12:43:47 ] INFO TR_J_pseudogene: TRUE
[ 2018-04-11 12:43:47 ] INFO IG_C_gene: FALSE
[ 2018-04-11 12:43:47 ] INFO IG_C_pseudogene: TRUE
[ 2018-04-11 12:43:47 ] INFO IG_J_gene: FALSE
[ 2018-04-11 12:43:47 ] INFO IG_J_pseudogene: TRUE
[ 2018-04-11 12:43:47 ] INFO IG_D_gene: FALSE
[ 2018-04-11 12:43:47 ] INFO IG_V_gene: FALSE
[ 2018-04-11 12:43:47 ] INFO IG_V_pseudogene: TRUE
[ 2018-04-11 12:43:47 ] INFO Filter application: postnorm
[ 2018-04-11 12:43:47 ] INFO Normalization algorithm: edger
[ 2018-04-11 12:43:47 ] INFO Normalization arguments:
[ 2018-04-11 12:43:47 ] INFO method: TMM
[ 2018-04-11 12:43:47 ] INFO logratioTrim: 0.3
[ 2018-04-11 12:43:47 ] INFO sumTrim: 0.05
[ 2018-04-11 12:43:47 ] INFO doWeighting: TRUE
[ 2018-04-11 12:43:47 ] INFO Acutoff: -1e+10
[ 2018-04-11 12:43:47 ] INFO p: 0.75
[ 2018-04-11 12:43:47 ] INFO Statistical algorithm: edger
[ 2018-04-11 12:43:47 ] INFO Statistical arguments:
[ 2018-04-11 12:43:47 ] INFO edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1)
[ 2018-04-11 12:43:47 ] INFO Meta-analysis method: none
[ 2018-04-11 12:43:47 ] INFO Multiple testing correction: BH
[ 2018-04-11 12:43:47 ] INFO p-value threshold: 0.05
[ 2018-04-11 12:43:47 ] INFO Logarithmic transformation offset: 1
[ 2018-04-11 12:43:47 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap
[ 2018-04-11 12:43:47 ] INFO Figure format: png, pdf
[ 2018-04-11 12:43:47 ] INFO Output directory: /data/images/proton2/run391/www/metaseqr_run391
[ 2018-04-11 12:43:47 ] INFO Output data: flags, annotation, p.value, adj.p.value, fold.change, stats, counts, flags
[ 2018-04-11 12:43:47 ] INFO Output scale(s): log2, rpgm
[ 2018-04-11 12:43:47 ] INFO Output values: normalized
[ 2018-04-11 12:43:47 ] INFO Output statistics: mean, median, sd, mad, cv, rcv
[ 2018-04-11 12:43:47 ] INFO Downloading gene annotation for hg19...
[ 2018-04-11 12:43:47 ] WARN R package RMySQL is not present! Annotation will be retrieved by downloading temporary files from UCSC and the usage of a temporary SQLite database...
[ 2018-04-11 12:43:47 ] INFO Retrieving tables for temporary SQLite refseq hg19 gene subset database
[ 2018-04-11 12:43:47 ] INFO Retrieving table refFlat
[ 2018-04-11 12:43:57 ] INFO Retrieving table knownToRefSeq
[ 2018-04-11 12:44:01 ] INFO Retrieving table knownCanonical
[ 2018-04-11 12:44:04 ] INFO Retrieving table knownToEnsembl
[ 2018-04-11 12:44:08 ] INFO Retrieving table ensemblSource
[ 2018-04-11 12:44:16 ] INFO Converting annotation to GenomicRanges object...
[ 2018-04-11 12:44:18 ] INFO Getting DNA sequences...
[ 2018-04-11 12:44:34 ] INFO Getting GC content...
[ 2018-04-11 12:44:36 ] INFO Converting annotation to GenomicRanges object...
[ 2018-04-11 12:44:36 ] INFO Reading bam file IT3R59-24-Prol.bam for sample with name IT3R59_24_Prol. This might take some time...
[ 2018-04-11 12:44:36 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded...
[ 2018-04-11 12:44:36 ] INFO Reading bam file IT3R63-28-Prol.bam for sample with name IT3R63_28_Prol. This might take some time...
[ 2018-04-11 12:44:36 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded...
[ 2018-04-11 12:44:36 ] INFO Reading bam file IT3R60-25-D4plus.bam for sample with name IT3R60_25_D4plus. This might take some time...
[ 2018-04-11 12:44:36 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded...
[ 2018-04-11 12:44:36 ] INFO Reading bam file IT3R65-30-D4plus.bam for sample with name IT3R65_30_D4plus. This might take some time...
[ 2018-04-11 12:44:36 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded...
[ 2018-04-11 12:45:06 ] INFO Counting reads overlapping with given annotation...
[ 2018-04-11 12:45:06 ] INFO ...for single-end reads...
[ 2018-04-11 12:45:06 ] INFO ...ignoring strandedness...
[ 2018-04-11 12:45:08 ] INFO Counting reads overlapping with given annotation...
[ 2018-04-11 12:45:08 ] INFO ...for single-end reads...
[ 2018-04-11 12:45:08 ] INFO ...ignoring strandedness...
[ 2018-04-11 12:45:08 ] INFO Counting reads overlapping with given annotation...
[ 2018-04-11 12:45:08 ] INFO ...for single-end reads...
[ 2018-04-11 12:45:08 ] INFO ...ignoring strandedness...
[ 2018-04-11 12:45:17 ] INFO Counting reads overlapping with given annotation...
[ 2018-04-11 12:45:17 ] INFO ...for single-end reads...
[ 2018-04-11 12:45:17 ] INFO ...ignoring strandedness...
[ 2018-04-11 12:45:49 ] INFO Reading bam file IT3R67-32-D8plus.bam for sample with name IT3R67_32_D8plus. This might take some time...
[ 2018-04-11 12:45:49 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded...
[ 2018-04-11 12:45:57 ] INFO Reading bam file IT3R62-27-D8plus.bam for sample with name IT3R62_27_D8plus. This might take some time...
[ 2018-04-11 12:45:57 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded...
[ 2018-04-11 12:45:58 ] INFO Reading bam file IT3R66-31-D8minus.bam for sample with name IT3R66_31_D8minus. This might take some time...
[ 2018-04-11 12:45:58 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded...
[ 2018-04-11 12:46:06 ] INFO Counting reads overlapping with given annotation...
[ 2018-04-11 12:46:06 ] INFO ...for single-end reads...
[ 2018-04-11 12:46:06 ] INFO ...ignoring strandedness...
[ 2018-04-11 12:46:11 ] INFO Counting reads overlapping with given annotation...
[ 2018-04-11 12:46:11 ] INFO ...for single-end reads...
[ 2018-04-11 12:46:11 ] INFO ...ignoring strandedness...
[ 2018-04-11 12:46:12 ] INFO Counting reads overlapping with given annotation...
[ 2018-04-11 12:46:12 ] INFO ...for single-end reads...
[ 2018-04-11 12:46:12 ] INFO ...ignoring strandedness...
[ 2018-04-11 12:47:14 ] INFO Reading bam file IT3R61-26-D8minus.bam for sample with name IT3R61_26_D8minus. This might take some time...
[ 2018-04-11 12:47:14 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded...
[ 2018-04-11 12:47:24 ] INFO Counting reads overlapping with given annotation...
[ 2018-04-11 12:47:24 ] INFO ...for single-end reads...
[ 2018-04-11 12:47:24 ] INFO ...ignoring strandedness...
[ 2018-04-11 12:47:52 ] INFO Reading bam file IT3R64-29-D2plus.bam for sample with name IT3R64_29_D2plus. This might take some time...
[ 2018-04-11 12:47:52 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded...
[ 2018-04-11 12:47:59 ] INFO Counting reads overlapping with given annotation...
[ 2018-04-11 12:47:59 ] INFO ...for single-end reads...
[ 2018-04-11 12:47:59 ] INFO ...ignoring strandedness...
[ 2018-04-11 12:48:26 ] INFO Exporting raw read counts table to /data/images/proton2/run391/www/metaseqr_run391/lists/raw_counts_table.txt.gz
[ 2018-04-11 12:48:27 ] INFO Saving gene model to /data/images/proton2/run391/www/metaseqr_run391/data/gene_model.RData
[ 2018-04-11 12:48:27 ] INFO Removing genes with zero counts in all samples...
[ 2018-04-11 12:48:27 ] INFO Normalizing with: edger
[ 2018-04-11 12:48:28 ] INFO Applying gene filter length...
[ 2018-04-11 12:48:28 ] INFO Threshold below which ignored: 500
[ 2018-04-11 12:48:28 ] INFO Applying gene filter avg.reads...
[ 2018-04-11 12:48:28 ] INFO Threshold below which ignored: 0.0266798024526509
[ 2018-04-11 12:48:28 ] INFO Applying gene filter expression...
[ 2018-04-11 12:48:28 ] INFO Threshold below which ignored: 40
[ 2018-04-11 12:48:28 ] INFO Applying gene filter biotype...
[ 2018-04-11 12:48:28 ] INFO Biotypes ignored: rRNA, TR_V_pseudogene, TR_J_pseudogene, IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene
[ 2018-04-11 12:48:28 ] INFO 10732 genes filtered out
[ 2018-04-11 12:48:28 ] INFO 11334 genes remain after filtering
[ 2018-04-11 12:48:28 ] INFO Running statistical tests with: edger
[ 2018-04-11 12:48:29 ] INFO Contrast: Prol_vs_D2plus
[ 2018-04-11 12:48:31 ] INFO Contrast: Prol_vs_D4plus
[ 2018-04-11 12:48:33 ] INFO Contrast: Prol_vs_D8minus
[ 2018-04-11 12:48:35 ] INFO Contrast: Prol_vs_D8plus
[ 2018-04-11 12:48:37 ] INFO Contrast Prol_vs_D2plus: found 911 genes
[ 2018-04-11 12:48:37 ] INFO Contrast Prol_vs_D4plus: found 402 genes
[ 2018-04-11 12:48:37 ] INFO Contrast Prol_vs_D8minus: found 571 genes
[ 2018-04-11 12:48:37 ] INFO Contrast Prol_vs_D8plus: found 655 genes
[ 2018-04-11 12:48:37 ] INFO Exporting and compressing normalized read counts table to /data/images/proton2/run391/www/metaseqr_run391/lists/normalized_counts_table.txt
[ 2018-04-11 12:48:38 ] INFO Building output files...
[ 2018-04-11 12:48:38 ] INFO Contrast: Prol_vs_D2plus
[ 2018-04-11 12:48:38 ] INFO Adding non-filtered data...
[ 2018-04-11 12:48:38 ] INFO binding annotation...
[ 2018-04-11 12:48:38 ] INFO binding p-values...
[ 2018-04-11 12:48:38 ] INFO binding FDRs...
[ 2018-04-11 12:48:39 ] INFO binding log2 normalized fold changes...
[ 2018-04-11 12:48:39 ] INFO binding normalized mean counts...
[ 2018-04-11 12:48:39 ] INFO binding normalized median counts...
[ 2018-04-11 12:48:41 ] INFO binding normalized count sds...
[ 2018-04-11 12:48:42 ] INFO binding normalized count MADs...
[ 2018-04-11 12:48:45 ] INFO binding normalized count CVs...
[ 2018-04-11 12:48:46 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:48:50 ] INFO binding normalized mean counts...
[ 2018-04-11 12:48:51 ] INFO binding normalized median counts...
[ 2018-04-11 12:48:52 ] INFO binding normalized count sds...
[ 2018-04-11 12:48:53 ] INFO binding normalized count MADs...
[ 2018-04-11 12:48:55 ] INFO binding normalized count CVs...
[ 2018-04-11 12:48:56 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:48:59 ] INFO binding all normalized counts for Prol...
[ 2018-04-11 12:49:00 ] INFO binding all normalized counts for D2plus...
[ 2018-04-11 12:49:00 ] INFO binding filtering flags...
[ 2018-04-11 12:49:00 ] INFO Writing output...
[ 2018-04-11 12:49:01 ] INFO Adding filtered data...
[ 2018-04-11 12:49:01 ] INFO binding annotation...
[ 2018-04-11 12:49:01 ] INFO binding p-values...
[ 2018-04-11 12:49:01 ] INFO binding FDRs...
[ 2018-04-11 12:49:01 ] INFO binding log2 normalized fold changes...
[ 2018-04-11 12:49:01 ] INFO binding normalized mean counts...
[ 2018-04-11 12:49:01 ] INFO binding normalized median counts...
[ 2018-04-11 12:49:03 ] INFO binding normalized count sds...
[ 2018-04-11 12:49:04 ] INFO binding normalized count MADs...
[ 2018-04-11 12:49:06 ] INFO binding normalized count CVs...
[ 2018-04-11 12:49:07 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:49:11 ] INFO binding normalized mean counts...
[ 2018-04-11 12:49:11 ] INFO binding normalized median counts...
[ 2018-04-11 12:49:12 ] INFO binding normalized count sds...
[ 2018-04-11 12:49:13 ] INFO binding normalized count MADs...
[ 2018-04-11 12:49:15 ] INFO binding normalized count CVs...
[ 2018-04-11 12:49:16 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:49:19 ] INFO binding all normalized counts for Prol...
[ 2018-04-11 12:49:19 ] INFO binding all normalized counts for D2plus...
[ 2018-04-11 12:49:19 ] INFO binding filtering flags...
[ 2018-04-11 12:49:19 ] INFO Writing output...
[ 2018-04-11 12:49:21 ] INFO Contrast: Prol_vs_D4plus
[ 2018-04-11 12:49:21 ] INFO Adding non-filtered data...
[ 2018-04-11 12:49:21 ] INFO binding annotation...
[ 2018-04-11 12:49:21 ] INFO binding p-values...
[ 2018-04-11 12:49:21 ] INFO binding FDRs...
[ 2018-04-11 12:49:21 ] INFO binding log2 normalized fold changes...
[ 2018-04-11 12:49:21 ] INFO binding normalized mean counts...
[ 2018-04-11 12:49:22 ] INFO binding normalized median counts...
[ 2018-04-11 12:49:24 ] INFO binding normalized count sds...
[ 2018-04-11 12:49:25 ] INFO binding normalized count MADs...
[ 2018-04-11 12:49:27 ] INFO binding normalized count CVs...
[ 2018-04-11 12:49:29 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:49:33 ] INFO binding normalized mean counts...
[ 2018-04-11 12:49:34 ] INFO binding normalized median counts...
[ 2018-04-11 12:49:36 ] INFO binding normalized count sds...
[ 2018-04-11 12:49:37 ] INFO binding normalized count MADs...
[ 2018-04-11 12:49:39 ] INFO binding normalized count CVs...
[ 2018-04-11 12:49:41 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:49:45 ] INFO binding all normalized counts for Prol...
[ 2018-04-11 12:49:45 ] INFO binding all normalized counts for D4plus...
[ 2018-04-11 12:49:45 ] INFO binding filtering flags...
[ 2018-04-11 12:49:46 ] INFO Writing output...
[ 2018-04-11 12:49:46 ] INFO Adding filtered data...
[ 2018-04-11 12:49:46 ] INFO binding annotation...
[ 2018-04-11 12:49:46 ] INFO binding p-values...
[ 2018-04-11 12:49:46 ] INFO binding FDRs...
[ 2018-04-11 12:49:46 ] INFO binding log2 normalized fold changes...
[ 2018-04-11 12:49:46 ] INFO binding normalized mean counts...
[ 2018-04-11 12:49:46 ] INFO binding normalized median counts...
[ 2018-04-11 12:49:48 ] INFO binding normalized count sds...
[ 2018-04-11 12:49:49 ] INFO binding normalized count MADs...
[ 2018-04-11 12:49:51 ] INFO binding normalized count CVs...
[ 2018-04-11 12:49:52 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:49:56 ] INFO binding normalized mean counts...
[ 2018-04-11 12:49:56 ] INFO binding normalized median counts...
[ 2018-04-11 12:49:58 ] INFO binding normalized count sds...
[ 2018-04-11 12:49:59 ] INFO binding normalized count MADs...
[ 2018-04-11 12:50:01 ] INFO binding normalized count CVs...
[ 2018-04-11 12:50:02 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:50:06 ] INFO binding all normalized counts for Prol...
[ 2018-04-11 12:50:06 ] INFO binding all normalized counts for D4plus...
[ 2018-04-11 12:50:06 ] INFO binding filtering flags...
[ 2018-04-11 12:50:06 ] INFO Writing output...
[ 2018-04-11 12:50:08 ] INFO Contrast: Prol_vs_D8minus
[ 2018-04-11 12:50:08 ] INFO Adding non-filtered data...
[ 2018-04-11 12:50:08 ] INFO binding annotation...
[ 2018-04-11 12:50:08 ] INFO binding p-values...
[ 2018-04-11 12:50:08 ] INFO binding FDRs...
[ 2018-04-11 12:50:09 ] INFO binding log2 normalized fold changes...
[ 2018-04-11 12:50:09 ] INFO binding normalized mean counts...
[ 2018-04-11 12:50:09 ] INFO binding normalized median counts...
[ 2018-04-11 12:50:11 ] INFO binding normalized count sds...
[ 2018-04-11 12:50:12 ] INFO binding normalized count MADs...
[ 2018-04-11 12:50:15 ] INFO binding normalized count CVs...
[ 2018-04-11 12:50:16 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:50:21 ] INFO binding normalized mean counts...
[ 2018-04-11 12:50:21 ] INFO binding normalized median counts...
[ 2018-04-11 12:50:23 ] INFO binding normalized count sds...
[ 2018-04-11 12:50:24 ] INFO binding normalized count MADs...
[ 2018-04-11 12:50:27 ] INFO binding normalized count CVs...
[ 2018-04-11 12:50:28 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:50:32 ] INFO binding all normalized counts for Prol...
[ 2018-04-11 12:50:32 ] INFO binding all normalized counts for D8minus...
[ 2018-04-11 12:50:33 ] INFO binding filtering flags...
[ 2018-04-11 12:50:33 ] INFO Writing output...
[ 2018-04-11 12:50:33 ] INFO Adding filtered data...
[ 2018-04-11 12:50:33 ] INFO binding annotation...
[ 2018-04-11 12:50:33 ] INFO binding p-values...
[ 2018-04-11 12:50:33 ] INFO binding FDRs...
[ 2018-04-11 12:50:33 ] INFO binding log2 normalized fold changes...
[ 2018-04-11 12:50:33 ] INFO binding normalized mean counts...
[ 2018-04-11 12:50:34 ] INFO binding normalized median counts...
[ 2018-04-11 12:50:35 ] INFO binding normalized count sds...
[ 2018-04-11 12:50:36 ] INFO binding normalized count MADs...
[ 2018-04-11 12:50:38 ] INFO binding normalized count CVs...
[ 2018-04-11 12:50:40 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:50:43 ] INFO binding normalized mean counts...
[ 2018-04-11 12:50:44 ] INFO binding normalized median counts...
[ 2018-04-11 12:50:45 ] INFO binding normalized count sds...
[ 2018-04-11 12:50:46 ] INFO binding normalized count MADs...
[ 2018-04-11 12:50:49 ] INFO binding normalized count CVs...
[ 2018-04-11 12:50:50 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:50:53 ] INFO binding all normalized counts for Prol...
[ 2018-04-11 12:50:53 ] INFO binding all normalized counts for D8minus...
[ 2018-04-11 12:50:53 ] INFO binding filtering flags...
[ 2018-04-11 12:50:53 ] INFO Writing output...
[ 2018-04-11 12:50:55 ] INFO Contrast: Prol_vs_D8plus
[ 2018-04-11 12:50:55 ] INFO Adding non-filtered data...
[ 2018-04-11 12:50:55 ] INFO binding annotation...
[ 2018-04-11 12:50:56 ] INFO binding p-values...
[ 2018-04-11 12:50:56 ] INFO binding FDRs...
[ 2018-04-11 12:50:56 ] INFO binding log2 normalized fold changes...
[ 2018-04-11 12:50:56 ] INFO binding normalized mean counts...
[ 2018-04-11 12:50:57 ] INFO binding normalized median counts...
[ 2018-04-11 12:50:58 ] INFO binding normalized count sds...
[ 2018-04-11 12:51:00 ] INFO binding normalized count MADs...
[ 2018-04-11 12:51:02 ] INFO binding normalized count CVs...
[ 2018-04-11 12:51:04 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:51:08 ] INFO binding normalized mean counts...
[ 2018-04-11 12:51:09 ] INFO binding normalized median counts...
[ 2018-04-11 12:51:10 ] INFO binding normalized count sds...
[ 2018-04-11 12:51:12 ] INFO binding normalized count MADs...
[ 2018-04-11 12:51:14 ] INFO binding normalized count CVs...
[ 2018-04-11 12:51:16 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:51:20 ] INFO binding all normalized counts for Prol...
[ 2018-04-11 12:51:21 ] INFO binding all normalized counts for D8plus...
[ 2018-04-11 12:51:21 ] INFO binding filtering flags...
[ 2018-04-11 12:51:21 ] INFO Writing output...
[ 2018-04-11 12:51:21 ] INFO Adding filtered data...
[ 2018-04-11 12:51:21 ] INFO binding annotation...
[ 2018-04-11 12:51:21 ] INFO binding p-values...
[ 2018-04-11 12:51:21 ] INFO binding FDRs...
[ 2018-04-11 12:51:22 ] INFO binding log2 normalized fold changes...
[ 2018-04-11 12:51:22 ] INFO binding normalized mean counts...
[ 2018-04-11 12:51:22 ] INFO binding normalized median counts...
[ 2018-04-11 12:51:23 ] INFO binding normalized count sds...
[ 2018-04-11 12:51:24 ] INFO binding normalized count MADs...
[ 2018-04-11 12:51:27 ] INFO binding normalized count CVs...
[ 2018-04-11 12:51:28 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:51:32 ] INFO binding normalized mean counts...
[ 2018-04-11 12:51:32 ] INFO binding normalized median counts...
[ 2018-04-11 12:51:33 ] INFO binding normalized count sds...
[ 2018-04-11 12:51:34 ] INFO binding normalized count MADs...
[ 2018-04-11 12:51:37 ] INFO binding normalized count CVs...
[ 2018-04-11 12:51:38 ] INFO binding normalized counts RCVs...
[ 2018-04-11 12:51:42 ] INFO binding all normalized counts for Prol...
[ 2018-04-11 12:51:42 ] INFO binding all normalized counts for D8plus...
[ 2018-04-11 12:51:42 ] INFO binding filtering flags...
[ 2018-04-11 12:51:42 ] INFO Writing output...
[ 2018-04-11 12:51:44 ] INFO Creating quality control graphs...
[ 2018-04-11 12:51:44 ] INFO Plotting in png format...
[ 2018-04-11 12:51:44 ] INFO Plotting mds...
[ 2018-04-11 12:51:44 ] INFO Plotting biodetection...
[ 2018-04-11 12:51:45 ] INFO Plotting countsbio...
[ 2018-04-11 12:51:47 ] INFO Plotting saturation...
[ 2018-04-11 12:51:53 ] INFO Plotting readnoise...
[ 2018-04-11 12:51:55 ] INFO Plotting correl...
[ 2018-04-11 12:51:55 ] INFO Plotting pairwise...
[ 2018-04-11 12:52:18 ] INFO Plotting boxplot...
[ 2018-04-11 12:52:18 ] INFO Plotting gcbias...
[ 2018-04-11 12:52:19 ] INFO Plotting lengthbias...
[ 2018-04-11 12:52:19 ] INFO Plotting meandiff...
[ 2018-04-11 12:52:20 ] WARN Cannot create a mean-difference plot with one sample per condition! Skipping...
[ 2018-04-11 12:52:20 ] INFO Plotting meanvar...
[ 2018-04-11 12:52:24 ] WARN Cannot create a mean-variance plot with one sample per condition! Skipping...
[ 2018-04-11 12:52:24 ] INFO Plotting boxplot...
[ 2018-04-11 12:52:25 ] INFO Plotting gcbias...
[ 2018-04-11 12:52:25 ] INFO Plotting lengthbias...
[ 2018-04-11 12:52:26 ] INFO Plotting meandiff...
[ 2018-04-11 12:52:27 ] WARN Cannot create a mean-difference plot with one sample per condition! Skipping...
[ 2018-04-11 12:52:27 ] INFO Plotting meanvar...
[ 2018-04-11 12:52:32 ] WARN Cannot create a mean-variance plot with one sample per condition! Skipping...
[ 2018-04-11 12:52:32 ] INFO Plotting biodist...
[ 2018-04-11 12:52:32 ] INFO Contrast: Prol_vs_D2plus
[ 2018-04-11 12:52:32 ] INFO Contrast: Prol_vs_D4plus
[ 2018-04-11 12:52:32 ] INFO Contrast: Prol_vs_D8minus
[ 2018-04-11 12:52:32 ] INFO Contrast: Prol_vs_D8plus
[ 2018-04-11 12:52:33 ] INFO Plotting volcano...
[ 2018-04-11 12:52:33 ] INFO Contrast: Prol_vs_D2plus
[ 2018-04-11 12:52:33 ] INFO Contrast: Prol_vs_D4plus
[ 2018-04-11 12:52:34 ] INFO Contrast: Prol_vs_D8minus
[ 2018-04-11 12:52:34 ] INFO Contrast: Prol_vs_D8plus
[ 2018-04-11 12:52:34 ] INFO Plotting deheatmap...
[ 2018-04-11 12:52:34 ] INFO Contrast: Prol_vs_D2plus
[ 2018-04-11 12:52:57 ] INFO Contrast: Prol_vs_D4plus
[ 2018-04-11 12:53:19 ] INFO Contrast: Prol_vs_D8minus
[ 2018-04-11 12:53:41 ] INFO Contrast: Prol_vs_D8plus
[ 2018-04-11 12:54:02 ] INFO Plotting filtered...
[ 2018-04-11 12:54:02 ] INFO Plotting in pdf format...
[ 2018-04-11 12:54:02 ] INFO Plotting mds...
[ 2018-04-11 12:54:03 ] INFO Plotting biodetection...
[ 2018-04-11 12:54:03 ] INFO Plotting countsbio...
[ 2018-04-11 12:54:04 ] INFO Plotting saturation...
[ 2018-04-11 12:54:09 ] INFO Plotting readnoise...
[ 2018-04-11 12:54:10 ] INFO Plotting correl...
[ 2018-04-11 12:54:10 ] INFO Plotting pairwise...
[ 2018-04-11 12:54:21 ] INFO Plotting boxplot...
[ 2018-04-11 12:54:21 ] INFO Plotting gcbias...
[ 2018-04-11 12:54:22 ] INFO Plotting lengthbias...
[ 2018-04-11 12:54:23 ] INFO Plotting meandiff...
[ 2018-04-11 12:54:24 ] WARN Cannot create a mean-difference plot with one sample per condition! Skipping...
[ 2018-04-11 12:54:24 ] INFO Plotting meanvar...
[ 2018-04-11 12:54:28 ] WARN Cannot create a mean-variance plot with one sample per condition! Skipping...
[ 2018-04-11 12:54:28 ] INFO Plotting boxplot...
[ 2018-04-11 12:54:28 ] INFO Plotting gcbias...
[ 2018-04-11 12:54:29 ] INFO Plotting lengthbias...
[ 2018-04-11 12:54:30 ] INFO Plotting meandiff...
[ 2018-04-11 12:54:31 ] WARN Cannot create a mean-difference plot with one sample per condition! Skipping...
[ 2018-04-11 12:54:31 ] INFO Plotting meanvar...
[ 2018-04-11 12:54:36 ] WARN Cannot create a mean-variance plot with one sample per condition! Skipping...
[ 2018-04-11 12:54:36 ] INFO Plotting biodist...
[ 2018-04-11 12:54:36 ] INFO Contrast: Prol_vs_D2plus
[ 2018-04-11 12:54:36 ] INFO Contrast: Prol_vs_D4plus
[ 2018-04-11 12:54:36 ] INFO Contrast: Prol_vs_D8minus
[ 2018-04-11 12:54:37 ] INFO Contrast: Prol_vs_D8plus
[ 2018-04-11 12:54:37 ] INFO Plotting volcano...
[ 2018-04-11 12:54:37 ] INFO Contrast: Prol_vs_D2plus
[ 2018-04-11 12:54:37 ] INFO Contrast: Prol_vs_D4plus
[ 2018-04-11 12:54:38 ] INFO Contrast: Prol_vs_D8minus
[ 2018-04-11 12:54:38 ] INFO Contrast: Prol_vs_D8plus
[ 2018-04-11 12:54:39 ] INFO Plotting deheatmap...
[ 2018-04-11 12:54:39 ] INFO Contrast: Prol_vs_D2plus
[ 2018-04-11 12:55:00 ] INFO Contrast: Prol_vs_D4plus
[ 2018-04-11 12:55:21 ] INFO Contrast: Prol_vs_D8minus
[ 2018-04-11 12:55:43 ] INFO Contrast: Prol_vs_D8plus
[ 2018-04-11 12:56:05 ] INFO Plotting filtered...
[ 2018-04-11 12:56:05 ] INFO Creating HTML report...
[ 2018-04-11 12:56:05 ] INFO Compressing figures...

Figures

Multidimensional scaling

The Multi-Dimensional Scaling (MDS) plots comprise a means of visualizing the level of similarity of individual cases of a dataset. It is similar to Principal Component Analysis (PCA), but instead of using the covariance matrix to find similarities among cases, MDS uses absolute distance metrics such as the classical Euclidean distance. Because of the relative linear relations among sequencing samples, it provides a more realistic clustering among samples. MDS serves quality control and it can be interpreted as follows: when the distance among samples of the same biological condition in the MDS space is small, this is an indication of high correlation and reproducibility among them. When this distance is larger or heterogeneous (e.g. the 3rd sample of a triplicate set is further from the other 2), this constitutes an indication of low correlation and reproducibility among samples. It can help exclude poor samples from further analysis.

Biotype detection

The biotype detection bar diagrams are a set of quality control charts that show the percentage of each biotype in the genome (i.e. in the whole set of features provided, for example, protein coding genes, non coding RNAs or pseudogenes) in grey bars, which proportion has been detected in a sample before normalization and after a basic filtering by removing features with zero counts in red lined bars, and the percentage of each biotype within the sample in solid red bars. The difference between grey bars and solid red bars is that the grey bars show the percentage of a feature in the genome while the solid red bars show the percentage in the sample. Thus, the solid red bars may be sometimes higher than the grey bars because certain features (e.g. protein coding genes) may be detected within a sample with a higher proportion relatively to their presence in the genome, as compared with other features. For example, while the percentage of protein coding genes in the whole genome is already higher than other biotypes, this percentage is expected to be even higher in an RNA-Seq experiment where one expects protein-coding genes to exhibit greater abundance. The vertical green line separates the most abundant biotypes (on the left-hand side, corresponding to the left axis scale) from the rest (on the right-hand side, corresponding to the right axis scale). Otherwise, the lower abundance biotypes would be indistinguishable. Unexpected outcomes in this quality control chart (e.g. very low detection of protein coding genes) would signify possible low quality of a sample.

Biotype detection counts

The biotype detection counts boxplots are a set of quality control charts that depict both the biological classification for the detected features and the actual distribution of the read counts for each biological type. The boxplot comprises a means of summarizing the read counts distribution of a sample in the form of a bar with extending lines, as commonly used way of graphically presenting groups of numerical data. A boxplot also indicates which observations, if any, might be considered outliers and is able to visually show different types of populations, without making any assumptions of the underlying statistical distribution. The spacing between the different parts of the box help indicate variance, skewness and identify outliers. The thick bar inside the colored box is the median of the observations while the box extends over the Interquartile Range of the observations. The whiskers extend up (down) to +/-1.5xIQR. Unexpected outcomes (e.g. protein coding read count distribution similar to pseudogene read count distribution) indicates poor sample quality.

Read and biotype saturation

The read and biotype saturation plots are a set of quality control charts that depict the read count saturation levels at several sequencing depths. Thus, they comprise a means of assessing whether the sequencing depth of an RNA-Seq experiment is sufficient in order to detect the biological features under investigation. These quality control charts are separated in two subgroups: the first subgroup (read saturation per biotype for all samples) is a set of plots, one for each biological feature (e.g. protein coding, pseudogene, lincRNA, etc.), that depict the number of detected features in different sequencing depths and for all samples in the same plot. The second subgroup (read saturation per sample for all biotypes) is a set of plots similar to the above, but with, there is one pair of plots with two panels for each sample, presenting all biological features. The left panel depicts the saturation levels for the less abundatnt features, while the right panel, the saturation for the more abundant features, as placing them all together would make the less abundant features indistinguishable. All the saturation plots should be interpreted as follows: if the read counts for a biotype tend to be saturated, the respective curve should tend to reach a plateau at higher depths. Otherwise, more sequencing is needed for the specific biotype.

Read saturation per biotype for all samples

Read saturation per sample for all biotypes

RNA-Seq reads noise

The read noise plots depict the percentage of biological features detected when subsampling the total number of reads. Very steep curves in read noise plots indicate that although the sequencing depth reaches its maximum, a relatively small percentage of total features is detected, indicating that the level of background noise is relatively high. Less steep RNA composition curves, indicate less noise. When a sample's curve deviate from the rest, it could indicate lower or higher quality, depending on the curves of the rest of the samples.

Correlation plots

The sample correlation plots depict the accordance among the RNA-Seq samples, as this is manifested through the read counts table used with the metaseqr pipeline, with two representations that both use the correlation matrix (a matrix which depicts all the pairwise correlations between each pair of samples) of the read counts matrix. The first is a correlation clustered heatmap which depicts the correlations among samples as color-scaled image and the hierarchical clustering tree depicts the grouping of the samples according to their correlation. Samples from the same group that are not clustered together provides an indication that there might be a quality problem with the dataset. The second is a 'correlogram' plot, where again the samples are hierarchically clustered and grouped but this time correlations are presented as ellipses inside each cell. Each cell represents a pairwise comparison and each correlation coefficient is represented by an ellipse whose 'diameter', direction and color depict the accordance for that pair of samples. Highly correlated samples are depicted as ellipses with narrow diameter, while poorly correlated samples are depicted as ellipses with wide diameters. Also, highly correlated samples are depicted as ellipses with a left-to-right upwards direction while poorly correlated samples are depicted as ellipses with a right-to-left upwards direction.

Correlation heatmap

Data correlogram

Pairwise scatterplots

The pairwise comparison plots are split in three parts: the upper diagonal consists of simple scatterplots for all pairwise sample comparisons, together with their Pearson correlation coefficient. It is a simple measure of between sample correlation using all the available data points instead of only the correlation matrix. The lower diagonal consists of mean-difference plots for all pairwise sample comparisons. A mean-difference plot (or a Bland-Altman plots) is a method of data plotting used in analyzing the agreement between two different assays/variables. In this graphical method the differences (or alternatively the ratios) between the two variables are plotted against the averages of the two. Such a plot is useful, for example, for analyzing data with strong correlation between x and y axes, when the (x,y) dots on the plot are close to the diagonal x=y. In this case, the value of the transformed variable X is about the same as x and y and the variable Y shows the difference between x and y. In both represantations, irregular shapes of the red smoother lines are an indication of poor correlation between samples or of other systematic bias sources, which is usually corrected through data normalization.

Boxplots

The boxplot comprises a means of summarizing the read counts distribution of a sample in the form of a bar with extending lines, as a commonly used way of graphically presenting groups of numerical data. A boxplot also indicates which observations, if any, might be considered outliers and is able to visually show different types of populations, without making any assumptions about the underlying statistical distribution. The spacings between the different parts of the box help indicate variance, skewness and identify outliers. The thick bar inside the colored box is the median of the observations while the box extends over the Interquartile Range of the observations. The whiskers extend up (down) to +/-1.5xIQR. Boxplots at similar levels indicate good quality of the normalization. If boxplots remain at different levels after normalization, maybe another normalization algorithm may have to be examined. The un-normalized boxplots show the need for data normalization in order for the data from different samples to follow the same underlying distribution and statistical testing becoming possible.

Boxplot of un-normalized data

Boxplot of normalized data

GC content bias

The GC-content bias plot is a quality control chart that shows the possible dependence of the read counts (in log2 scale) under a gene to the GC content percentage of that gene. In order for the statistical tests to be able to detect statistical significance which occurs due to real biological effects and not by other systematic biases present in the data (e.g. a possible GC-content bias), the latter should be accounted for by the applied normalization algorithm. Although the tests are performed for each gene across biological conditions one could assume that the GC content does not represent a bias, as it is the same for the tested gene across samples and conditions. However, Risso et al. (2011) showed that the GC-content could have an impact in the statistical testing procedure. The GC-content bias plot depicts the dependence of the read counts to the GC content before and after normalization. The smoothing lines for each sample, should be as 'straight' as possible after normalization. In addition, if the smoothing lines differ significantly between biological conditions, this would constitute a possible quality warning.

GC content bias un-normalized

GC content bias normalized

Gene/transcript length bias

The gene/transcript length bias plot is a quality control chart that shows the possible dependence of the read counts (in log2 scale) under a gene to the length that gene (whole gene or sum of exons depending on the analysis). In order for the statistical tests to be able to detect statistical significance which occurs due to real biological effects and not by other systematic biases present in the data (e.g. a possible length bias), the latter should be accounted for by the applied normalization algorithm. Although the tests are performed for each gene across bioogical conditions, one could assume that the gene length does not represent a bias as it's the same for the tested gene across samples and conditions. However, it has been shown in several studies that the gene length could have an impact on the statistical testing procedure. The length bias plot depicts the dependence of the read counts to the gene/transcript length before and after normalization. The smoothing lines for each sample, should be as 'straight' as possible after normalization. In addition, if the smoothing lines differ significantly among biological conditions, this would constitute a possible quality warning.

Gene/transcript length bias un-normalized

Gene/transcript length bias normalized

Mean-difference

A mean-difference plot (or a Bland-Altman plot) is a method of data plotting used in analyzing the agreement between two different assays/variables. In this graphical method the differences (or alternatively the ratios) between the two variables are plotted against the averages of the two. Such a plot is useful, for example, for analyzing data with strong correlation between x and y axes, when the (x,y) dots on the plot are close to the diagonal x=y. In this case, the value of the transformed variable X is about the same as x and y and the variable Y shows the difference between x and y. When the data cloud in a mean difference plot is centered around the horizontal zero line, this is an indication of good data quality and good normalization results. On the other hand, when the data cloud deviates from the center line or has a 'banana' shape, this constitutes an indication of systematic biases present in the data and that either the chosen normalization algorithm has not worked well, or that data are not normalized. The smoothing curve that traverses the data (red curve) summarizes the above trends.

Mean-difference plots for the replicates of Prol

Mean-difference plots for the replicates of D4plus

Mean-difference plots for the replicates of D8minus

Mean-difference plots for the replicates of D8plus

Mean-variance

The mean-variance plot comprises a graphical means of displaying a possible relationship between the means of gene expression (counts) values and their variances across replicates of the same biological condition. Thus data can be inspected for possible overdispersion (greater variability in a dataset than would be expected based on a given simple statistical model). In such plots for RNA-Seq data, overdispersion is usually manifested as increasing variance with increasing gene expression (counts) and it is summarized through a smoothing curve (red curve). The following is taken from the EDASeq package vignette: '...although the Poisson distribution is a natural and simple way to model count data, it has the limitation of assuming equality of the mean and variance. For this reason, the negative binomial distribution has been proposed as an alternative when the data show over-dispersion...' If overdispersion is not present, the data cloud is expected to be evenly scattered around the smoothing curve.

Mean-variance plots for the replicates of Prol

Mean-variance plots for the replicates of D4plus

Mean-variance plots for the replicates of D8minus

Mean-variance plots for the replicates of D8plus

Chromosome and biotype distribution of filtered genes

The chromosome and biotype distribution of filtered genes is a quality control chart with two rows and four panels: on the left panel of the first row, the bar chart depicts the numbers of filtered genes per chromosome (actual numbers shown above the bars). On the right panel of the first row, the bar chart depicts the numbers of filtered genes per biotype (actual numbers shown above the bars). On the left panel of the second row, the bar chart depicts the fraction of the filtered genes to the total genes per chromosome (actual percentages shown above the bars). On the right panel of the second row, the bar chart depicts the fraction of the filtered genes to the total genes per biotype (actual percentages shown above the bars). This plot should indicate possible quality problems when for example the filtered genes for a specific chromosome (or the fraction) is extremely higher than the rest. Generally, the fractions per chromosome should be uniform and the fractions per biotype should be proportional to the biotype fraction relative to the genome.

Volcano plots

A volcano plot is a scatterplot that is often used when analyzing high-throughput -omics data (e.g. microarray data, RNA-Seq data) to give an overview of interesting genes. The log2 fold change is plotted on the x-axis and the negative log10 p-value is plotted on the y-axis. A volcano plot combines the results of a statistical test (aka, p-values) with the magnitude of the change enabling quick visual identification of those genes that display large-magnitude changes that are also statistically significant. The horizontal dashed line sets the threshold for statistical significance, while the vertical dashed lines set the thresholds for biological significance. It should be noted that the volcano plots become harder to interpret when using more than one statistical algorithm and performing meta-analysis. This happens because the genes that have stronger evidence of being differentially expressed obtain lower p-values while the rest either remain at similar levels or obtain higher p-values. The result is a 'warped' volcano plot, with two main data clouds: one in the upper part of the plot, and one in the lower part of the plot. You can always zoom in when using interacting mode (the default).

Volcano plot for the contrast Prol_vs_D2plus

Volcano plot for the contrast Prol_vs_D4plus

Volcano plot for the contrast Prol_vs_D8minus

Volcano plot for the contrast Prol_vs_D8plus

DEG heatmaps

The Differentially Expressed Genes (DEGs) heatmaps depict how well samples from different conditions cluster together according to their expression values after normalization and statistical testing, for each requested statistical contrast. If samples from the same biological condition do not cluster together, this would constitute a warning sign regarding the quality of the samples. In addition, DEG heatmaps provide an initial view of possible clusters of co-expressed genes.

DEG heatmap for the contrast Prol_vs_D2plus

DEG heatmap for the contrast Prol_vs_D4plus

DEG heatmap for the contrast Prol_vs_D8minus

DEG heatmap for the contrast Prol_vs_D8plus

Chromosome and biotype distributions of DEGs

The chromosome and biotype distributions bar diagram for Differentially Expressed Genes (DEGs) is split in two panels: i) on the left panel DEGs are distributed per chromosome and the percentage of each chromosome in the genome is presented in grey bars, the percentage of DEGs in each chromosome is presented in red lined bars and the percentage of certain chromosomes in the distribution of DEGs is presented in solid red bars. ii) on the right panel, DEGs are distributed per biotype and the percentage of each biotype in the genome (i.e. in the whole set of features provided, for example, protein coding genes, non coding RNAs or pseudogenes) is presented in grey bars, the percentage of DEGs in each biotype is presented in blue lined bars and the percentage of each biotype in DEGs is presented in solid blue lines. The vertical green line separates the most abundant biotypes (on the left-hand side, corresponding to the left axis scale), from the rest (on the right-hand side, corresponding to the right axis scale). Otherwise, the lower abundance, biotypes would be indistinguishable.

Biotype distribution in DEG for the contrast Prol_vs_D2plus

Biotype distribution in DEG for the contrast Prol_vs_D4plus

Biotype distribution in DEG for the contrast Prol_vs_D8minus

Biotype distribution in DEG for the contrast Prol_vs_D8plus

Get all the figures in png, pdf format.

Results

DEG table for the contrast Prol_vs_D2plus

The following table presents the top 10% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Prol_vs_D2plus. The fields of the table correspond to the requested features to be exported. The table can be searched using the search field on the top right.

chromosome	start	end	gene_id	gc_content	strand	gene_name	biotype	p-value_edger	FDR_edger	log2_normalized_fold_change_Prol_vs_D2plus	log2_normalized_mean_counts_Prol	rpgm_normalized_mean_counts_Prol	log2_normalized_median_counts_Prol	rpgm_normalized_median_counts_Prol	log2_normalized_sd_counts_Prol	rpgm_normalized_sd_counts_Prol	log2_normalized_mad_counts_Prol	rpgm_normalized_mad_counts_Prol	log2_normalized_cv_counts_Prol	rpgm_normalized_cv_counts_Prol	log2_normalized_rcv_counts_Prol	rpgm_normalized_rcv_counts_Prol	log2_normalized_mean_counts_D2plus	rpgm_normalized_mean_counts_D2plus	log2_normalized_median_counts_D2plus	rpgm_normalized_median_counts_D2plus	log2_normalized_sd_counts_D2plus	rpgm_normalized_sd_counts_D2plus	log2_normalized_cv_counts_D2plus	rpgm_normalized_cv_counts_D2plus	log2_normalized_counts_IT3R59_24_Prol	log2_normalized_counts_IT3R63_28_Prol	rpgm_normalized_counts_IT3R59_24_Prol	rpgm_normalized_counts_IT3R63_28_Prol	log2_normalized_counts_IT3R64_29_D2plus	rpgm_normalized_counts_IT3R64_29_D2plus
chr2	72356366	72374991	NM_019885	0.5985	-	CYP26B1	protein_coding	3.82e-29	4.33e-25	9.24139	1.95e+00	1.61e-04	1.95e+00	1.61e-04	5.21e-01	7.59e-05	5.46e-01	7.96e-05	2.67e-01	4.71e-01	2.80e-01	4.94e-01	1.12e+01	1.30e-01	1.12e+01	1.30e-01	NA	NA	NA	NA	2.32e+00	1.58e+00	2.15e-04	1.07e-04	1.12e+01	1.30e-01
chr10	94833646	94837641	NM_000783	0.5168	+	CYP26A1	protein_coding	1.26e-18	7.13e-15	9.38226	5.00e-01	1.25e-04	5.00e-01	1.25e-04	7.07e-01	1.77e-04	7.41e-01	1.86e-04	1.41e+00	1.41e+00	1.48e+00	1.48e+00	9.97e+00	2.50e-01	9.97e+00	2.50e-01	NA	NA	NA	NA	0.00e+00	1.00e+00	0.00e+00	2.50e-04	9.97e+00	2.50e-01
chr1	12627938	12677737	NM_004753	0.5131	-	DHRS3	protein_coding	2.63e-18	9.92e-15	6.75207	3.20e+00	1.71e-04	3.20e+00	1.71e-04	5.50e-01	7.10e-05	5.76e-01	7.44e-05	1.72e-01	4.16e-01	1.80e-01	4.36e-01	1.00e+01	2.05e-02	1.00e+01	2.05e-02	NA	NA	NA	NA	2.81e+00	3.58e+00	1.20e-04	2.21e-04	1.00e+01	2.05e-02
chr14	24708850	24711880	NM_001099274	0.5332	-	TINF2	protein_coding	3.54e-11	1.00e-07	4.13043	6.14e+00	2.34e-02	6.14e+00	2.34e-02	4.31e-01	7.00e-03	4.52e-01	7.34e-03	7.03e-02	2.99e-01	7.37e-02	3.13e-01	1.03e+01	4.16e-01	1.03e+01	4.16e-01	NA	NA	NA	NA	6.44e+00	5.83e+00	2.84e-02	1.85e-02	1.03e+01	4.16e-01
chr4	107842958	107957453	NM_014421	0.3622	-	DKK2	protein_coding	1.10e-09	2.49e-06	4.53478	4.17e+00	1.62e-04	4.17e+00	1.62e-04	8.27e-01	9.26e-05	8.67e-01	9.71e-05	1.98e-01	5.73e-01	2.08e-01	6.01e-01	8.82e+00	3.94e-03	8.82e+00	3.94e-03	NA	NA	NA	NA	3.58e+00	4.75e+00	9.61e-05	2.27e-04	8.82e+00	3.94e-03
chr12	64660762	64784345	NM_001170633	0.4157	-	C12orf56	protein_coding	2.88e-09	5.45e-06	3.91343	5.42e+00	3.48e-04	5.42e+00	3.48e-04	4.72e-01	1.14e-04	4.95e-01	1.20e-04	8.71e-02	3.29e-01	9.13e-02	3.45e-01	9.37e+00	5.36e-03	9.37e+00	5.36e-03	NA	NA	NA	NA	5.75e+00	5.09e+00	4.29e-04	2.67e-04	9.37e+00	5.36e-03
chrX	102317580	102319168	NM_018476	0.5683	-	BEX1	protein_coding	1.06e-08	1.71e-05	3.48852	1.04e+01	8.60e-01	1.04e+01	8.60e-01	1.81e-01	1.08e-01	1.90e-01	1.13e-01	1.74e-02	1.25e-01	1.82e-02	1.31e-01	1.39e+01	9.65e+00	1.39e+01	9.65e+00	NA	NA	NA	NA	1.05e+01	1.03e+01	9.36e-01	7.83e-01	1.39e+01	9.65e+00
chr6	149639435	149732749	NM_015093	0.3640	+	TAB2	protein_coding	1.82e-08	2.58e-05	3.57204	8.58e+00	4.20e-03	8.58e+00	4.20e-03	4.90e-01	1.40e-03	5.14e-01	1.47e-03	5.71e-02	3.34e-01	5.99e-02	3.50e-01	1.22e+01	5.00e-02	1.22e+01	5.00e-02	NA	NA	NA	NA	8.92e+00	8.23e+00	5.19e-03	3.20e-03	1.22e+01	5.00e-02
chr5	110831731	110848295	NM_139164	0.3617	-	STARD4	protein_coding	9.83e-08	1.24e-04	3.95777	5.26e+00	2.69e-03	5.26e+00	2.69e-03	1.23e+00	2.09e-03	1.29e+00	2.19e-03	2.33e-01	7.79e-01	2.45e-01	8.16e-01	9.47e+00	4.26e-02	9.47e+00	4.26e-02	NA	NA	NA	NA	6.13e+00	4.39e+00	4.17e-03	1.21e-03	9.47e+00	4.26e-02
chr1	156669399	156675459	NM_001878	0.5516	-	CRABP2	protein_coding	1.51e-07	1.71e-04	4.17821	9.15e+00	9.37e-02	9.15e+00	9.37e-02	1.94e-01	1.26e-02	2.04e-01	1.32e-02	2.12e-02	1.34e-01	2.23e-02	1.41e-01	1.33e+01	1.70e+00	1.33e+01	1.70e+00	NA	NA	NA	NA	9.28e+00	9.01e+00	1.03e-01	8.48e-02	1.33e+01	1.70e+00
chrX	53111541	53117728	NM_022117	0.5250	+	TSPYL2	protein_coding	2.23e-07	2.30e-04	3.47063	5.00e+00	5.50e-03	5.00e+00	5.50e-03	8.64e-01	3.20e-03	9.06e-01	3.35e-03	1.73e-01	5.82e-01	1.81e-01	6.10e-01	8.60e+00	6.26e-02	8.60e+00	6.26e-02	NA	NA	NA	NA	4.39e+00	5.61e+00	3.23e-03	7.76e-03	8.60e+00	6.26e-02
chr11	30431617	30602040	NM_001584	0.3944	-	MPPED2	protein_coding	3.02e-07	2.85e-04	3.03536	6.03e+00	3.78e-04	6.03e+00	3.78e-04	7.79e-02	2.07e-05	8.17e-02	2.17e-05	1.29e-02	5.48e-02	1.35e-02	5.75e-02	9.07e+00	3.15e-03	9.07e+00	3.15e-03	NA	NA	NA	NA	6.09e+00	5.98e+00	3.93e-04	3.64e-04	9.07e+00	3.15e-03
chr12	55038374	55042277	NM_053283	0.4908	-	DCD	protein_coding	4.40e-07	3.84e-04	3.79751	4.37e+00	5.12e-03	4.37e+00	5.12e-03	3.93e-01	1.45e-03	4.12e-01	1.52e-03	9.01e-02	2.83e-01	9.45e-02	2.97e-01	8.19e+00	7.46e-02	8.19e+00	7.46e-02	NA	NA	NA	NA	4.64e+00	4.09e+00	6.15e-03	4.10e-03	8.19e+00	7.46e-02
chr11	111126706	111157129	NM_198498	0.4140	+	C11orf53	protein_coding	5.54e-07	4.49e-04	4.61471	1.00e+00	3.29e-05	1.00e+00	3.29e-05	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.61e+00	1.58e-03	5.61e+00	1.58e-03	NA	NA	NA	NA	1.00e+00	1.00e+00	3.29e-05	3.29e-05	5.61e+00	1.58e-03
chr9	87283372	87641985	NM_006180	0.4094	+	NTRK2	protein_coding	9.21e-07	6.96e-04	3.30666	4.81e+00	7.67e-05	4.81e+00	7.67e-05	3.25e-01	1.77e-05	3.41e-01	1.86e-05	6.75e-02	2.31e-01	7.07e-02	2.43e-01	8.14e+00	7.84e-04	8.14e+00	7.84e-04	NA	NA	NA	NA	4.58e+00	5.04e+00	6.41e-05	8.92e-05	8.14e+00	7.84e-04
chr4	48499379	48782316	NM_015030	0.3694	-	FRYL	protein_coding	1.14e-06	7.22e-04	3.19841	9.73e+00	3.03e-03	9.73e+00	3.03e-03	3.33e-01	6.95e-04	3.50e-01	7.28e-04	3.43e-02	2.29e-01	3.59e-02	2.40e-01	1.29e+01	2.78e-02	1.29e+01	2.78e-02	NA	NA	NA	NA	9.96e+00	9.49e+00	3.52e-03	2.54e-03	1.29e+01	2.78e-02
chr20	31219426	31261743	NM_182584	0.5034	-	C20orf203	lincRNA	1.18e-06	7.22e-04	3.73909	4.06e+00	3.78e-04	4.06e+00	3.78e-04	3.64e-01	1.00e-04	3.81e-01	1.05e-04	8.95e-02	2.65e-01	9.38e-02	2.78e-01	7.83e+00	5.34e-03	7.83e+00	5.34e-03	NA	NA	NA	NA	3.81e+00	4.32e+00	3.07e-04	4.49e-04	7.83e+00	5.34e-03
chr8	29920527	29940724	NM_016127	0.4020	-	SARAF	protein_coding	1.20e-06	7.22e-04	3.06320	8.28e+00	1.58e-02	8.28e+00	1.58e-02	5.19e-01	5.60e-03	5.45e-01	5.87e-03	6.27e-02	3.54e-01	6.58e-02	3.71e-01	1.14e+01	1.33e-01	1.14e+01	1.33e-01	NA	NA	NA	NA	8.65e+00	7.91e+00	1.98e-02	1.19e-02	1.14e+01	1.33e-01
chr16	1560427	1662109	NM_014714	0.5444	-	IFT140	protein_coding	1.21e-06	7.22e-04	3.25078	7.05e+00	1.30e-03	7.05e+00	1.30e-03	1.23e-01	1.11e-04	1.29e-01	1.17e-04	1.74e-02	8.57e-02	1.83e-02	8.99e-02	1.03e+01	1.24e-02	1.03e+01	1.24e-02	NA	NA	NA	NA	6.97e+00	7.14e+00	1.22e-03	1.38e-03	1.03e+01	1.24e-02
chr2	7052406	7058813	NR_033997	0.5117	-	RNF144A-AS1	antisense	2.53e-06	1.43e-03	3.02191	4.61e+00	3.67e-03	4.61e+00	3.67e-03	2.09e-01	5.52e-04	2.19e-01	5.79e-04	4.53e-02	1.50e-01	4.75e-02	1.58e-01	7.64e+00	3.09e-02	7.64e+00	3.09e-02	NA	NA	NA	NA	4.46e+00	4.75e+00	3.28e-03	4.06e-03	7.64e+00	3.09e-02
chr2	202241929	202316319	NM_015049	0.3774	-	TRAK2	protein_coding	2.67e-06	1.44e-03	2.76517	6.85e+00	1.55e-03	6.85e+00	1.55e-03	3.09e-01	3.33e-04	3.24e-01	3.49e-04	4.51e-02	2.14e-01	4.73e-02	2.25e-01	9.63e+00	1.06e-02	9.63e+00	1.06e-02	NA	NA	NA	NA	6.63e+00	7.07e+00	1.32e-03	1.79e-03	9.63e+00	1.06e-02
chr12	132379278	132407707	NM_003565	0.6236	+	ULK1	protein_coding	3.00e-06	1.54e-03	2.96176	8.47e+00	1.29e-02	8.47e+00	1.29e-02	5.69e-01	4.97e-03	5.96e-01	5.22e-03	6.72e-02	3.85e-01	7.04e-02	4.04e-01	1.15e+01	1.01e-01	1.15e+01	1.01e-01	NA	NA	NA	NA	8.07e+00	8.87e+00	9.39e-03	1.64e-02	1.15e+01	1.01e-01
chr11	64532075	64545938	NM_001178030	0.4882	-	SF1	protein_coding	3.12e-06	1.54e-03	2.78151	1.11e+01	1.59e-01	1.11e+01	1.59e-01	2.18e-01	2.40e-02	2.29e-01	2.52e-02	1.97e-02	1.51e-01	2.06e-02	1.58e-01	1.39e+01	1.10e+00	1.39e+01	1.10e+00	NA	NA	NA	NA	1.09e+01	1.13e+01	1.42e-01	1.76e-01	1.39e+01	1.10e+00
chr17	40177593	40190044	NM_001242704	0.5224	-	ZNF385C	processed_transcript	4.45e-06	2.03e-03	3.93860	3.39e+00	7.63e-04	3.39e+00	7.63e-04	9.72e-02	5.68e-05	1.02e-01	5.95e-05	2.87e-02	7.44e-02	3.01e-02	7.80e-02	7.33e+00	1.29e-02	7.33e+00	1.29e-02	NA	NA	NA	NA	3.32e+00	3.46e+00	7.23e-04	8.03e-04	7.33e+00	1.29e-02
chr3	105085556	105295757	NM_001627	0.3532	+	ALCAM	protein_coding	4.47e-06	2.03e-03	3.05753	9.68e+00	3.91e-03	9.68e+00	3.91e-03	8.06e-02	2.19e-04	8.45e-02	2.29e-04	8.32e-03	5.59e-02	8.72e-03	5.86e-02	1.27e+01	3.26e-02	1.27e+01	3.26e-02	NA	NA	NA	NA	9.63e+00	9.74e+00	3.76e-03	4.07e-03	1.27e+01	3.26e-02
chr2	75059781	75120481	NM_000189	0.4771	+	HK2	protein_coding	6.12e-06	2.67e-03	-3.56605	7.56e+00	3.11e-03	7.56e+00	3.11e-03	1.67e-01	3.61e-04	1.75e-01	3.79e-04	2.21e-02	1.16e-01	2.32e-02	1.22e-01	4.00e+00	2.47e-04	4.00e+00	2.47e-04	NA	NA	NA	NA	7.68e+00	7.44e+00	3.36e-03	2.85e-03	4.00e+00	2.47e-04
chr7	120628750	120937498	NM_024913	0.3660	+	CPED1	protein_coding	7.59e-06	3.16e-03	2.69674	5.90e+00	1.91e-04	5.90e+00	1.91e-04	2.39e-01	3.21e-05	2.51e-01	3.36e-05	4.05e-02	1.68e-01	4.25e-02	1.76e-01	8.60e+00	1.26e-03	8.60e+00	1.26e-03	NA	NA	NA	NA	5.73e+00	6.07e+00	1.68e-04	2.14e-04	8.60e+00	1.26e-03
chr11	77850838	77885023	NR_102280	0.4736	+	KCTD21-AS1	antisense	7.81e-06	3.16e-03	3.01381	4.70e+00	7.31e-04	4.70e+00	7.31e-04	7.85e-02	4.14e-05	8.23e-02	4.34e-05	1.67e-02	5.66e-02	1.75e-02	5.93e-02	7.71e+00	6.11e-03	7.71e+00	6.11e-03	NA	NA	NA	NA	4.75e+00	4.64e+00	7.61e-04	7.02e-04	7.71e+00	6.11e-03
chr2	27714749	27718126	NM_022823	0.5802	-	FNDC4	protein_coding	9.94e-06	3.89e-03	2.80075	6.77e+00	3.21e-02	6.77e+00	3.21e-02	2.80e-02	6.28e-04	2.93e-02	6.59e-04	4.13e-03	1.96e-02	4.33e-03	2.05e-02	9.58e+00	2.26e-01	9.58e+00	2.26e-01	NA	NA	NA	NA	6.75e+00	6.79e+00	3.17e-02	3.26e-02	9.58e+00	2.26e-01
chr10	100175954	100206720	NM_000195	0.4973	-	HPS1	protein_coding	1.13e-05	4.26e-03	2.71621	6.61e+00	3.27e-03	6.61e+00	3.27e-03	5.67e-01	1.26e-03	5.94e-01	1.33e-03	8.58e-02	3.87e-01	8.99e-02	4.06e-01	9.38e+00	2.16e-02	9.38e+00	2.16e-02	NA	NA	NA	NA	6.21e+00	7.01e+00	2.37e-03	4.16e-03	9.38e+00	2.16e-02
chr5	59783758	59822245	NR_028509	0.3980	+	PART1	lincRNA	1.24e-05	4.54e-03	4.49185	1.00e+00	2.60e-05	1.00e+00	2.60e-05	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.49e+00	1.14e-03	5.49e+00	1.14e-03	NA	NA	NA	NA	1.00e+00	1.00e+00	2.60e-05	2.60e-05	5.49e+00	1.14e-03
chr22	50312277	50321188	NM_001135101	0.5867	+	CRELD2	protein_coding	1.29e-05	4.58e-03	2.85783	7.34e+00	1.81e-02	7.34e+00	1.81e-02	9.42e-02	1.19e-03	9.88e-02	1.25e-03	1.28e-02	6.57e-02	1.35e-02	6.89e-02	1.02e+01	1.32e-01	1.02e+01	1.32e-01	NA	NA	NA	NA	7.41e+00	7.28e+00	1.90e-02	1.73e-02	1.02e+01	1.32e-01
chr16	57279037	57287545	NM_012106	0.4536	+	ARL2BP	protein_coding	1.35e-05	4.63e-03	2.59516	6.14e+00	8.17e-03	6.14e+00	8.17e-03	1.30e-01	7.48e-04	1.37e-01	7.84e-04	2.13e-02	9.16e-02	2.23e-02	9.60e-02	8.73e+00	5.00e-02	8.73e+00	5.00e-02	NA	NA	NA	NA	6.23e+00	6.04e+00	8.70e-03	7.64e-03	8.73e+00	5.00e-02
chr1	229728865	229761794	NM_014409	0.4191	-	TAF5L	protein_coding	1.60e-05	5.34e-03	2.59904	6.07e+00	2.03e-03	6.07e+00	2.03e-03	3.33e-01	4.72e-04	3.49e-01	4.95e-04	5.49e-02	2.32e-01	5.75e-02	2.43e-01	8.69e+00	1.25e-02	8.69e+00	1.25e-02	NA	NA	NA	NA	5.83e+00	6.30e+00	1.70e-03	2.37e-03	8.69e+00	1.25e-02
chr15	74466904	74469212	NM_201526	0.6072	+	ISLR	protein_coding	1.70e-05	5.51e-03	4.58496	2.16e+00	1.52e-03	2.16e+00	1.52e-03	2.28e-01	3.06e-04	2.39e-01	3.21e-04	1.05e-01	2.02e-01	1.10e-01	2.12e-01	6.75e+00	4.64e-02	6.75e+00	4.64e-02	NA	NA	NA	NA	2.00e+00	2.32e+00	1.30e-03	1.73e-03	6.75e+00	4.64e-02
chr19	1107632	1174282	NM_014963	0.6318	-	SBNO2	protein_coding	2.12e-05	6.68e-03	2.58646	7.30e+00	2.39e-03	7.30e+00	2.39e-03	4.19e-01	6.90e-04	4.39e-01	7.23e-04	5.74e-02	2.88e-01	6.02e-02	3.02e-01	9.91e+00	1.44e-02	9.91e+00	1.44e-02	NA	NA	NA	NA	7.59e+00	7.00e+00	2.88e-03	1.91e-03	9.91e+00	1.44e-02
chr3	25469753	25639422	NM_000965	0.4175	+	RARB	protein_coding	2.24e-05	6.86e-03	3.43296	4.91e+00	1.71e-04	4.91e+00	1.71e-04	6.80e-02	8.34e-06	7.13e-02	8.74e-06	1.39e-02	4.88e-02	1.45e-02	5.11e-02	8.34e+00	1.90e-03	8.34e+00	1.90e-03	NA	NA	NA	NA	4.95e+00	4.86e+00	1.77e-04	1.65e-04	8.34e+00	1.90e-03
chr11	83166055	85338314	NM_001142699	0.3701	-	DLG2	protein_coding	2.32e-05	6.92e-03	2.91511	8.73e+00	2.01e-04	8.73e+00	2.01e-04	4.97e-01	6.80e-05	5.21e-01	7.13e-05	5.69e-02	3.39e-01	5.97e-02	3.55e-01	1.17e+01	1.52e-03	1.17e+01	1.52e-03	NA	NA	NA	NA	8.38e+00	9.08e+00	1.53e-04	2.49e-04	1.17e+01	1.52e-03
chr8	22436253	22451810	NM_021630	0.5888	+	PDLIM2	protein_coding	3.08e-05	8.73e-03	-4.54432	6.13e+00	4.44e-03	6.13e+00	4.44e-03	2.91e-02	9.09e-05	3.06e-02	9.53e-05	4.76e-03	2.05e-02	4.99e-03	2.15e-02	1.58e+00	1.29e-04	1.58e+00	1.29e-04	NA	NA	NA	NA	6.11e+00	6.15e+00	4.37e-03	4.50e-03	1.58e+00	1.29e-04
chr11	64844926	64851615	NM_080668	0.5202	-	CDCA5	protein_coding	3.08e-05	8.73e-03	2.77409	6.96e+00	1.91e-02	6.96e+00	1.91e-02	4.94e-01	6.45e-03	5.18e-01	6.76e-03	7.09e-02	3.38e-01	7.43e-02	3.55e-01	9.78e+00	1.31e-01	9.78e+00	1.31e-01	NA	NA	NA	NA	6.61e+00	7.31e+00	1.45e-02	2.36e-02	9.78e+00	1.31e-01
chr5	45255051	45696220	NM_021072	0.3473	-	HCN1	protein_coding	4.50e-05	1.24e-02	2.69426	6.13e+00	1.61e-04	6.13e+00	1.61e-04	4.61e-01	5.13e-05	4.83e-01	5.38e-05	7.52e-02	3.19e-01	7.88e-02	3.34e-01	8.86e+00	1.05e-03	8.86e+00	1.05e-03	NA	NA	NA	NA	6.46e+00	5.81e+00	1.97e-04	1.25e-04	8.86e+00	1.05e-03
chr18	61637262	61656608	NM_002640	0.4249	+	SERPINB8	protein_coding	4.64e-05	1.25e-02	4.12653	2.35e+00	3.36e-04	2.35e+00	3.36e-04	1.91e+00	4.02e-04	2.00e+00	4.21e-04	8.12e-01	1.20e+00	8.52e-01	1.25e+00	7.03e+00	6.72e-03	7.03e+00	6.72e-03	NA	NA	NA	NA	1.00e+00	3.70e+00	5.17e-05	6.20e-04	7.03e+00	6.72e-03
chr12	65563350	65642141	NM_014319	0.3553	+	LEMD3	protein_coding	4.86e-05	1.27e-02	2.49508	6.18e+00	9.33e-04	6.18e+00	9.33e-04	4.59e-01	2.96e-04	4.82e-01	3.10e-04	7.43e-02	3.17e-01	7.79e-02	3.33e-01	8.71e+00	5.32e-03	8.71e+00	5.32e-03	NA	NA	NA	NA	5.86e+00	6.51e+00	7.23e-04	1.14e-03	8.71e+00	5.32e-03
chr12	57998404	58003587	NM_178502	0.5561	+	DTX3	protein_coding	4.92e-05	1.27e-02	2.39056	9.03e+00	1.02e-01	9.03e+00	1.02e-01	2.19e-01	1.54e-02	2.30e-01	1.62e-02	2.43e-02	1.52e-01	2.55e-02	1.59e-01	1.14e+01	5.33e-01	1.14e+01	5.33e-01	NA	NA	NA	NA	8.88e+00	9.19e+00	9.07e-02	1.12e-01	1.14e+01	5.33e-01
chr10	48425778	48439138	NM_004962	0.5292	-	GDF10	protein_coding	5.16e-05	1.30e-02	4.16993	5.00e-01	3.74e-05	5.00e-01	3.74e-05	7.07e-01	5.29e-05	7.41e-01	5.55e-05	1.41e+00	1.41e+00	1.48e+00	1.48e+00	4.75e+00	1.95e-03	4.75e+00	1.95e-03	NA	NA	NA	NA	0.00e+00	1.00e+00	0.00e+00	7.49e-05	4.75e+00	1.95e-03
chr16	21689834	21772050	NM_144672	0.4495	+	OTOA	protein_coding	6.68e-05	1.65e-02	3.19265	3.80e+00	1.58e-04	3.80e+00	1.58e-04	1.46e-01	1.72e-05	1.53e-01	1.80e-05	3.84e-02	1.09e-01	4.02e-02	1.14e-01	7.00e+00	1.54e-03	7.00e+00	1.54e-03	NA	NA	NA	NA	3.91e+00	3.70e+00	1.70e-04	1.46e-04	7.00e+00	1.54e-03
chr7	41724711	41742706	NM_002192	0.4168	-	INHBA	protein_coding	7.08e-05	1.71e-02	2.66458	4.45e+00	1.25e-03	4.45e+00	1.25e-03	7.73e-01	6.68e-04	8.10e-01	7.00e-04	1.74e-01	5.34e-01	1.82e-01	5.60e-01	7.22e+00	8.22e-03	7.22e+00	8.22e-03	NA	NA	NA	NA	5.00e+00	3.91e+00	1.72e-03	7.78e-04	7.22e+00	8.22e-03
chr3	158787040	159615155	NM_001197113	0.3906	+	IQCJ-SCHIP1	protein_coding	8.47e-05	2.00e-02	2.45051	9.40e+00	8.18e-04	9.40e+00	8.18e-04	1.36e-01	7.68e-05	1.42e-01	8.06e-05	1.44e-02	9.40e-02	1.51e-02	9.85e-02	1.19e+01	4.47e-03	1.19e+01	4.47e-03	NA	NA	NA	NA	9.50e+00	9.31e+00	8.72e-04	7.63e-04	1.19e+01	4.47e-03
chr18	70203914	70211723	NM_182511	0.4942	-	CBLN2	protein_coding	8.69e-05	2.01e-02	2.86555	4.82e+00	3.65e-03	4.82e+00	3.65e-03	6.05e-01	1.54e-03	6.34e-01	1.61e-03	1.26e-01	4.22e-01	1.32e-01	4.42e-01	7.75e+00	2.74e-02	7.75e+00	2.74e-02	NA	NA	NA	NA	4.39e+00	5.25e+00	2.56e-03	4.74e-03	7.75e+00	2.74e-02
chr8	2792874	4852328	NM_033225	0.3847	-	CSMD1	protein_coding	1.17e-04	2.65e-02	2.83162	7.29e+00	7.72e-05	7.29e+00	7.72e-05	4.54e-01	2.40e-05	4.76e-01	2.52e-05	6.23e-02	3.11e-01	6.53e-02	3.26e-01	1.02e+01	5.53e-04	1.02e+01	5.53e-04	NA	NA	NA	NA	6.97e+00	7.61e+00	6.02e-05	9.42e-05	1.02e+01	5.53e-04
chr18	9546788	9614605	NM_001042388	0.3877	-	PPP4R1	protein_coding	1.25e-04	2.78e-02	2.24286	7.49e+00	2.64e-03	7.49e+00	2.64e-03	1.59e-01	2.92e-04	1.67e-01	3.06e-04	2.12e-02	1.11e-01	2.23e-02	1.16e-01	9.73e+00	1.25e-02	9.73e+00	1.25e-02	NA	NA	NA	NA	7.38e+00	7.60e+00	2.43e-03	2.85e-03	9.73e+00	1.25e-02
chr19	47123724	47128354	NM_000960	0.5902	-	PTGIR	protein_coding	1.28e-04	2.79e-02	2.80735	3.79e+00	3.24e-03	3.79e+00	3.24e-03	1.12e+00	2.44e-03	1.17e+00	2.56e-03	2.96e-01	7.54e-01	3.10e-01	7.91e-01	6.81e+00	2.40e-02	6.81e+00	2.40e-02	NA	NA	NA	NA	4.58e+00	3.00e+00	4.97e-03	1.51e-03	6.81e+00	2.40e-02
chr9	114803060	114937577	NM_022486	0.4275	-	SUSD1	protein_coding	1.35e-04	2.88e-02	2.31194	5.83e+00	4.24e-04	5.83e+00	4.24e-04	4.28e-01	1.26e-04	4.49e-01	1.32e-04	7.35e-02	2.98e-01	7.71e-02	3.12e-01	8.17e+00	2.13e-03	8.17e+00	2.13e-03	NA	NA	NA	NA	5.52e+00	6.13e+00	3.35e-04	5.13e-04	8.17e+00	2.13e-03
chr10	103892750	103910090	NM_015062	0.5198	+	PPRC1	protein_coding	1.51e-04	3.18e-02	2.62312	6.63e+00	5.68e-03	6.63e+00	5.68e-03	1.13e-01	4.49e-04	1.18e-01	4.70e-04	1.70e-02	7.90e-02	1.78e-02	8.28e-02	9.26e+00	3.53e-02	9.26e+00	3.53e-02	NA	NA	NA	NA	6.55e+00	6.71e+00	5.36e-03	6.00e-03	9.26e+00	3.53e-02
chr14	96343108	96391908	NR_038861	0.4713	+	TUNAR	lincRNA	1.87e-04	3.85e-02	-4.71425	5.68e+00	1.06e-03	5.68e+00	1.06e-03	4.14e-01	3.04e-04	4.34e-01	3.19e-04	7.28e-02	2.88e-01	7.63e-02	3.02e-01	1.00e+00	2.05e-05	1.00e+00	2.05e-05	NA	NA	NA	NA	5.98e+00	5.39e+00	1.27e-03	8.40e-04	1.00e+00	2.05e-05
chr12	107385142	107487635	NM_004075	0.3763	-	CRY1	protein_coding	1.91e-04	3.85e-02	2.16559	6.76e+00	1.07e-03	6.76e+00	1.07e-03	4.29e-01	3.17e-04	4.50e-01	3.33e-04	6.34e-02	2.96e-01	6.65e-02	3.10e-01	8.96e+00	4.85e-03	8.96e+00	4.85e-03	NA	NA	NA	NA	6.46e+00	7.07e+00	8.49e-04	1.30e-03	8.96e+00	4.85e-03
chr1	192778168	192781407	NM_002923	0.4083	+	RGS2	protein_coding	1.95e-04	3.85e-02	2.55548	7.53e+00	5.82e-02	7.53e+00	5.82e-02	4.88e-01	1.94e-02	5.12e-01	2.04e-02	6.49e-02	3.34e-01	6.80e-02	3.50e-01	1.01e+01	3.44e-01	1.01e+01	3.44e-01	NA	NA	NA	NA	7.87e+00	7.18e+00	7.19e-02	4.45e-02	1.01e+01	3.44e-01
chr16	12995476	13334273	NM_001145204	0.4322	+	SHISA9	protein_coding	1.97e-04	3.85e-02	2.39296	5.71e+00	1.55e-04	5.71e+00	1.55e-04	4.06e-01	4.38e-05	4.25e-01	4.59e-05	7.10e-02	2.83e-01	7.44e-02	2.97e-01	8.13e+00	8.26e-04	8.13e+00	8.26e-04	NA	NA	NA	NA	5.43e+00	6.00e+00	1.24e-04	1.86e-04	8.13e+00	8.26e-04
chr11	34172533	34379555	NM_145804	0.4792	-	ABTB2	protein_coding	2.18e-04	4.20e-02	2.90364	5.42e+00	2.10e-04	5.42e+00	2.10e-04	5.89e-01	8.54e-05	6.17e-01	8.95e-05	1.09e-01	4.06e-01	1.14e-01	4.26e-01	8.38e+00	1.60e-03	8.38e+00	1.60e-03	NA	NA	NA	NA	5.00e+00	5.83e+00	1.50e-04	2.71e-04	8.38e+00	1.60e-03
chr5	172741725	172756506	NM_003714	0.5093	-	STC2	protein_coding	2.22e-04	4.20e-02	-5.28309	7.79e+00	2.10e-02	7.79e+00	2.10e-02	1.79e+00	2.10e-02	1.87e+00	2.20e-02	2.30e-01	1.00e+00	2.41e-01	1.05e+00	3.00e+00	4.74e-04	3.00e+00	4.74e-04	NA	NA	NA	NA	6.52e+00	9.05e+00	6.16e-03	3.59e-02	3.00e+00	4.74e-04
chrX	119560002	119603204	NM_001122606	0.3861	-	LAMP2	protein_coding	2.30e-04	4.28e-02	2.22322	7.94e+00	5.72e-03	7.94e+00	5.72e-03	2.56e-01	1.01e-03	2.69e-01	1.06e-03	3.23e-02	1.77e-01	3.38e-02	1.86e-01	1.02e+01	2.68e-02	1.02e+01	2.68e-02	NA	NA	NA	NA	8.12e+00	7.76e+00	6.43e-03	5.00e-03	1.02e+01	2.68e-02
chrX	153626405	153630680	NM_006013	0.5248	+	RPL10	protein_coding	2.47e-04	4.50e-02	2.59460	1.06e+01	3.72e-01	1.06e+01	3.72e-01	2.64e-01	6.78e-02	2.77e-01	7.11e-02	2.49e-02	1.82e-01	2.61e-02	1.91e-01	1.32e+01	2.25e+00	1.32e+01	2.25e+00	NA	NA	NA	NA	1.08e+01	1.04e+01	4.20e-01	3.24e-01	1.32e+01	2.25e+00
chr3	122283184	122294049	NM_138287	0.4422	+	DTX3L	protein_coding	2.54e-04	4.50e-02	2.40651	5.70e+00	4.79e-03	5.70e+00	4.79e-03	3.90e-01	1.30e-03	4.08e-01	1.36e-03	6.83e-02	2.72e-01	7.16e-02	2.85e-01	8.13e+00	2.58e-02	8.13e+00	2.58e-02	NA	NA	NA	NA	5.43e+00	5.98e+00	3.87e-03	5.71e-03	8.13e+00	2.58e-02
chr2	136871918	136875725	NM_003467	0.5200	-	CXCR4	protein_coding	2.54e-04	4.50e-02	-3.08746	9.21e+00	1.56e-01	9.21e+00	1.56e-01	2.31e-01	2.49e-02	2.42e-01	2.61e-02	2.51e-02	1.60e-01	2.63e-02	1.67e-01	6.13e+00	1.81e-02	6.13e+00	1.81e-02	NA	NA	NA	NA	9.37e+00	9.04e+00	1.74e-01	1.38e-01	6.13e+00	1.81e-02
chr10	74033676	74035794	NM_019058	0.5866	+	DDIT4	protein_coding	2.94e-04	5.13e-02	-4.10254	7.52e+00	1.13e-01	7.52e+00	1.13e-01	1.57e+00	1.04e-01	1.65e+00	1.09e-01	2.09e-01	9.18e-01	2.19e-01	9.63e-01	3.81e+00	6.14e-03	3.81e+00	6.14e-03	NA	NA	NA	NA	6.41e+00	8.63e+00	3.97e-02	1.86e-01	3.81e+00	6.14e-03
chr1	67773046	67862583	NM_001559	0.4165	+	IL12RB2	protein_coding	3.39e-04	5.82e-02	4.16993	1.66e+00	2.79e-05	1.66e+00	2.79e-05	9.35e-01	2.37e-05	9.80e-01	2.48e-05	5.63e-01	8.49e-01	5.90e-01	8.90e-01	5.98e+00	6.92e-04	5.98e+00	6.92e-04	NA	NA	NA	NA	2.32e+00	1.00e+00	4.47e-05	1.12e-05	5.98e+00	6.92e-04
chr13	24153485	24243412	NM_018647	0.4018	+	TNFRSF19	protein_coding	3.59e-04	6.07e-02	3.05585	3.14e+00	9.45e-05	3.14e+00	9.45e-05	7.89e-01	5.50e-05	8.27e-01	5.77e-05	2.51e-01	5.82e-01	2.63e-01	6.10e-01	6.30e+00	8.67e-04	6.30e+00	8.67e-04	NA	NA	NA	NA	2.58e+00	3.70e+00	5.56e-05	1.33e-04	6.30e+00	8.67e-04
chr8	42010463	42028701	NM_006803	0.4138	+	AP3M2	protein_coding	3.78e-04	6.30e-02	2.03857	7.67e+00	1.11e-02	7.67e+00	1.11e-02	3.02e-02	2.33e-04	3.16e-02	2.44e-04	3.93e-03	2.10e-02	4.12e-03	2.20e-02	9.70e+00	4.57e-02	9.70e+00	4.57e-02	NA	NA	NA	NA	7.64e+00	7.69e+00	1.09e-02	1.12e-02	9.70e+00	4.57e-02
chr12	110906231	110928192	NM_013300	0.4372	+	FAM216A	protein_coding	4.00e-04	6.57e-02	-2.49185	8.81e+00	2.04e-02	8.81e+00	2.04e-02	1.91e-01	2.70e-03	2.00e-01	2.84e-03	2.17e-02	1.32e-01	2.27e-02	1.39e-01	6.32e+00	3.60e-03	6.32e+00	3.60e-03	NA	NA	NA	NA	8.94e+00	8.67e+00	2.24e-02	1.85e-02	6.32e+00	3.60e-03
chr17	72199794	72206019	NM_001035258	0.4863	+	RPL38	protein_coding	4.77e-04	7.70e-02	2.16389	1.21e+01	6.90e-01	1.21e+01	6.90e-01	1.07e-02	5.11e-03	1.12e-02	5.36e-03	8.85e-04	7.41e-03	9.28e-04	7.76e-03	1.42e+01	3.09e+00	1.42e+01	3.09e+00	NA	NA	NA	NA	1.21e+01	1.21e+01	6.87e-01	6.94e-01	1.42e+01	3.09e+00
chr9	34521039	34523037	NM_198573	0.6288	-	ENHO	protein_coding	4.82e-04	7.70e-02	-3.52356	6.07e+00	3.40e-02	6.07e+00	3.40e-02	4.82e-01	1.13e-02	5.05e-01	1.19e-02	7.94e-02	3.33e-01	8.32e-02	3.49e-01	2.58e+00	2.50e-03	2.58e+00	2.50e-03	NA	NA	NA	NA	6.41e+00	5.73e+00	4.20e-02	2.60e-02	2.58e+00	2.50e-03
chr3	141595433	141645390	NM_001679	0.4034	+	ATP1B3	nonsense_mediated_decay	5.04e-04	7.93e-02	2.31021	9.13e+00	1.21e-02	9.13e+00	1.21e-02	8.02e-01	6.41e-03	8.41e-01	6.72e-03	8.78e-02	5.30e-01	9.21e-02	5.56e-01	1.16e+01	6.01e-02	1.16e+01	6.01e-02	NA	NA	NA	NA	9.70e+00	8.57e+00	1.66e-02	7.57e-03	1.16e+01	6.01e-02
chr8	87586162	87755903	NM_019098	0.3809	-	CNGB3	protein_coding	5.26e-04	8.16e-02	3.23266	2.32e+00	2.36e-05	2.32e+00	2.36e-05	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.55e+00	2.71e-04	5.55e+00	2.71e-04	NA	NA	NA	NA	2.32e+00	2.32e+00	2.36e-05	2.36e-05	5.55e+00	2.71e-04
chr12	49458458	49463808	NM_144593	0.4971	-	RHEBL1	protein_coding	5.37e-04	8.22e-02	-2.60706	8.34e+00	6.13e-02	8.34e+00	6.13e-02	3.38e-01	1.43e-02	3.54e-01	1.50e-02	4.05e-02	2.33e-01	4.25e-02	2.44e-01	5.75e+00	9.91e-03	5.75e+00	9.91e-03	NA	NA	NA	NA	8.58e+00	8.10e+00	7.14e-02	5.12e-02	5.75e+00	9.91e-03
chr12	103351451	103354294	NM_004316	0.5130	+	ASCL1	protein_coding	5.73e-04	8.65e-02	-3.90689	7.52e+00	7.88e-02	7.52e+00	7.88e-02	1.36e+00	6.52e-02	1.42e+00	6.83e-02	1.81e-01	8.27e-01	1.90e-01	8.67e-01	3.91e+00	4.92e-03	3.91e+00	4.92e-03	NA	NA	NA	NA	6.55e+00	8.48e+00	3.27e-02	1.25e-01	3.91e+00	4.92e-03
chr5	33440881	33468196	NM_001258438	0.3836	+	TARS	protein_coding	6.21e-04	9.26e-02	-2.45943	9.09e+00	2.05e-02	9.09e+00	2.05e-02	4.85e-01	6.78e-03	5.09e-01	7.11e-03	5.34e-02	3.31e-01	5.60e-02	3.47e-01	6.67e+00	3.70e-03	6.67e+00	3.70e-03	NA	NA	NA	NA	8.75e+00	9.43e+00	1.57e-02	2.53e-02	6.67e+00	3.70e-03
chr14	105939274	105946507	NM_001270837	0.6953	+	CRIP2	protein_coding	6.44e-04	9.37e-02	2.20246	7.83e+00	3.15e-02	7.83e+00	3.15e-02	2.60e-01	5.67e-03	2.72e-01	5.94e-03	3.32e-02	1.80e-01	3.48e-02	1.89e-01	1.00e+01	1.46e-01	1.00e+01	1.46e-01	NA	NA	NA	NA	7.64e+00	8.01e+00	2.75e-02	3.55e-02	1.00e+01	1.46e-01
chr18	57098170	57364644	NM_133459	0.4278	-	CCBE1	protein_coding	6.45e-04	9.37e-02	2.10639	5.58e+00	1.80e-04	5.58e+00	1.80e-04	4.66e-01	5.84e-05	4.88e-01	6.12e-05	8.35e-02	3.24e-01	8.76e-02	3.40e-01	7.72e+00	7.88e-04	7.72e+00	7.88e-04	NA	NA	NA	NA	5.25e+00	5.91e+00	1.39e-04	2.21e-04	7.72e+00	7.88e-04
chr19	44790500	44809178	NM_004234	0.3832	-	ZNF235	protein_coding	6.54e-04	9.39e-02	2.55706	5.44e+00	2.28e-03	5.44e+00	2.28e-03	7.04e-02	1.14e-04	7.38e-02	1.19e-04	1.29e-02	4.99e-02	1.36e-02	5.23e-02	8.00e+00	1.37e-02	8.00e+00	1.37e-02	NA	NA	NA	NA	5.39e+00	5.49e+00	2.20e-03	2.36e-03	8.00e+00	1.37e-02
chr1	149900542	149908791	NM_001145862	0.5001	-	MTMR11	protein_coding	6.68e-04	9.47e-02	3.72247	2.20e+00	4.85e-04	2.20e+00	4.85e-04	8.64e-01	3.43e-04	9.06e-01	3.59e-04	3.94e-01	7.07e-01	4.13e-01	7.41e-01	6.04e+00	7.88e-03	6.04e+00	7.88e-03	NA	NA	NA	NA	2.81e+00	1.58e+00	7.27e-04	2.42e-04	6.04e+00	7.88e-03
chr1	35734567	35887545	NM_005095	0.3865	+	ZMYM4	protein_coding	7.07e-04	9.89e-02	2.40087	8.51e+00	2.38e-03	8.51e+00	2.38e-03	8.12e-02	1.34e-04	8.51e-02	1.41e-04	9.54e-03	5.64e-02	1.00e-02	5.91e-02	1.09e+01	1.26e-02	1.09e+01	1.26e-02	NA	NA	NA	NA	8.57e+00	8.45e+00	2.47e-03	2.28e-03	1.09e+01	1.26e-02
chr2	201735678	201753849	NM_032472	0.4138	-	PPIL3	protein_coding	7.38e-04	1.02e-01	2.19898	6.73e+00	5.81e-03	6.73e+00	5.81e-03	2.21e-01	8.95e-04	2.32e-01	9.38e-04	3.29e-02	1.54e-01	3.45e-02	1.62e-01	8.93e+00	2.69e-02	8.93e+00	2.69e-02	NA	NA	NA	NA	6.57e+00	6.88e+00	5.17e-03	6.44e-03	8.93e+00	2.69e-02
chr7	151574126	151576308	NR_038926	0.6010	+	PRKAG2-AS1	antisense	8.23e-04	1.12e-01	-2.70966	7.27e+00	7.15e-02	7.27e+00	7.15e-02	3.54e-01	1.75e-02	3.72e-01	1.83e-02	4.87e-02	2.45e-01	5.11e-02	2.57e-01	4.58e+00	1.05e-02	4.58e+00	1.05e-02	NA	NA	NA	NA	7.02e+00	7.52e+00	5.91e-02	8.39e-02	4.58e+00	1.05e-02
chr3	64501330	64673365	NM_182920	0.4003	-	ADAMTS9	protein_coding	8.34e-04	1.13e-01	2.55848	8.72e+00	2.44e-03	8.72e+00	2.44e-03	3.63e-02	6.17e-05	3.81e-02	6.46e-05	4.16e-03	2.52e-02	4.37e-03	2.64e-02	1.13e+01	1.44e-02	1.13e+01	1.44e-02	NA	NA	NA	NA	8.69e+00	8.74e+00	2.40e-03	2.49e-03	1.13e+01	1.44e-02
chr7	36552548	36764154	NM_001177506	0.4156	-	AOAH	protein_coding	8.48e-04	1.13e-01	2.26127	5.06e+00	1.56e-04	5.06e+00	1.56e-04	3.64e-01	4.01e-05	3.81e-01	4.20e-05	7.18e-02	2.57e-01	7.53e-02	2.70e-01	7.35e+00	7.66e-04	7.35e+00	7.66e-04	NA	NA	NA	NA	4.81e+00	5.32e+00	1.28e-04	1.84e-04	7.35e+00	7.66e-04
chr2	74648849	74652882	NM_032118	0.5436	+	WDR54	protein_coding	9.02e-04	1.18e-01	2.16506	8.43e+00	8.57e-02	8.43e+00	8.57e-02	1.39e-01	8.24e-03	1.45e-01	8.64e-03	1.64e-02	9.62e-02	1.72e-02	1.01e-01	1.06e+01	3.85e-01	1.06e+01	3.85e-01	NA	NA	NA	NA	8.53e+00	8.34e+00	9.15e-02	7.98e-02	1.06e+01	3.85e-01
chr2	73300509	73340146	NM_015470	0.5435	-	RAB11FIP5	protein_coding	9.08e-04	1.18e-01	-2.74416	6.61e+00	2.51e-03	6.61e+00	2.51e-03	4.86e-01	8.38e-04	5.10e-01	8.79e-04	7.35e-02	3.34e-01	7.71e-02	3.50e-01	3.91e+00	3.53e-04	3.91e+00	3.53e-04	NA	NA	NA	NA	6.95e+00	6.27e+00	3.10e-03	1.92e-03	3.91e+00	3.53e-04
chr12	39687029	39837192	NM_001173464	0.3622	-	KIF21A	protein_coding	9.21e-04	1.19e-01	2.52739	1.05e+01	9.92e-03	1.05e+01	9.92e-03	3.75e-01	2.55e-03	3.93e-01	2.68e-03	3.57e-02	2.57e-01	3.74e-02	2.70e-01	1.31e+01	5.72e-02	1.31e+01	5.72e-02	NA	NA	NA	NA	1.08e+01	1.03e+01	1.17e-02	8.12e-03	1.31e+01	5.72e-02
chr9	21454266	21559797	NR_027054	0.3760	-	MIR31HG	sense_overlapping	9.50e-04	1.21e-01	3.29956	2.45e+00	5.21e-05	2.45e+00	5.21e-05	1.23e+00	4.69e-05	1.29e+00	4.92e-05	5.01e-01	9.00e-01	5.25e-01	9.43e-01	6.00e+00	5.97e-04	6.00e+00	5.97e-04	NA	NA	NA	NA	1.58e+00	3.32e+00	1.90e-05	8.53e-05	6.00e+00	5.97e-04
chr19	36236477	36238420	NM_172341	0.5000	+	PSENEN	protein_coding	9.82e-04	1.24e-01	2.00286	6.97e+00	6.43e-02	6.97e+00	6.43e-02	1.79e-01	8.01e-03	1.87e-01	8.39e-03	2.56e-02	1.24e-01	2.69e-02	1.30e-01	8.98e+00	2.59e-01	8.98e+00	2.59e-01	NA	NA	NA	NA	7.10e+00	6.85e+00	7.00e-02	5.87e-02	8.98e+00	2.59e-01
chr16	81069457	81080951	NM_015251	0.4462	+	ATMIN	protein_coding	1.02e-03	1.27e-01	1.90215	8.39e+00	2.91e-02	8.39e+00	2.91e-02	9.12e-03	1.85e-04	9.56e-03	1.93e-04	1.09e-03	6.34e-03	1.14e-03	6.65e-03	1.03e+01	1.09e-01	1.03e+01	1.09e-01	NA	NA	NA	NA	8.40e+00	8.38e+00	2.92e-02	2.90e-02	1.03e+01	1.09e-01
chr3	35721278	35835988	NM_001267619	0.3664	+	ARPP21	protein_coding	1.04e-03	1.27e-01	2.89812	2.29e+00	3.92e-05	2.29e+00	3.92e-05	1.00e+00	3.08e-05	1.05e+00	3.23e-05	4.36e-01	7.86e-01	4.58e-01	8.24e-01	5.36e+00	3.49e-04	5.36e+00	3.49e-04	NA	NA	NA	NA	1.58e+00	3.00e+00	1.74e-05	6.10e-05	5.36e+00	3.49e-04

Download the DEG result list for Prol_vs_D2plus.
Download the whole result list for Prol_vs_D2plus.

DEG table for the contrast Prol_vs_D4plus

The following table presents the top 10% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Prol_vs_D4plus. The fields of the table correspond to the requested features to be exported. The table can be searched using the search field on the top right.

chromosome	start	end	gene_id	gc_content	strand	gene_name	biotype	p-value_edger	FDR_edger	log2_normalized_fold_change_Prol_vs_D4plus	log2_normalized_mean_counts_Prol	rpgm_normalized_mean_counts_Prol	log2_normalized_median_counts_Prol	rpgm_normalized_median_counts_Prol	log2_normalized_sd_counts_Prol	rpgm_normalized_sd_counts_Prol	log2_normalized_mad_counts_Prol	rpgm_normalized_mad_counts_Prol	log2_normalized_cv_counts_Prol	rpgm_normalized_cv_counts_Prol	log2_normalized_rcv_counts_Prol	rpgm_normalized_rcv_counts_Prol	log2_normalized_mean_counts_D4plus	rpgm_normalized_mean_counts_D4plus	log2_normalized_median_counts_D4plus	rpgm_normalized_median_counts_D4plus	log2_normalized_sd_counts_D4plus	rpgm_normalized_sd_counts_D4plus	log2_normalized_mad_counts_D4plus	rpgm_normalized_mad_counts_D4plus	log2_normalized_cv_counts_D4plus	rpgm_normalized_cv_counts_D4plus	log2_normalized_rcv_counts_D4plus	rpgm_normalized_rcv_counts_D4plus	log2_normalized_counts_IT3R59_24_Prol	log2_normalized_counts_IT3R63_28_Prol	rpgm_normalized_counts_IT3R59_24_Prol	rpgm_normalized_counts_IT3R63_28_Prol	log2_normalized_counts_IT3R60_25_D4plus	log2_normalized_counts_IT3R65_30_D4plus	rpgm_normalized_counts_IT3R60_25_D4plus	rpgm_normalized_counts_IT3R65_30_D4plus
chr2	72356366	72374991	NM_019885	0.5985	-	CYP26B1	protein_coding	5.12e-33	5.80e-29	9.82615	1.95e+00	1.61e-04	1.95e+00	1.61e-04	5.21e-01	7.59e-05	5.46e-01	7.96e-05	2.67e-01	4.71e-01	2.80e-01	4.94e-01	1.18e+01	1.95e-01	1.18e+01	1.95e-01	2.02e-01	2.73e-02	2.12e-01	2.86e-02	1.71e-02	1.40e-01	1.80e-02	1.47e-01	2.32e+00	1.58e+00	2.15e-04	1.07e-04	1.20e+01	1.17e+01	2.14e-01	1.76e-01
chr10	94833646	94837641	NM_000783	0.5168	+	CYP26A1	protein_coding	1.66e-21	9.41e-18	10.16281	5.00e-01	1.25e-04	5.00e-01	1.25e-04	7.07e-01	1.77e-04	7.41e-01	1.86e-04	1.41e+00	1.41e+00	1.48e+00	1.48e+00	1.06e+01	4.30e-01	1.06e+01	4.30e-01	9.99e-01	2.76e-01	1.05e+00	2.90e-01	9.44e-02	6.42e-01	9.90e-02	6.73e-01	0.00e+00	1.00e+00	0.00e+00	2.50e-04	1.13e+01	9.87e+00	6.26e-01	2.35e-01
chr1	12627938	12677737	NM_004753	0.5131	-	DHRS3	protein_coding	6.53e-21	2.47e-17	7.03690	3.20e+00	1.71e-04	3.20e+00	1.71e-04	5.50e-01	7.10e-05	5.76e-01	7.44e-05	1.72e-01	4.16e-01	1.80e-01	4.36e-01	1.03e+01	2.50e-02	1.03e+01	2.50e-02	2.72e-01	4.70e-03	2.85e-01	4.93e-03	2.65e-02	1.88e-01	2.78e-02	1.97e-01	2.81e+00	3.58e+00	1.20e-04	2.21e-04	1.01e+01	1.05e+01	2.17e-02	2.84e-02
chr9	87283372	87641985	NM_006180	0.4094	+	NTRK2	protein_coding	3.86e-10	1.09e-06	3.99048	4.81e+00	7.67e-05	4.81e+00	7.67e-05	3.25e-01	1.77e-05	3.41e-01	1.86e-05	6.75e-02	2.31e-01	7.07e-02	2.43e-01	8.82e+00	1.26e-03	8.82e+00	1.26e-03	9.47e-02	8.28e-05	9.92e-02	8.68e-05	1.07e-02	6.57e-02	1.12e-02	6.89e-02	4.58e+00	5.04e+00	6.41e-05	8.92e-05	8.75e+00	8.89e+00	1.20e-03	1.32e-03
chr11	111126706	111157129	NM_198498	0.4140	+	C11orf53	protein_coding	1.41e-09	3.19e-06	5.09803	1.00e+00	3.29e-05	1.00e+00	3.29e-05	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.05e+00	2.22e-03	6.05e+00	2.22e-03	5.01e-01	7.67e-04	5.26e-01	8.04e-04	8.28e-02	3.46e-01	8.68e-02	3.62e-01	1.00e+00	1.00e+00	3.29e-05	3.29e-05	6.41e+00	5.70e+00	2.76e-03	1.68e-03
chr1	156669399	156675459	NM_001878	0.5516	-	CRABP2	protein_coding	1.67e-08	3.16e-05	4.21997	9.15e+00	9.37e-02	9.15e+00	9.37e-02	1.94e-01	1.26e-02	2.04e-01	1.32e-02	2.12e-02	1.34e-01	2.23e-02	1.41e-01	1.33e+01	1.75e+00	1.33e+01	1.75e+00	5.07e-01	6.03e-01	5.32e-01	6.32e-01	3.80e-02	3.44e-01	3.99e-02	3.61e-01	9.28e+00	9.01e+00	1.03e-01	8.48e-02	1.37e+01	1.30e+01	2.18e+00	1.32e+00
chr8	120569316	120651106	NM_006209	0.3892	-	ENPP2	protein_coding	2.30e-08	3.72e-05	5.41302	3.71e+00	1.59e-04	3.71e+00	1.59e-04	7.62e-01	8.65e-05	7.99e-01	9.06e-05	2.06e-01	5.44e-01	2.15e-01	5.70e-01	8.66e+00	7.28e-03	8.66e+00	7.28e-03	1.91e+00	7.56e-03	2.00e+00	7.93e-03	2.20e-01	1.04e+00	2.31e-01	1.09e+00	4.25e+00	3.17e+00	2.20e-04	9.78e-05	1.00e+01	7.31e+00	1.26e-02	1.93e-03
chr10	48425778	48439138	NM_004962	0.5292	-	GDF10	protein_coding	1.12e-07	1.52e-04	5.33390	5.00e-01	3.74e-05	5.00e-01	3.74e-05	7.07e-01	5.29e-05	7.41e-01	5.55e-05	1.41e+00	1.41e+00	1.48e+00	1.48e+00	5.67e+00	4.45e-03	5.67e+00	4.45e-03	1.22e+00	3.44e-03	1.28e+00	3.61e-03	2.16e-01	7.72e-01	2.26e-01	8.10e-01	0.00e+00	1.00e+00	0.00e+00	7.49e-05	4.81e+00	6.54e+00	2.02e-03	6.89e-03
chr4	107842958	107957453	NM_014421	0.3622	-	DKK2	protein_coding	1.21e-07	1.52e-04	3.55695	4.17e+00	1.62e-04	4.17e+00	1.62e-04	8.27e-01	9.26e-05	8.67e-01	9.71e-05	1.98e-01	5.73e-01	2.08e-01	6.01e-01	7.84e+00	2.00e-03	7.84e+00	2.00e-03	4.45e-03	6.18e-06	4.66e-03	6.47e-06	5.67e-04	3.09e-03	5.94e-04	3.24e-03	3.58e+00	4.75e+00	9.61e-05	2.27e-04	7.85e+00	7.84e+00	2.00e-03	1.99e-03
chr1	11917520	11918992	NM_002521	0.5451	-	NPPB	protein_coding	1.32e-06	1.48e-03	4.17880	2.08e+00	2.38e-03	2.08e+00	2.38e-03	7.07e-01	1.44e-03	7.41e-01	1.51e-03	3.39e-01	6.06e-01	3.56e-01	6.35e-01	6.27e+00	5.47e-02	6.27e+00	5.47e-02	6.61e-01	2.45e-02	6.92e-01	2.57e-02	1.05e-01	4.48e-01	1.10e-01	4.70e-01	1.58e+00	2.58e+00	1.36e-03	3.40e-03	5.81e+00	6.74e+00	3.74e-02	7.20e-02
chr5	172741725	172756506	NM_003714	0.5093	-	STC2	protein_coding	1.43e-06	1.48e-03	-4.69813	7.79e+00	2.10e-02	7.79e+00	2.10e-02	1.79e+00	2.10e-02	1.87e+00	2.20e-02	2.30e-01	1.00e+00	2.41e-01	1.05e+00	2.73e+00	7.44e-04	2.73e+00	7.44e-04	2.45e+00	9.57e-04	2.56e+00	1.00e-03	8.96e-01	1.29e+00	9.39e-01	1.35e+00	6.52e+00	9.05e+00	6.16e-03	3.59e-02	1.00e+00	4.46e+00	6.77e-05	1.42e-03
chr12	103351451	103354294	NM_004316	0.5130	+	ASCL1	protein_coding	2.96e-06	2.80e-03	-3.85958	7.52e+00	7.88e-02	7.52e+00	7.88e-02	1.36e+00	6.52e-02	1.42e+00	6.83e-02	1.81e-01	8.27e-01	1.90e-01	8.67e-01	3.76e+00	5.10e-03	3.76e+00	5.10e-03	1.08e+00	3.73e-03	1.13e+00	3.91e-03	2.86e-01	7.31e-01	3.00e-01	7.67e-01	6.55e+00	8.48e+00	3.27e-02	1.25e-01	3.00e+00	4.52e+00	2.46e-03	7.74e-03
chr2	136871918	136875725	NM_003467	0.5200	-	CXCR4	protein_coding	5.84e-06	4.79e-03	-2.76553	9.21e+00	1.56e-01	9.21e+00	1.56e-01	2.31e-01	2.49e-02	2.42e-01	2.61e-02	2.51e-02	1.60e-01	2.63e-02	1.67e-01	6.34e+00	2.27e-02	6.34e+00	2.27e-02	8.23e-01	1.24e-02	8.63e-01	1.30e-02	1.30e-01	5.48e-01	1.36e-01	5.74e-01	9.37e+00	9.04e+00	1.74e-01	1.38e-01	6.92e+00	5.75e+00	3.15e-02	1.39e-02
chr7	120628750	120937498	NM_024913	0.3660	+	CPED1	protein_coding	6.31e-06	4.79e-03	2.43962	5.90e+00	1.91e-04	5.90e+00	1.91e-04	2.39e-01	3.21e-05	2.51e-01	3.36e-05	4.05e-02	1.68e-01	4.25e-02	1.76e-01	8.34e+00	1.05e-03	8.34e+00	1.05e-03	2.36e-01	1.72e-04	2.48e-01	1.80e-04	2.83e-02	1.63e-01	2.97e-02	1.71e-01	5.73e+00	6.07e+00	1.68e-04	2.14e-04	8.50e+00	8.17e+00	1.17e-03	9.30e-04
chr3	139654026	140286919	NM_022131	0.4268	+	CLSTN2	protein_coding	6.34e-06	4.79e-03	2.73128	5.47e+00	6.87e-05	5.47e+00	6.87e-05	2.07e-01	1.01e-05	2.17e-01	1.05e-05	3.79e-02	1.46e-01	3.97e-02	1.53e-01	8.15e+00	4.65e-04	8.15e+00	4.65e-04	5.78e-01	1.82e-04	6.06e-01	1.91e-04	7.09e-02	3.91e-01	7.43e-02	4.10e-01	5.61e+00	5.32e+00	7.58e-05	6.16e-05	7.74e+00	8.56e+00	3.37e-04	5.94e-04
chr11	30431617	30602040	NM_001584	0.3944	-	MPPED2	protein_coding	8.11e-06	5.74e-03	2.35675	6.03e+00	3.78e-04	6.03e+00	3.78e-04	7.79e-02	2.07e-05	8.17e-02	2.17e-05	1.29e-02	5.48e-02	1.35e-02	5.75e-02	8.38e+00	1.96e-03	8.38e+00	1.96e-03	2.35e-01	3.19e-04	2.47e-01	3.35e-04	2.81e-02	1.63e-01	2.94e-02	1.71e-01	6.09e+00	5.98e+00	3.93e-04	3.64e-04	8.21e+00	8.55e+00	1.74e-03	2.19e-03
chr3	25469753	25639422	NM_000965	0.4175	+	RARB	protein_coding	1.01e-05	6.73e-03	3.29278	4.91e+00	1.71e-04	4.91e+00	1.71e-04	6.80e-02	8.34e-06	7.13e-02	8.74e-06	1.39e-02	4.88e-02	1.45e-02	5.11e-02	8.09e+00	1.73e-03	8.09e+00	1.73e-03	8.19e-01	9.34e-04	8.58e-01	9.79e-04	1.01e-01	5.41e-01	1.06e-01	5.67e-01	4.95e+00	4.86e+00	1.77e-04	1.65e-04	7.51e+00	8.67e+00	1.07e-03	2.39e-03
chr11	111169270	111179460	NM_001271458	0.4525	+	COLCA2	protein_coding	1.12e-05	7.07e-03	4.64386	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	NaN	NaN	NaN	NaN	4.45e+00	2.36e-03	4.45e+00	2.36e-03	1.07e+00	1.67e-03	1.12e+00	1.75e-03	2.40e-01	7.07e-01	2.51e-01	7.41e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.70e+00	5.21e+00	1.18e-03	3.53e-03
chr1	852197	855072	NR_026874	0.6127	-	LOC100130417	lincRNA	1.24e-05	7.40e-03	-4.93074	4.55e+00	1.03e-02	4.55e+00	1.03e-02	1.54e+00	9.59e-03	1.62e+00	1.01e-02	3.39e-01	9.35e-01	3.56e-01	9.80e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	NaN	NaN	NaN	NaN	3.46e+00	5.64e+00	3.48e-03	1.70e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr10	90043858	90343082	NM_001031709	0.3674	-	RNLS	protein_coding	2.44e-05	1.36e-02	-5.54226	7.22e+00	2.33e-03	7.22e+00	2.33e-03	4.55e+00	3.23e-03	4.77e+00	3.38e-03	6.30e-01	1.38e+00	6.61e-01	1.45e+00	3.91e+00	4.68e-05	3.91e+00	4.68e-05	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	4.00e+00	1.04e+01	5.01e-05	4.62e-03	3.91e+00	3.91e+00	4.68e-05	4.68e-05
chr6	1610680	1614129	NM_001453	0.5333	+	FOXC1	protein_coding	2.52e-05	1.36e-02	2.25813	8.31e+00	9.22e-02	8.31e+00	9.22e-02	1.41e-01	9.02e-03	1.48e-01	9.46e-03	1.70e-02	9.78e-02	1.78e-02	1.03e-01	1.06e+01	4.42e-01	1.06e+01	4.42e-01	3.08e-02	9.43e-03	3.22e-02	9.89e-03	2.91e-03	2.13e-02	3.05e-03	2.24e-02	8.21e+00	8.41e+00	8.58e-02	9.86e-02	1.06e+01	1.06e+01	4.35e-01	4.49e-01
chr2	238768186	238820759	NM_005855	0.5227	+	RAMP1	protein_coding	4.04e-05	2.00e-02	2.28784	6.61e+00	1.85e-03	6.61e+00	1.85e-03	2.39e-01	3.09e-04	2.51e-01	3.24e-04	3.62e-02	1.67e-01	3.79e-02	1.75e-01	8.90e+00	9.13e-03	8.90e+00	9.13e-03	2.13e-01	1.34e-03	2.23e-01	1.41e-03	2.39e-02	1.47e-01	2.51e-02	1.54e-01	6.44e+00	6.78e+00	1.64e-03	2.07e-03	9.05e+00	8.75e+00	1.01e-02	8.18e-03
chr10	120789227	120793244	NM_199461	0.5087	+	NANOS1	protein_coding	4.05e-05	2.00e-02	2.21036	6.38e+00	2.12e-02	6.38e+00	2.12e-02	5.08e-01	7.39e-03	5.33e-01	7.75e-03	7.97e-02	3.49e-01	8.35e-02	3.66e-01	8.61e+00	9.88e-02	8.61e+00	9.88e-02	3.63e-01	2.46e-02	3.80e-01	2.58e-02	4.21e-02	2.49e-01	4.41e-02	2.61e-01	6.02e+00	6.74e+00	1.59e-02	2.64e-02	8.87e+00	8.36e+00	1.16e-01	8.14e-02
chr11	34172533	34379555	NM_145804	0.4792	-	ABTB2	protein_coding	4.79e-05	2.26e-02	2.92301	5.42e+00	2.10e-04	5.42e+00	2.10e-04	5.89e-01	8.54e-05	6.17e-01	8.95e-05	1.09e-01	4.06e-01	1.14e-01	4.26e-01	8.19e+00	1.63e-03	8.19e+00	1.63e-03	1.12e+00	1.15e-03	1.17e+00	1.21e-03	1.37e-01	7.08e-01	1.43e-01	7.42e-01	5.00e+00	5.83e+00	1.50e-04	2.71e-04	7.40e+00	8.98e+00	8.12e-04	2.44e-03
chr5	52084135	52249485	NM_181501	0.3674	+	ITGA1	protein_coding	6.51e-05	2.95e-02	2.12295	6.32e+00	4.87e-04	6.32e+00	4.87e-04	4.19e-01	1.41e-04	4.39e-01	1.48e-04	6.63e-02	2.90e-01	6.95e-02	3.04e-01	8.47e+00	2.14e-03	8.47e+00	2.14e-03	1.21e-01	1.80e-04	1.27e-01	1.88e-04	1.43e-02	8.39e-02	1.50e-02	8.80e-02	6.61e+00	6.02e+00	5.87e-04	3.87e-04	8.38e+00	8.55e+00	2.01e-03	2.27e-03
chr2	233344536	233352569	NM_004826	0.6487	-	ECEL1	protein_coding	7.22e-05	3.15e-02	4.70044	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	NaN	NaN	NaN	NaN	4.05e+00	3.11e-03	4.05e+00	3.11e-03	2.08e+00	3.52e-03	2.18e+00	3.69e-03	5.13e-01	1.13e+00	5.37e-01	1.19e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.52e+00	2.58e+00	5.60e-03	6.22e-04
chr2	7052406	7058813	NR_033997	0.5117	-	RNF144A-AS1	antisense	1.01e-04	4.25e-02	2.20547	4.61e+00	3.67e-03	4.61e+00	3.67e-03	2.09e-01	5.52e-04	2.19e-01	5.79e-04	4.53e-02	1.50e-01	4.75e-02	1.58e-01	6.79e+00	1.75e-02	6.79e+00	1.75e-02	3.84e-01	4.64e-03	4.02e-01	4.86e-03	5.65e-02	2.65e-01	5.92e-02	2.78e-01	4.46e+00	4.75e+00	3.28e-03	4.06e-03	7.07e+00	6.52e+00	2.08e-02	1.42e-02
chr2	174937174	175113398	NM_013341	0.3649	-	OLA1	protein_coding	1.05e-04	4.25e-02	4.57132	8.63e+00	2.26e-03	8.63e+00	2.26e-03	1.56e-01	2.45e-04	1.64e-01	2.57e-04	1.81e-02	1.09e-01	1.90e-02	1.14e-01	1.12e+01	5.38e-02	1.12e+01	5.38e-02	4.23e+00	7.37e-02	4.43e+00	7.72e-02	3.77e-01	1.37e+00	3.96e-01	1.44e+00	8.74e+00	8.52e+00	2.43e-03	2.08e-03	1.42e+01	8.21e+00	1.06e-01	1.67e-03
chr4	147560044	147563623	NM_004575	0.4944	+	POU4F2	protein_coding	1.11e-04	4.33e-02	-4.34577	4.28e+00	8.24e-03	4.28e+00	8.24e-03	2.08e+00	9.29e-03	2.19e+00	9.73e-03	4.87e-01	1.13e+00	5.10e-01	1.18e+00	5.00e-01	1.40e-04	5.00e-01	1.40e-04	7.07e-01	1.98e-04	7.41e-01	2.07e-04	1.41e+00	1.41e+00	1.48e+00	1.48e+00	5.75e+00	2.81e+00	1.48e-02	1.68e-03	1.00e+00	0.00e+00	2.79e-04	0.00e+00
chr5	121647763	121799914	NM_005460	0.3913	+	SNCAIP	protein_coding	1.16e-04	4.36e-02	2.90689	3.29e+00	5.92e-05	3.29e+00	5.92e-05	4.14e-01	1.86e-05	4.34e-01	1.95e-05	1.26e-01	3.14e-01	1.32e-01	3.29e-01	6.20e+00	4.86e-04	6.20e+00	4.86e-04	3.85e-01	1.30e-04	4.04e-01	1.36e-04	6.21e-02	2.68e-01	6.51e-02	2.80e-01	3.00e+00	3.58e+00	4.60e-05	7.23e-05	5.93e+00	6.48e+00	3.94e-04	5.78e-04
chr2	30945637	31030311	NM_144575	0.4603	-	CAPN13	protein_coding	1.25e-04	4.58e-02	3.54432	1.50e+00	2.36e-05	1.50e+00	2.36e-05	7.07e-01	1.67e-05	7.41e-01	1.75e-05	4.71e-01	7.07e-01	4.94e-01	7.41e-01	5.11e+00	4.02e-04	5.11e+00	4.02e-04	3.53e-01	1.00e-04	3.70e-01	1.05e-04	6.92e-02	2.50e-01	7.25e-02	2.62e-01	1.00e+00	2.00e+00	1.18e-05	3.54e-05	4.86e+00	5.36e+00	3.31e-04	4.72e-04
chr10	74033676	74035794	NM_019058	0.5866	+	DDIT4	protein_coding	1.30e-04	4.61e-02	-2.95570	7.52e+00	1.13e-01	7.52e+00	1.13e-01	1.57e+00	1.04e-01	1.65e+00	1.09e-01	2.09e-01	9.18e-01	2.19e-01	9.63e-01	4.95e+00	1.42e-02	4.95e+00	1.42e-02	1.98e-01	2.00e-03	2.08e-01	2.10e-03	4.00e-02	1.41e-01	4.20e-02	1.48e-01	6.41e+00	8.63e+00	3.97e-02	1.86e-01	5.09e+00	4.81e+00	1.56e-02	1.27e-02
chr8	97505881	97624037	NM_002998	0.4136	+	SDC2	protein_coding	1.39e-04	4.76e-02	-2.02337	8.62e+00	3.41e-03	8.62e+00	3.41e-03	4.70e-01	1.10e-03	4.92e-01	1.15e-03	5.45e-02	3.21e-01	5.71e-02	3.36e-01	6.61e+00	8.34e-04	6.61e+00	8.34e-04	3.63e-01	2.09e-04	3.80e-01	2.20e-04	5.48e-02	2.51e-01	5.75e-02	2.63e-01	8.95e+00	8.29e+00	4.19e-03	2.64e-03	6.36e+00	6.87e+00	6.86e-04	9.82e-04
chr1	87794150	87814607	NM_006769	0.4255	+	LMO4	protein_coding	1.47e-04	4.86e-02	-2.86790	6.16e+00	3.52e-03	6.16e+00	3.52e-03	3.96e-01	9.68e-04	4.15e-01	1.01e-03	6.43e-02	2.75e-01	6.74e-02	2.88e-01	3.32e+00	4.40e-04	3.32e+00	4.40e-04	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.88e+00	6.44e+00	2.84e-03	4.20e-03	3.32e+00	3.32e+00	4.40e-04	4.40e-04
chr2	12856997	12882858	NM_021643	0.4771	+	TRIB2	protein_coding	1.50e-04	4.86e-02	1.95679	9.25e+00	2.35e-02	9.25e+00	2.35e-02	3.34e-03	5.47e-05	3.51e-03	5.73e-05	3.61e-04	2.32e-03	3.79e-04	2.43e-03	1.12e+01	9.15e-02	1.12e+01	9.15e-02	6.90e-02	4.37e-03	7.23e-02	4.59e-03	6.15e-03	4.78e-02	6.45e-03	5.01e-02	9.25e+00	9.26e+00	2.35e-02	2.36e-02	1.12e+01	1.13e+01	8.84e-02	9.46e-02
chr10	21068902	21186531	NM_006393	0.3712	-	NEBL	protein_coding	1.57e-04	4.94e-02	1.95936	6.56e+00	7.95e-04	6.56e+00	7.95e-04	1.84e-01	1.02e-04	1.93e-01	1.07e-04	2.81e-02	1.29e-01	2.94e-02	1.35e-01	8.52e+00	3.12e-03	8.52e+00	3.12e-03	5.83e-02	1.26e-04	6.11e-02	1.32e-04	6.84e-03	4.05e-02	7.17e-03	4.25e-02	6.69e+00	6.43e+00	8.67e-04	7.23e-04	8.56e+00	8.48e+00	3.20e-03	3.03e-03
chr5	146770370	146889619	NM_001197294	0.4143	-	DPYSL3	protein_coding	2.01e-04	6.15e-02	2.19876	9.79e+00	7.49e-03	9.79e+00	7.49e-03	2.77e-01	1.43e-03	2.90e-01	1.50e-03	2.82e-02	1.91e-01	2.96e-02	2.00e-01	1.20e+01	3.44e-02	1.20e+01	3.44e-02	3.59e-01	8.49e-03	3.77e-01	8.90e-03	3.00e-02	2.46e-01	3.14e-02	2.58e-01	9.99e+00	9.60e+00	8.50e-03	6.48e-03	1.17e+01	1.22e+01	2.84e-02	4.04e-02
chr11	64879325	64883707	NM_003273	0.6035	+	TM7SF2	protein_coding	2.32e-04	6.91e-02	2.14923	5.87e+00	1.31e-02	5.87e+00	1.31e-02	8.72e-02	8.07e-04	9.15e-02	8.46e-04	1.49e-02	6.15e-02	1.56e-02	6.45e-02	8.01e+00	5.90e-02	8.01e+00	5.90e-02	2.89e-01	1.18e-02	3.03e-01	1.23e-02	3.61e-02	2.00e-01	3.78e-02	2.09e-01	5.93e+00	5.81e+00	1.37e-02	1.26e-02	8.21e+00	7.80e+00	6.73e-02	5.07e-02
chr3	158787040	159615155	NM_001197113	0.3906	+	IQCJ-SCHIP1	protein_coding	2.55e-04	7.40e-02	2.02609	9.40e+00	8.18e-04	9.40e+00	8.18e-04	1.36e-01	7.68e-05	1.42e-01	8.06e-05	1.44e-02	9.40e-02	1.51e-02	9.85e-02	1.14e+01	3.33e-03	1.14e+01	3.33e-03	1.72e-01	3.97e-04	1.81e-01	4.16e-04	1.51e-02	1.19e-01	1.58e-02	1.25e-01	9.50e+00	9.31e+00	8.72e-04	7.63e-04	1.13e+01	1.15e+01	3.05e-03	3.61e-03
chr21	22370613	22915648	NM_004540	0.3403	+	NCAM2	protein_coding	2.78e-04	7.63e-02	2.79918	7.12e+00	2.53e-04	7.12e+00	2.53e-04	7.34e-02	1.30e-05	7.70e-02	1.36e-05	1.03e-02	5.12e-02	1.08e-02	5.37e-02	9.76e+00	1.77e-03	9.76e+00	1.77e-03	9.81e-01	1.12e-03	1.03e+00	1.18e-03	1.01e-01	6.33e-01	1.05e-01	6.63e-01	7.07e+00	7.17e+00	2.44e-04	2.62e-04	9.06e+00	1.05e+01	9.80e-04	2.57e-03
chr12	51785100	51909547	NM_001258401	0.4272	+	SLC4A8	retained_intron	2.82e-04	7.63e-02	3.77259	1.50e+00	1.61e-05	1.50e+00	1.61e-05	7.07e-01	1.14e-05	7.41e-01	1.19e-05	4.71e-01	7.07e-01	4.94e-01	7.41e-01	4.90e+00	3.21e-04	4.90e+00	3.21e-04	1.70e+00	3.18e-04	1.79e+00	3.34e-04	3.47e-01	9.90e-01	3.64e-01	1.04e+00	1.00e+00	2.00e+00	8.04e-06	2.41e-05	3.70e+00	6.11e+00	9.64e-05	5.46e-04

Download the DEG result list for Prol_vs_D4plus.
Download the whole result list for Prol_vs_D4plus.

DEG table for the contrast Prol_vs_D8minus

The following table presents the top 10% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Prol_vs_D8minus. The fields of the table correspond to the requested features to be exported. The table can be searched using the search field on the top right.

chromosome	start	end	gene_id	gc_content	strand	gene_name	biotype	p-value_edger	FDR_edger	log2_normalized_fold_change_Prol_vs_D8minus	log2_normalized_mean_counts_Prol	rpgm_normalized_mean_counts_Prol	log2_normalized_median_counts_Prol	rpgm_normalized_median_counts_Prol	log2_normalized_sd_counts_Prol	rpgm_normalized_sd_counts_Prol	log2_normalized_mad_counts_Prol	rpgm_normalized_mad_counts_Prol	log2_normalized_cv_counts_Prol	rpgm_normalized_cv_counts_Prol	log2_normalized_rcv_counts_Prol	rpgm_normalized_rcv_counts_Prol	log2_normalized_mean_counts_D8minus	rpgm_normalized_mean_counts_D8minus	log2_normalized_median_counts_D8minus	rpgm_normalized_median_counts_D8minus	log2_normalized_sd_counts_D8minus	rpgm_normalized_sd_counts_D8minus	log2_normalized_mad_counts_D8minus	rpgm_normalized_mad_counts_D8minus	log2_normalized_cv_counts_D8minus	rpgm_normalized_cv_counts_D8minus	log2_normalized_rcv_counts_D8minus	rpgm_normalized_rcv_counts_D8minus	log2_normalized_counts_IT3R59_24_Prol	log2_normalized_counts_IT3R63_28_Prol	rpgm_normalized_counts_IT3R59_24_Prol	rpgm_normalized_counts_IT3R63_28_Prol	log2_normalized_counts_IT3R61_26_D8minus	log2_normalized_counts_IT3R66_31_D8minus	rpgm_normalized_counts_IT3R61_26_D8minus	rpgm_normalized_counts_IT3R66_31_D8minus
chr9	138594030	138684993	NM_020822	0.6170	+	KCNT1	protein_coding	2.79e-08	0.000317	-4.82018	5.81e+00	6.10e-04	5.81e+00	6.10e-04	2.36e-01	1.01e-04	2.47e-01	1.06e-04	4.06e-02	1.66e-01	4.25e-02	1.74e-01	7.92e-01	1.10e-05	7.92e-01	1.10e-05	1.12e+00	1.55e-05	1.17e+00	1.63e-05	1.414214	1.414214	1.482600	1.482600	5.98e+00	5.64e+00	6.82e-04	5.39e-04	0.00e+00	1.58e+00	0.00e+00	2.20e-05
chr1	2985741	3355185	NM_022114	0.5758	+	PRDM16	protein_coding	2.30e-06	0.009250	11.39395	3.81e+00	3.65e-05	3.81e+00	3.65e-05	5.02e-01	1.34e-05	5.27e-01	1.40e-05	1.32e-01	3.67e-01	1.38e-01	3.84e-01	9.13e+00	1.06e-01	9.13e+00	1.06e-01	1.01e+01	1.49e-01	1.06e+01	1.57e-01	1.104280	1.414105	1.157680	1.482486	3.46e+00	4.17e+00	2.71e-05	4.60e-05	1.63e+01	2.00e+00	2.11e-01	8.12e-06
chr4	113434671	113437328	NM_024019	0.5658	-	NEUROG2	protein_coding	2.45e-06	0.009250	4.74595	1.50e+00	7.53e-04	1.50e+00	7.53e-04	7.07e-01	5.32e-04	7.41e-01	5.58e-04	4.71e-01	7.07e-01	4.94e-01	7.41e-01	6.31e+00	2.99e-02	6.31e+00	2.99e-02	3.72e-01	7.72e-03	3.90e-01	8.09e-03	0.058911	0.257938	0.061759	0.270411	1.00e+00	2.00e+00	3.76e-04	1.13e-03	6.04e+00	6.57e+00	2.45e-02	3.54e-02
chr9	77112251	77302117	NM_006914	0.3770	+	RORB	protein_coding	5.76e-06	0.016327	-3.46538	6.80e+00	6.35e-04	6.80e+00	6.35e-04	8.62e-01	3.61e-04	9.04e-01	3.79e-04	1.27e-01	5.69e-01	1.33e-01	5.97e-01	3.40e+00	5.27e-05	3.40e+00	5.27e-05	5.71e-01	2.23e-05	5.98e-01	2.34e-05	0.167726	0.424264	0.175837	0.444780	6.19e+00	7.41e+00	3.79e-04	8.90e-04	3.81e+00	3.00e+00	6.85e-05	3.69e-05
chr5	136310986	136835018	NM_004598	0.4276	-	SPOCK1	protein_coding	1.19e-05	0.021478	2.62945	6.17e+00	1.40e-04	6.17e+00	1.40e-04	5.17e-01	4.99e-05	5.42e-01	5.23e-05	8.38e-02	3.56e-01	8.79e-02	3.73e-01	8.83e+00	8.78e-04	8.83e+00	8.78e-04	2.90e-01	1.75e-04	3.04e-01	1.84e-04	0.032782	0.199835	0.034368	0.209498	5.81e+00	6.54e+00	1.05e-04	1.76e-04	8.63e+00	9.04e+00	7.54e-04	1.00e-03
chrX	119392504	119445391	NM_017938	0.4318	-	TMEM255A	protein_coding	1.19e-05	0.021478	-6.28540	5.62e+00	2.93e-03	5.62e+00	2.93e-03	3.71e+00	3.96e-03	3.89e+00	4.15e-03	6.60e-01	1.35e+00	6.92e-01	1.42e+00	7.92e-01	1.89e-05	7.92e-01	1.89e-05	1.12e+00	2.67e-05	1.17e+00	2.80e-05	1.414214	1.414214	1.482600	1.482600	8.25e+00	3.00e+00	5.73e-03	1.32e-04	1.58e+00	0.00e+00	3.78e-05	0.00e+00
chr11	63304272	63313930	NM_004585	0.4851	+	RARRES3	protein_coding	1.49e-05	0.021478	8.26913	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	NaN	NaN	NaN	NaN	4.63e+00	3.18e-02	4.63e+00	3.18e-02	6.55e+00	4.50e-02	6.87e+00	4.72e-02	1.414214	1.414214	1.482600	1.482600	0.00e+00	0.00e+00	0.00e+00	0.00e+00	9.27e+00	0.00e+00	6.37e-02	0.00e+00
chr5	90664448	90679190	NM_020801	0.3575	-	ARRDC3	protein_coding	1.52e-05	0.021478	-2.55152	7.87e+00	1.58e-02	7.87e+00	1.58e-02	1.35e-01	1.49e-03	1.42e-01	1.56e-03	1.72e-02	9.39e-02	1.80e-02	9.84e-02	5.32e+00	2.65e-03	5.32e+00	2.65e-03	1.53e-01	2.88e-04	1.61e-01	3.02e-04	0.028829	0.108786	0.030223	0.114046	7.97e+00	7.77e+00	1.69e-02	1.48e-02	5.21e+00	5.43e+00	2.44e-03	2.85e-03
chr5	137588068	137610253	NM_001496	0.4737	-	GFRA3	protein_coding	2.36e-05	0.029452	2.89269	6.62e+00	4.71e-03	6.62e+00	4.71e-03	7.58e-01	2.39e-03	7.95e-01	2.51e-03	1.14e-01	5.07e-01	1.20e-01	5.32e-01	9.55e+00	3.53e-02	9.55e+00	3.53e-02	6.04e-01	1.44e-02	6.34e-01	1.51e-02	0.063267	0.407547	0.066326	0.427254	6.09e+00	7.16e+00	3.02e-03	6.40e-03	9.98e+00	9.12e+00	4.54e-02	2.51e-02
chr1	156830670	156851642	NM_002529	0.5514	+	NTRK1	protein_coding	2.99e-05	0.029452	-2.90378	6.85e+00	5.48e-03	6.85e+00	5.48e-03	2.47e-01	9.44e-04	2.59e-01	9.90e-04	3.61e-02	1.72e-01	3.79e-02	1.80e-01	3.94e+00	6.91e-04	3.94e+00	6.91e-04	3.32e-01	1.69e-04	3.48e-01	1.77e-04	0.084361	0.243830	0.088440	0.255621	7.02e+00	6.67e+00	6.15e-03	4.82e-03	4.17e+00	3.70e+00	8.11e-04	5.72e-04
chr12	115108058	115121969	NM_016569	0.4727	-	TBX3	protein_coding	3.11e-05	0.029452	-2.56640	9.86e+00	7.76e-02	9.86e+00	7.76e-02	1.16e+00	5.65e-02	1.22e+00	5.93e-02	1.18e-01	7.28e-01	1.23e-01	7.63e-01	7.51e+00	1.30e-02	7.51e+00	1.30e-02	1.06e-01	9.66e-04	1.11e-01	1.01e-03	0.014155	0.074022	0.014840	0.077602	9.04e+00	1.07e+01	3.77e-02	1.18e-01	7.58e+00	7.43e+00	1.37e-02	1.24e-02
chr2	8822112	8824583	NM_002166	0.4494	+	ID2	protein_coding	3.12e-05	0.029452	-2.88319	7.98e+00	1.34e-01	7.98e+00	1.34e-01	1.57e+00	1.23e-01	1.65e+00	1.29e-01	1.97e-01	9.19e-01	2.07e-01	9.63e-01	5.48e+00	1.78e-02	5.48e+00	1.78e-02	2.28e-01	2.86e-03	2.39e-01	3.00e-03	0.041518	0.160706	0.043525	0.168477	6.87e+00	9.10e+00	4.69e-02	2.21e-01	5.64e+00	5.32e+00	1.98e-02	1.58e-02
chr10	90043858	90343082	NM_001031709	0.3674	-	RNLS	protein_coding	6.68e-05	0.058206	-5.23970	7.22e+00	2.33e-03	7.22e+00	2.33e-03	4.55e+00	3.23e-03	4.77e+00	3.38e-03	6.30e-01	1.38e+00	6.61e-01	1.45e+00	4.17e+00	5.85e-05	4.17e+00	5.85e-05	5.06e-01	2.13e-05	5.31e-01	2.23e-05	0.121580	0.363655	0.127459	0.381240	4.00e+00	1.04e+01	5.01e-05	4.62e-03	4.52e+00	3.81e+00	7.35e-05	4.34e-05
chr7	107788070	107880614	NM_001037132	0.3848	-	NRCAM	protein_coding	7.24e-05	0.058578	-2.19129	9.68e+00	9.00e-03	9.68e+00	9.00e-03	3.72e-01	2.30e-03	3.90e-01	2.41e-03	3.85e-02	2.56e-01	4.03e-02	2.68e-01	7.51e+00	1.96e-03	7.51e+00	1.96e-03	1.29e-01	1.76e-04	1.35e-01	1.84e-04	0.017145	0.089606	0.017974	0.093939	9.94e+00	9.42e+00	1.06e-02	7.37e-03	7.60e+00	7.42e+00	2.09e-03	1.84e-03
chr20	5525079	5591672	NM_019593	0.3924	-	GPCPD1	protein_coding	7.96e-05	0.060124	-2.55459	6.86e+00	1.75e-03	6.86e+00	1.75e-03	2.71e-01	3.29e-04	2.84e-01	3.45e-04	3.94e-02	1.88e-01	4.13e-02	1.97e-01	4.25e+00	2.85e-04	4.25e+00	2.85e-04	6.32e-01	1.27e-04	6.62e-01	1.34e-04	0.148454	0.446594	0.155632	0.468189	7.06e+00	6.67e+00	1.98e-03	1.52e-03	3.81e+00	4.70e+00	1.95e-04	3.75e-04
chr4	41362647	41702061	NM_014988	0.4044	+	LIMCH1	protein_coding	9.96e-05	0.068379	-2.23832	1.00e+01	3.08e-03	1.00e+01	3.08e-03	1.85e-01	3.94e-04	1.93e-01	4.13e-04	1.84e-02	1.28e-01	1.93e-02	1.34e-01	7.74e+00	6.51e-04	7.74e+00	6.51e-04	5.85e-01	2.58e-04	6.14e-01	2.71e-04	0.075668	0.396748	0.079327	0.415933	9.90e+00	1.02e+01	2.80e-03	3.36e-03	7.32e+00	8.15e+00	4.68e-04	8.34e-04
chr1	55315299	55352921	NM_014762	0.4771	-	DHCR24	protein_coding	1.04e-04	0.068379	2.30134	7.49e+00	4.85e-03	7.49e+00	4.85e-03	4.23e-01	1.41e-03	4.43e-01	1.48e-03	5.65e-02	2.91e-01	5.92e-02	3.05e-01	9.71e+00	2.40e-02	9.71e+00	2.40e-02	7.97e-01	1.26e-02	8.36e-01	1.33e-02	0.082081	0.526710	0.086050	0.552180	7.79e+00	7.19e+00	5.85e-03	3.85e-03	1.03e+01	9.15e+00	3.30e-02	1.51e-02
chr11	62283373	62314332	NM_001620	0.5274	-	AHNAK	protein_coding	1.12e-04	0.068379	-2.41504	7.32e+00	5.14e-03	7.32e+00	5.14e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	4.73e+00	9.37e-04	4.73e+00	9.37e-04	1.03e+00	6.40e-04	1.08e+00	6.70e-04	0.218189	0.682724	0.228740	0.715738	7.32e+00	7.32e+00	5.14e-03	5.14e-03	5.46e+00	4.00e+00	1.39e-03	4.85e-04
chr10	127700953	128077127	NM_003474	0.4312	-	ADAM12	protein_coding	1.15e-04	0.068379	-2.00000	8.65e+00	1.07e-03	8.65e+00	1.07e-03	1.53e-01	1.13e-04	1.60e-01	1.18e-04	1.76e-02	1.06e-01	1.85e-02	1.11e-01	6.65e+00	2.65e-04	6.65e+00	2.65e-04	3.05e-02	5.64e-06	3.19e-02	5.91e-06	0.004579	0.021320	0.004800	0.022351	8.54e+00	8.75e+00	9.86e-04	1.15e-03	6.67e+00	6.63e+00	2.68e-04	2.61e-04
chr10	48425778	48439138	NM_004962	0.5292	-	GDF10	protein_coding	1.79e-04	0.101683	3.54432	5.00e-01	3.74e-05	5.00e-01	3.74e-05	7.07e-01	5.29e-05	7.41e-01	5.55e-05	1.41e+00	1.41e+00	1.48e+00	1.48e+00	3.88e+00	1.24e-03	3.88e+00	1.24e-03	1.24e+00	1.01e-03	1.30e+00	1.05e-03	0.320029	0.814244	0.335504	0.853618	0.00e+00	1.00e+00	0.00e+00	7.49e-05	4.75e+00	3.00e+00	1.95e-03	5.24e-04
chr10	54073942	54077417	NM_012242	0.4537	+	DKK1	protein_coding	1.96e-04	0.105819	-3.18161	7.54e+00	5.32e-02	7.54e+00	5.32e-02	1.21e-01	4.48e-03	1.27e-01	4.69e-03	1.60e-02	8.41e-02	1.68e-02	8.82e-02	4.32e+00	5.61e-03	4.32e+00	5.61e-03	4.55e-01	1.83e-03	4.77e-01	1.92e-03	0.105341	0.326357	0.110435	0.342138	7.62e+00	7.45e+00	5.64e-02	5.01e-02	4.64e+00	4.00e+00	6.91e-03	4.32e-03
chr7	93514708	93520303	NM_006528	0.3933	-	TFPI2	protein_coding	2.54e-04	0.131062	-3.09565	6.94e+00	2.35e-02	6.94e+00	2.35e-02	8.19e-01	1.28e-02	8.59e-01	1.34e-02	1.18e-01	5.43e-01	1.24e-01	5.69e-01	3.61e+00	2.59e-03	3.61e+00	2.59e-03	1.46e+00	2.40e-03	1.53e+00	2.52e-03	0.402793	0.926554	0.422270	0.971359	7.52e+00	6.36e+00	3.25e-02	1.45e-02	4.64e+00	2.58e+00	4.29e-03	8.94e-04
chr20	30193085	30194317	NM_002165	0.5864	+	ID1	protein_coding	2.95e-04	0.145135	-2.07276	8.60e+00	3.46e-01	8.60e+00	3.46e-01	8.94e-01	2.02e-01	9.37e-01	2.12e-01	1.04e-01	5.84e-01	1.09e-01	6.13e-01	6.66e+00	8.16e-02	6.66e+00	8.16e-02	1.51e-01	8.61e-03	1.58e-01	9.03e-03	0.022673	0.105538	0.023770	0.110642	7.97e+00	9.24e+00	2.03e-01	4.89e-01	6.77e+00	6.55e+00	8.77e-02	7.55e-02
chr12	103351451	103354294	NM_004316	0.5130	+	ASCL1	protein_coding	3.23e-04	0.145502	-2.83650	7.52e+00	7.88e-02	7.52e+00	7.88e-02	1.36e+00	6.52e-02	1.42e+00	6.83e-02	1.81e-01	8.27e-01	1.90e-01	8.67e-01	4.89e+00	1.07e-02	4.89e+00	1.07e-02	7.07e-01	5.22e-03	7.41e-01	5.48e-03	0.144534	0.486860	0.151523	0.510403	6.55e+00	8.48e+00	3.27e-02	1.25e-01	5.39e+00	4.39e+00	1.44e-02	7.03e-03
chr2	113587336	113594356	NM_000576	0.4556	-	IL1B	protein_coding	3.24e-04	0.145502	5.18322	5.00e-01	7.12e-05	5.00e-01	7.12e-05	7.07e-01	1.01e-04	7.41e-01	1.06e-04	1.41e+00	1.41e+00	1.48e+00	1.48e+00	3.38e+00	7.62e-03	3.38e+00	7.62e-03	4.78e+00	1.08e-02	5.01e+00	1.13e-02	1.414214	1.414214	1.482600	1.482600	1.00e+00	0.00e+00	1.42e-04	0.00e+00	6.75e+00	0.00e+00	1.52e-02	0.00e+00
chrX	151999510	152037907	NM_015922	0.4602	+	NSDHL	protein_coding	3.34e-04	0.145502	2.04999	5.28e+00	9.90e-04	5.28e+00	9.90e-04	1.05e-01	7.37e-05	1.10e-01	7.72e-05	1.98e-02	7.44e-02	2.08e-02	7.80e-02	7.32e+00	4.18e-03	7.32e+00	4.18e-03	2.86e-01	8.29e-04	3.00e-01	8.69e-04	0.039079	0.198254	0.040969	0.207841	5.21e+00	5.36e+00	9.38e-04	1.04e-03	7.52e+00	7.12e+00	4.77e-03	3.59e-03
chr11	15133969	15268756	NM_001031853	0.4370	+	INSC	protein_coding	3.72e-04	0.156335	-4.51006	5.98e+00	1.18e-03	5.98e+00	1.18e-03	3.22e+00	1.54e-03	3.38e+00	1.61e-03	5.39e-01	1.31e+00	5.65e-01	1.37e+00	2.52e+00	4.45e-05	2.52e+00	4.45e-05	1.33e+00	4.20e-05	1.39e+00	4.40e-05	0.525514	0.942809	0.550926	0.988400	3.70e+00	8.26e+00	8.90e-05	2.26e-03	1.58e+00	3.46e+00	1.48e-05	7.42e-05
chr1	149856009	149858232	NM_003528	0.4793	-	HIST2H2BE	protein_coding	4.29e-04	0.172664	2.44626	4.32e+00	8.55e-03	4.32e+00	8.55e-03	1.02e-01	6.36e-04	1.07e-01	6.67e-04	2.36e-02	7.44e-02	2.48e-02	7.80e-02	6.62e+00	4.86e-02	6.62e+00	4.86e-02	9.41e-01	2.99e-02	9.87e-01	3.13e-02	0.142195	0.615445	0.149071	0.645206	4.25e+00	4.39e+00	8.10e-03	9.00e-03	7.29e+00	5.95e+00	6.97e-02	2.74e-02
chr1	208195587	208417665	NM_025179	0.4798	-	PLXNA2	protein_coding	4.42e-04	0.172664	-2.11548	8.41e+00	1.61e-03	8.41e+00	1.61e-03	6.71e-01	7.23e-04	7.03e-01	7.58e-04	7.98e-02	4.50e-01	8.37e-02	4.72e-01	6.33e+00	3.67e-04	6.33e+00	3.67e-04	4.39e-01	1.11e-04	4.61e-01	1.17e-04	0.069391	0.303665	0.072746	0.318350	7.93e+00	8.88e+00	1.09e-03	2.12e-03	6.64e+00	6.02e+00	4.46e-04	2.88e-04
chr6	153071931	153080902	NM_003381	0.3381	+	VIP	protein_coding	4.77e-04	0.180117	-3.52474	8.20e+00	3.39e-02	8.20e+00	3.39e-02	5.55e-01	1.28e-02	5.82e-01	1.34e-02	6.77e-02	3.77e-01	7.10e-02	3.95e-01	4.25e+00	2.84e-03	4.25e+00	2.84e-03	1.76e+00	2.92e-03	1.85e+00	3.06e-03	0.414987	1.025998	0.435055	1.075612	8.59e+00	7.81e+00	4.29e-02	2.49e-02	3.00e+00	5.49e+00	7.80e-04	4.90e-03
chr14	106383837	106398502	NR_026800	0.5591	+	FAM30A	protein_coding	5.14e-04	0.187836	-3.05889	5.57e+00	3.34e-03	5.57e+00	3.34e-03	6.77e-01	1.54e-03	7.09e-01	1.62e-03	1.22e-01	4.62e-01	1.27e-01	4.84e-01	2.50e+00	3.41e-04	2.50e+00	3.41e-04	7.07e-01	1.93e-04	7.41e-01	2.02e-04	0.282843	0.565685	0.296520	0.593040	6.04e+00	5.09e+00	4.43e-03	2.25e-03	3.00e+00	2.00e+00	4.77e-04	2.05e-04
chr13	32605436	32870776	NM_023037	0.3887	+	FRY	protein_coding	5.68e-04	0.198975	-2.21560	7.34e+00	6.61e-04	7.34e+00	6.61e-04	8.49e-01	3.70e-04	8.90e-01	3.88e-04	1.16e-01	5.60e-01	1.21e-01	5.87e-01	5.13e+00	1.39e-04	5.13e+00	1.39e-04	8.52e-01	7.99e-05	8.93e-01	8.38e-05	0.166144	0.573330	0.174178	0.601054	7.94e+00	6.74e+00	9.23e-04	3.99e-04	4.52e+00	5.73e+00	8.29e-05	1.96e-04
chr5	16067414	16179897	NM_001102562	0.3921	-	MARCH11	protein_coding	5.79e-04	0.198975	-1.90107	9.87e+00	8.51e-03	9.87e+00	8.51e-03	4.73e-01	2.74e-03	4.95e-01	2.87e-03	4.79e-02	3.22e-01	5.02e-02	3.38e-01	7.96e+00	2.27e-03	7.96e+00	2.27e-03	4.74e-01	7.36e-04	4.97e-01	7.71e-04	0.059473	0.323802	0.062348	0.339460	1.02e+01	9.53e+00	1.04e-02	6.57e-03	8.30e+00	7.63e+00	2.79e-03	1.75e-03
chr1	852197	855072	NR_026874	0.6127	-	LOC100130417	lincRNA	6.34e-04	0.211323	-3.93074	4.55e+00	1.03e-02	4.55e+00	1.03e-02	1.54e+00	9.59e-03	1.62e+00	1.01e-02	3.39e-01	9.35e-01	3.56e-01	9.80e-01	7.92e-01	3.48e-04	7.92e-01	3.48e-04	1.12e+00	4.92e-04	1.17e+00	5.16e-04	1.414214	1.414214	1.482600	1.482600	3.46e+00	5.64e+00	3.48e-03	1.70e-02	0.00e+00	1.58e+00	0.00e+00	6.96e-04
chr1	216676587	216896814	NM_001438	0.3662	-	ESRRG	protein_coding	6.72e-04	0.217577	-2.02008	8.68e+00	1.97e-03	8.68e+00	1.97e-03	6.77e-01	8.93e-04	7.10e-01	9.36e-04	7.80e-02	4.54e-01	8.18e-02	4.76e-01	6.62e+00	4.81e-04	6.62e+00	4.81e-04	8.46e-01	2.70e-04	8.87e-01	2.83e-04	0.127820	0.560349	0.134001	0.587445	8.20e+00	9.16e+00	1.33e-03	2.60e-03	6.02e+00	7.22e+00	2.91e-04	6.72e-04
chr2	17721806	17837706	NM_003385	0.4169	+	VSNL1	protein_coding	7.03e-04	0.221438	2.34628	4.55e+00	1.94e-04	4.55e+00	1.94e-04	4.34e-02	6.10e-06	4.55e-02	6.40e-06	9.53e-03	3.14e-02	9.99e-03	3.29e-02	6.90e+00	1.02e-03	6.90e+00	1.02e-03	1.11e-01	7.93e-05	1.16e-01	8.31e-05	0.016103	0.077573	0.016881	0.081324	4.52e+00	4.58e+00	1.90e-04	1.98e-04	6.82e+00	6.98e+00	9.66e-04	1.08e-03
chr13	77454303	77460540	NM_138444	0.4364	-	KCTD12	protein_coding	7.23e-04	0.221438	-2.86250	5.31e+00	6.25e-03	5.31e+00	6.25e-03	3.08e-01	1.36e-03	3.23e-01	1.43e-03	5.81e-02	2.18e-01	6.09e-02	2.28e-01	2.29e+00	7.22e-04	2.29e+00	7.22e-04	1.00e+00	5.67e-04	1.05e+00	5.94e-04	0.436463	0.785674	0.457569	0.823667	5.52e+00	5.09e+00	7.22e-03	5.29e-03	1.58e+00	3.00e+00	3.21e-04	1.12e-03
chr17	76108998	76124875	NM_001127198	0.6165	-	TMC6	protein_coding	7.55e-04	0.225316	-2.94190	6.02e+00	4.53e-03	6.02e+00	4.53e-03	9.94e-01	2.94e-03	1.04e+00	3.08e-03	1.65e-01	6.48e-01	1.73e-01	6.80e-01	3.25e+00	5.35e-04	3.25e+00	5.35e-04	1.07e-01	4.45e-05	1.13e-01	4.67e-05	0.033113	0.083189	0.034714	0.087212	6.73e+00	5.32e+00	6.61e-03	2.46e-03	3.32e+00	3.17e+00	5.67e-04	5.04e-04
chr6	154726432	154831793	NM_173515	0.4290	-	CNKSR3	protein_coding	8.74e-04	0.252476	-1.88164	7.07e+00	1.27e-03	7.07e+00	1.27e-03	9.87e-02	8.72e-05	1.03e-01	9.15e-05	1.40e-02	6.89e-02	1.46e-02	7.22e-02	5.19e+00	3.37e-04	5.19e+00	3.37e-04	8.39e-02	2.01e-05	8.80e-02	2.11e-05	0.016169	0.059756	0.016951	0.062645	7.14e+00	7.00e+00	1.33e-03	1.21e-03	5.25e+00	5.13e+00	3.51e-04	3.23e-04
chr7	80371851	80548667	NM_006379	0.3576	-	SEMA3C	protein_coding	8.91e-04	0.252476	-2.70352	7.63e+00	1.32e-03	7.63e+00	1.32e-03	1.23e+00	1.01e-03	1.29e+00	1.06e-03	1.61e-01	7.66e-01	1.69e-01	8.03e-01	5.15e+00	1.98e-04	5.15e+00	1.98e-04	3.43e-01	4.80e-05	3.60e-01	5.03e-05	0.066655	0.242437	0.069879	0.254160	8.50e+00	6.75e+00	2.04e-03	6.05e-04	5.39e+00	4.91e+00	2.32e-04	1.64e-04
chr16	67471916	67515089	NM_004691	0.5377	-	ATP6V0D1	protein_coding	9.47e-04	0.261665	1.85631	7.21e+00	3.43e-03	7.21e+00	3.43e-03	1.65e-01	3.93e-04	1.73e-01	4.12e-04	2.28e-02	1.15e-01	2.39e-02	1.20e-01	9.00e+00	1.25e-02	9.00e+00	1.25e-02	6.68e-01	5.59e-03	7.00e-01	5.86e-03	0.074187	0.447769	0.077774	0.469421	7.10e+00	7.33e+00	3.15e-03	3.71e-03	9.47e+00	8.53e+00	1.64e-02	8.52e-03
chr22	35796115	35820495	NM_006739	0.5270	+	MCM5	protein_coding	1.00e-03	0.270049	1.83988	8.92e+00	2.03e-02	8.92e+00	2.03e-02	4.18e-01	5.80e-03	4.38e-01	6.08e-03	4.68e-02	2.86e-01	4.91e-02	3.00e-01	1.07e+01	7.26e-02	1.07e+01	7.26e-02	6.06e-01	2.96e-02	6.35e-01	3.11e-02	0.056442	0.408054	0.059171	0.427786	8.63e+00	9.22e+00	1.62e-02	2.44e-02	1.12e+01	1.03e+01	9.36e-02	5.17e-02
chr3	122628039	122694981	NM_001256347	0.5022	-	SEMA5B	nonsense_mediated_decay	1.05e-03	0.272600	-3.80735	6.59e+00	1.55e-03	6.59e+00	1.55e-03	8.64e-01	8.87e-04	9.06e-01	9.30e-04	1.31e-01	5.71e-01	1.38e-01	5.99e-01	2.90e+00	9.71e-05	2.90e+00	9.71e-05	1.36e-01	1.06e-05	1.43e-01	1.11e-05	0.046913	0.108786	0.049182	0.114046	5.98e+00	7.20e+00	9.26e-04	2.18e-03	2.81e+00	3.00e+00	8.96e-05	1.05e-04
chrX	70145429	70150975	NM_032803	0.5048	-	SLC7A3	protein_coding	1.06e-03	0.272600	-3.04103	5.50e+00	9.47e-03	5.50e+00	9.47e-03	1.21e+00	7.27e-03	1.27e+00	7.62e-03	2.20e-01	7.68e-01	2.31e-01	8.05e-01	2.66e+00	9.92e-04	2.66e+00	9.92e-04	4.79e-01	3.82e-04	5.03e-01	4.01e-04	0.180186	0.385695	0.188899	0.404345	4.64e+00	6.36e+00	4.33e-03	1.46e-02	2.32e+00	3.00e+00	7.21e-04	1.26e-03
chr11	64532075	64545938	NM_001178030	0.4882	-	SF1	protein_coding	1.08e-03	0.272600	1.70563	1.11e+01	1.59e-01	1.11e+01	1.59e-01	2.18e-01	2.40e-02	2.29e-01	2.52e-02	1.97e-02	1.51e-01	2.06e-02	1.58e-01	1.28e+01	5.20e-01	1.28e+01	5.20e-01	2.35e-01	8.42e-02	2.46e-01	8.83e-02	0.018340	0.162087	0.019227	0.169925	1.09e+01	1.13e+01	1.42e-01	1.76e-01	1.26e+01	1.30e+01	4.60e-01	5.79e-01
chr2	173600524	173917620	NM_007023	0.4051	+	RAPGEF4	protein_coding	1.14e-03	0.279720	-1.98606	6.68e+00	3.22e-04	6.68e+00	3.22e-04	1.59e-01	3.57e-05	1.66e-01	3.74e-05	2.38e-02	1.11e-01	2.49e-02	1.16e-01	4.67e+00	7.88e-05	4.67e+00	7.88e-05	3.97e-01	2.23e-05	4.17e-01	2.34e-05	0.085017	0.282843	0.089129	0.296520	6.79e+00	6.57e+00	3.47e-04	2.96e-04	4.95e+00	4.39e+00	9.46e-05	6.31e-05
chr8	11561659	11617511	NM_002052	0.4736	+	GATA4	protein_coding	1.22e-03	0.289569	-2.15791	7.17e+00	2.66e-03	7.17e+00	2.66e-03	5.52e-01	1.00e-03	5.79e-01	1.05e-03	7.70e-02	3.76e-01	8.07e-02	3.94e-01	5.05e+00	5.82e-04	5.05e+00	5.82e-04	2.76e-01	1.14e-04	2.89e-01	1.19e-04	0.054569	0.195814	0.057208	0.205283	6.78e+00	7.56e+00	1.95e-03	3.37e-03	4.86e+00	5.25e+00	5.01e-04	6.62e-04
chr4	162305043	163085186	NM_020116	0.3382	-	FSTL5	protein_coding	1.23e-03	0.289569	-1.83611	7.99e+00	3.40e-04	7.99e+00	3.40e-04	6.42e-01	1.47e-04	6.73e-01	1.54e-04	8.04e-02	4.32e-01	8.42e-02	4.53e-01	6.19e+00	9.42e-05	6.19e+00	9.42e-05	4.31e-01	2.81e-05	4.52e-01	2.95e-05	0.069623	0.298236	0.072990	0.312657	8.44e+00	7.53e+00	4.44e-04	2.36e-04	5.88e+00	6.49e+00	7.43e-05	1.14e-04
chr5	36103413	36152015	NM_001007527	0.3602	-	LMBRD2	protein_coding	1.33e-03	0.299792	-2.89077	5.47e+00	8.95e-04	5.47e+00	8.95e-04	2.07e-01	1.31e-04	2.17e-01	1.37e-04	3.79e-02	1.46e-01	3.97e-02	1.53e-01	1.73e+00	1.03e-04	1.73e+00	1.03e-04	2.45e+00	1.45e-04	2.56e+00	1.53e-04	1.414214	1.414214	1.482600	1.482600	5.61e+00	5.32e+00	9.88e-04	8.02e-04	0.00e+00	3.46e+00	0.00e+00	2.06e-04
chr2	21224300	21266945	NM_000384	0.4297	-	APOB	protein_coding	1.34e-03	0.299792	-4.32193	4.12e+00	9.15e-04	4.12e+00	9.15e-04	3.00e+00	1.19e-03	3.15e+00	1.25e-03	7.28e-01	1.31e+00	7.64e-01	1.37e+00	7.92e-01	2.34e-05	7.92e-01	2.34e-05	1.12e+00	3.32e-05	1.17e+00	3.48e-05	1.414214	1.414214	1.482600	1.482600	6.25e+00	2.00e+00	1.76e-03	7.03e-05	1.58e+00	0.00e+00	4.69e-05	0.00e+00
chr6	154360545	154414655	NM_001008505	0.3729	+	OPRM1	protein_coding	1.38e-03	0.299792	-2.31703	7.01e+00	2.70e-03	7.01e+00	2.70e-03	1.06e+00	1.83e-03	1.11e+00	1.92e-03	1.51e-01	6.78e-01	1.58e-01	7.11e-01	4.71e+00	5.27e-04	4.71e+00	5.27e-04	1.01e+00	3.53e-04	1.06e+00	3.70e-04	0.213981	0.669891	0.224329	0.702284	6.27e+00	7.76e+00	1.40e-03	3.99e-03	4.00e+00	5.43e+00	2.77e-04	7.76e-04
chr4	7760439	7941653	NM_001134647	0.4639	-	AFAP1	protein_coding	1.38e-03	0.299792	-2.51785	5.92e+00	3.42e-04	5.92e+00	3.42e-04	6.00e-01	1.40e-04	6.29e-01	1.47e-04	1.01e-01	4.11e-01	1.06e-01	4.30e-01	3.08e+00	5.52e-05	3.08e+00	5.52e-05	1.53e+00	5.46e-05	1.61e+00	5.73e-05	0.497370	0.989949	0.521421	1.037820	5.49e+00	6.34e+00	2.43e-04	4.41e-04	4.17e+00	2.00e+00	9.38e-05	1.66e-05
chr11	5363743	5526882	NM_001005567	0.3927	-	OR51B5	processed_transcript	1.40e-03	0.299792	1.82736	7.64e+00	1.22e-03	7.64e+00	1.22e-03	7.67e-02	6.50e-05	8.04e-02	6.82e-05	1.00e-02	5.34e-02	1.05e-02	5.60e-02	9.32e+00	4.33e-03	9.32e+00	4.33e-03	9.47e-01	2.66e-03	9.93e-01	2.79e-03	0.101680	0.614093	0.106596	0.643788	7.58e+00	7.69e+00	1.17e-03	1.26e-03	9.99e+00	8.65e+00	6.22e-03	2.45e-03
chr20	54572412	54580528	NM_080617	0.4383	-	CBLN4	protein_coding	1.47e-03	0.307870	2.89885	3.38e+00	1.36e-03	3.38e+00	1.36e-03	1.12e+00	1.05e-03	1.17e+00	1.10e-03	3.32e-01	7.71e-01	3.48e-01	8.09e-01	6.42e+00	1.09e-02	6.42e+00	1.09e-02	6.23e-01	4.62e-03	6.53e-01	4.84e-03	0.097037	0.423465	0.101730	0.443942	2.58e+00	4.17e+00	6.16e-04	2.09e-03	5.98e+00	6.86e+00	7.64e-03	1.42e-02
chr5	15500304	15939905	NM_012304	0.3982	+	FBXL7	protein_coding	1.52e-03	0.312312	-1.80073	9.22e+00	1.36e-03	9.22e+00	1.36e-03	1.52e-01	1.43e-04	1.60e-01	1.50e-04	1.65e-02	1.06e-01	1.73e-02	1.11e-01	7.32e+00	3.88e-04	7.32e+00	3.88e-04	7.93e-01	2.04e-04	8.31e-01	2.14e-04	0.108412	0.526701	0.113655	0.552171	9.33e+00	9.11e+00	1.46e-03	1.26e-03	6.75e+00	7.88e+00	2.43e-04	5.32e-04
chr19	33865429	33873592	NM_001252296	0.4129	+	CEBPG	protein_coding	1.60e-03	0.322937	-1.92600	8.19e+00	3.83e-02	8.19e+00	3.83e-02	7.89e-01	2.00e-02	8.27e-01	2.10e-02	9.63e-02	5.23e-01	1.01e-01	5.48e-01	6.19e+00	9.98e-03	6.19e+00	9.98e-03	1.03e+00	6.67e-03	1.08e+00	6.99e-03	0.166739	0.668064	0.174802	0.700369	7.63e+00	8.74e+00	2.41e-02	5.24e-02	5.46e+00	6.92e+00	5.27e-03	1.47e-02
chr17	64298925	64806862	NM_002737	0.4385	+	PRKCA	protein_coding	1.68e-03	0.333943	-1.72165	1.04e+01	2.80e-03	1.04e+01	2.80e-03	4.12e-01	7.89e-04	4.32e-01	8.27e-04	3.95e-02	2.82e-01	4.14e-02	2.96e-01	8.75e+00	8.47e-04	8.75e+00	8.47e-04	1.90e-01	1.11e-04	1.99e-01	1.17e-04	0.021714	0.131555	0.022764	0.137916	1.02e+01	1.07e+01	2.24e-03	3.35e-03	8.88e+00	8.61e+00	9.25e-04	7.68e-04
chr8	11351520	11422108	NM_001715	0.4741	+	BLK	protein_coding	1.76e-03	0.344324	-2.46467	6.02e+00	9.63e-04	6.02e+00	9.63e-04	7.07e-01	4.61e-04	7.41e-01	4.83e-04	1.17e-01	4.78e-01	1.23e-01	5.01e-01	3.32e+00	1.63e-04	3.32e+00	1.63e-04	1.41e+00	1.50e-04	1.48e+00	1.58e-04	0.425721	0.922313	0.446307	0.966913	5.52e+00	6.52e+00	6.38e-04	1.29e-03	2.32e+00	4.32e+00	5.67e-05	2.69e-04

Download the DEG result list for Prol_vs_D8minus.
Download the whole result list for Prol_vs_D8minus.

DEG table for the contrast Prol_vs_D8plus

The following table presents the top 10% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Prol_vs_D8plus. The fields of the table correspond to the requested features to be exported. The table can be searched using the search field on the top right.

chromosome	start	end	gene_id	gc_content	strand	gene_name	biotype	p-value_edger	FDR_edger	log2_normalized_fold_change_Prol_vs_D8plus	log2_normalized_mean_counts_Prol	rpgm_normalized_mean_counts_Prol	log2_normalized_median_counts_Prol	rpgm_normalized_median_counts_Prol	log2_normalized_sd_counts_Prol	rpgm_normalized_sd_counts_Prol	log2_normalized_mad_counts_Prol	rpgm_normalized_mad_counts_Prol	log2_normalized_cv_counts_Prol	rpgm_normalized_cv_counts_Prol	log2_normalized_rcv_counts_Prol	rpgm_normalized_rcv_counts_Prol	log2_normalized_mean_counts_D8plus	rpgm_normalized_mean_counts_D8plus	log2_normalized_median_counts_D8plus	rpgm_normalized_median_counts_D8plus	log2_normalized_sd_counts_D8plus	rpgm_normalized_sd_counts_D8plus	log2_normalized_mad_counts_D8plus	rpgm_normalized_mad_counts_D8plus	log2_normalized_cv_counts_D8plus	rpgm_normalized_cv_counts_D8plus	log2_normalized_rcv_counts_D8plus	rpgm_normalized_rcv_counts_D8plus	log2_normalized_counts_IT3R59_24_Prol	log2_normalized_counts_IT3R63_28_Prol	rpgm_normalized_counts_IT3R59_24_Prol	rpgm_normalized_counts_IT3R63_28_Prol	log2_normalized_counts_IT3R62_27_D8plus	log2_normalized_counts_IT3R67_32_D8plus	rpgm_normalized_counts_IT3R62_27_D8plus	rpgm_normalized_counts_IT3R67_32_D8plus
chr2	72356366	72374991	NM_019885	0.5985	-	CYP26B1	protein_coding	2.99e-36	3.38e-32	10.555907	1.95e+00	1.61e-04	1.95e+00	1.61e-04	5.21e-01	7.59e-05	5.46e-01	7.96e-05	2.67e-01	4.71e-01	2.80e-01	4.94e-01	1.25e+01	3.23e-01	1.25e+01	3.23e-01	3.92e-01	8.67e-02	4.10e-01	9.09e-02	0.031247	0.268138	0.032758	0.281104	2.32e+00	1.58e+00	2.15e-04	1.07e-04	1.28e+01	1.23e+01	3.85e-01	2.62e-01
chr10	94833646	94837641	NM_000783	0.5168	+	CYP26A1	protein_coding	3.94e-20	1.77e-16	9.609794	5.00e-01	1.25e-04	5.00e-01	1.25e-04	7.07e-01	1.77e-04	7.41e-01	1.86e-04	1.41e+00	1.41e+00	1.48e+00	1.48e+00	1.00e+01	2.93e-01	1.00e+01	2.93e-01	1.02e+00	1.91e-01	1.07e+00	2.00e-01	0.101430	0.652157	0.106335	0.683693	0.00e+00	1.00e+00	0.00e+00	2.50e-04	1.07e+01	9.30e+00	4.28e-01	1.58e-01
chr1	12627938	12677737	NM_004753	0.5131	-	DHRS3	protein_coding	4.69e-20	1.77e-16	6.842185	3.20e+00	1.71e-04	3.20e+00	1.71e-04	5.50e-01	7.10e-05	5.76e-01	7.44e-05	1.72e-01	4.16e-01	1.80e-01	4.36e-01	1.01e+01	2.19e-02	1.01e+01	2.19e-02	1.73e-01	2.61e-03	1.81e-01	2.74e-03	0.017116	0.119474	0.017944	0.125252	2.81e+00	3.58e+00	1.20e-04	2.21e-04	9.96e+00	1.02e+01	2.00e-02	2.37e-02
chr9	87283372	87641985	NM_006180	0.4094	+	NTRK2	protein_coding	2.47e-10	7.00e-07	4.032843	4.81e+00	7.67e-05	4.81e+00	7.67e-05	3.25e-01	1.77e-05	3.41e-01	1.86e-05	6.75e-02	2.31e-01	7.07e-02	2.43e-01	8.82e+00	1.30e-03	8.82e+00	1.30e-03	5.21e-01	4.59e-04	5.46e-01	4.82e-04	0.059022	0.353933	0.061876	0.371048	4.58e+00	5.04e+00	6.41e-05	8.92e-05	8.45e+00	9.19e+00	9.73e-04	1.62e-03
chr11	111126706	111157129	NM_198498	0.4140	+	C11orf53	protein_coding	3.27e-10	7.42e-07	5.599913	1.00e+00	3.29e-05	1.00e+00	3.29e-05	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.60e+00	3.16e-03	6.60e+00	3.16e-03	6.31e-02	1.39e-04	6.62e-02	1.46e-04	0.009565	0.044194	0.010028	0.046331	1.00e+00	1.00e+00	3.29e-05	3.29e-05	6.64e+00	6.55e+00	3.25e-03	3.06e-03
chr10	48425778	48439138	NM_004962	0.5292	-	GDF10	protein_coding	4.44e-09	8.38e-06	6.037089	5.00e-01	3.74e-05	5.00e-01	3.74e-05	7.07e-01	5.29e-05	7.41e-01	5.55e-05	1.41e+00	1.41e+00	1.48e+00	1.48e+00	6.47e+00	7.30e-03	6.47e+00	7.30e-03	9.68e-01	4.60e-03	1.01e+00	4.83e-03	0.149654	0.630957	0.156891	0.661468	0.00e+00	1.00e+00	0.00e+00	7.49e-05	5.78e+00	7.15e+00	4.04e-03	1.06e-02
chr12	103351451	103354294	NM_004316	0.5130	+	ASCL1	protein_coding	2.06e-08	3.33e-05	-4.813781	7.52e+00	7.88e-02	7.52e+00	7.88e-02	1.36e+00	6.52e-02	1.42e+00	6.83e-02	1.81e-01	8.27e-01	1.90e-01	8.67e-01	3.00e+00	2.46e-03	3.00e+00	2.46e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.000000	0.000000	0.000000	0.000000	6.55e+00	8.48e+00	3.27e-02	1.25e-01	3.00e+00	3.00e+00	2.46e-03	2.46e-03
chr8	21971931	21988565	NM_005144	0.6065	-	HR	protein_coding	8.85e-08	1.25e-04	-4.898853	6.46e+00	5.32e-03	6.46e+00	5.32e-03	3.57e-01	1.32e-03	3.74e-01	1.38e-03	5.52e-02	2.48e-01	5.79e-02	2.60e-01	1.50e+00	1.20e-04	1.50e+00	1.20e-04	7.07e-01	8.50e-05	7.41e-01	8.91e-05	0.471405	0.707107	0.494200	0.741300	6.21e+00	6.71e+00	4.39e-03	6.25e-03	2.00e+00	1.00e+00	1.80e-04	6.01e-05
chr1	156669399	156675459	NM_001878	0.5516	-	CRABP2	protein_coding	1.68e-07	1.91e-04	3.844542	9.15e+00	9.37e-02	9.15e+00	9.37e-02	1.94e-01	1.26e-02	2.04e-01	1.32e-02	2.12e-02	1.34e-01	2.23e-02	1.41e-01	1.30e+01	1.35e+00	1.30e+01	1.35e+00	2.95e-02	2.75e-02	3.09e-02	2.89e-02	0.002266	0.020418	0.002376	0.021405	9.28e+00	9.01e+00	1.03e-01	8.48e-02	1.30e+01	1.30e+01	1.37e+00	1.33e+00
chr4	159045731	159094202	NM_001128424	0.3710	-	FAM198B	protein_coding	1.69e-07	1.91e-04	3.740568	3.73e+00	2.89e-04	3.73e+00	2.89e-04	1.03e+00	2.04e-04	1.08e+00	2.14e-04	2.77e-01	7.07e-01	2.90e-01	7.41e-01	7.54e+00	4.12e-03	7.54e+00	4.12e-03	7.96e-01	2.17e-03	8.35e-01	2.28e-03	0.105594	0.528115	0.110700	0.553653	4.46e+00	3.00e+00	4.33e-04	1.44e-04	8.10e+00	6.98e+00	5.65e-03	2.58e-03
chr8	120569316	120651106	NM_006209	0.3892	-	ENPP2	protein_coding	2.48e-07	2.53e-04	4.889613	3.71e+00	1.59e-04	3.71e+00	1.59e-04	7.62e-01	8.65e-05	7.99e-01	9.06e-05	2.06e-01	5.44e-01	2.15e-01	5.70e-01	8.34e+00	5.06e-03	8.34e+00	5.06e-03	1.48e+00	4.46e-03	1.56e+00	4.68e-03	0.177938	0.881321	0.186543	0.923939	4.25e+00	3.17e+00	2.20e-04	9.78e-05	9.39e+00	7.29e+00	8.22e-03	1.91e-03
chr4	107842958	107957453	NM_014421	0.3622	-	DKK2	protein_coding	2.68e-07	2.53e-04	3.439112	4.17e+00	1.62e-04	4.17e+00	1.62e-04	8.27e-01	9.26e-05	8.67e-01	9.71e-05	1.98e-01	5.73e-01	2.08e-01	6.01e-01	7.72e+00	1.84e-03	7.72e+00	1.84e-03	1.40e-01	1.79e-04	1.47e-01	1.88e-04	0.018145	0.097416	0.019022	0.102127	3.58e+00	4.75e+00	9.61e-05	2.27e-04	7.82e+00	7.62e+00	1.97e-03	1.71e-03
chr10	74033676	74035794	NM_019058	0.5866	+	DDIT4	protein_coding	7.51e-07	6.54e-04	-4.003002	7.52e+00	1.13e-01	7.52e+00	1.13e-01	1.57e+00	1.04e-01	1.65e+00	1.09e-01	2.09e-01	9.18e-01	2.19e-01	9.63e-01	3.89e+00	6.61e-03	3.89e+00	6.61e-03	2.74e-01	1.34e-03	2.87e-01	1.40e-03	0.070280	0.202031	0.073678	0.211800	6.41e+00	8.63e+00	3.97e-02	1.86e-01	4.09e+00	3.70e+00	7.55e-03	5.67e-03
chr3	139654026	140286919	NM_022131	0.4268	+	CLSTN2	protein_coding	1.05e-06	8.50e-04	2.989833	5.47e+00	6.87e-05	5.47e+00	6.87e-05	2.07e-01	1.01e-05	2.17e-01	1.05e-05	3.79e-02	1.46e-01	3.97e-02	1.53e-01	8.32e+00	5.57e-04	8.32e+00	5.57e-04	9.28e-01	3.36e-04	9.73e-01	3.53e-04	0.111483	0.603799	0.116874	0.632997	5.61e+00	5.32e+00	7.58e-05	6.16e-05	7.67e+00	8.98e+00	3.19e-04	7.95e-04
chr1	11917520	11918992	NM_002521	0.5451	-	NPPB	protein_coding	1.19e-06	8.81e-04	4.169925	2.08e+00	2.38e-03	2.08e+00	2.38e-03	7.07e-01	1.44e-03	7.41e-01	1.51e-03	3.39e-01	6.06e-01	3.56e-01	6.35e-01	6.01e+00	5.43e-02	6.01e+00	5.43e-02	1.43e+00	4.71e-02	1.50e+00	4.94e-02	0.237895	0.866206	0.249399	0.908092	1.58e+00	2.58e+00	1.36e-03	3.40e-03	5.00e+00	7.02e+00	2.11e-02	8.76e-02
chr3	25469753	25639422	NM_000965	0.4175	+	RARB	protein_coding	1.24e-06	8.81e-04	3.662965	4.91e+00	1.71e-04	4.91e+00	1.71e-04	6.80e-02	8.34e-06	7.13e-02	8.74e-06	1.39e-02	4.88e-02	1.45e-02	5.11e-02	8.34e+00	2.23e-03	8.34e+00	2.23e-03	1.19e+00	1.66e-03	1.24e+00	1.74e-03	0.142256	0.742555	0.149135	0.778463	4.95e+00	4.86e+00	1.77e-04	1.65e-04	7.50e+00	9.18e+00	1.06e-03	3.41e-03
chr2	113587336	113594356	NM_000576	0.4556	-	IL1B	protein_coding	1.33e-06	8.88e-04	7.238405	5.00e-01	7.12e-05	5.00e-01	7.12e-05	7.07e-01	1.01e-04	7.41e-01	1.06e-04	1.41e+00	1.41e+00	1.48e+00	1.48e+00	7.24e+00	3.21e-02	7.24e+00	3.21e-02	1.96e+00	3.39e-02	2.05e+00	3.56e-02	0.270246	1.056741	0.283314	1.107841	1.00e+00	0.00e+00	1.42e-04	0.00e+00	8.63e+00	5.86e+00	5.61e-02	8.12e-03
chr11	111169270	111179460	NM_001271458	0.4525	+	COLCA2	protein_coding	3.30e-06	2.08e-03	4.930737	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	NaN	NaN	NaN	NaN	4.77e+00	2.89e-03	4.77e+00	2.89e-03	9.70e-01	1.87e-03	1.02e+00	1.96e-03	0.203234	0.647182	0.213062	0.678478	0.00e+00	0.00e+00	0.00e+00	0.00e+00	4.09e+00	5.46e+00	1.57e-03	4.22e-03
chr4	141481049	141489959	NM_021833	0.4023	-	UCP1	protein_coding	9.16e-06	5.24e-03	4.375039	1.00e+00	1.12e-04	1.00e+00	1.12e-04	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.10e+00	4.55e-03	5.10e+00	4.55e-03	1.31e+00	3.73e-03	1.37e+00	3.91e-03	0.257032	0.820593	0.269462	0.860274	1.00e+00	1.00e+00	1.12e-04	1.12e-04	6.02e+00	4.17e+00	7.18e-03	1.91e-03
chr7	1272017	1276962	NM_001080461	0.6638	+	UNCX	protein_coding	9.25e-06	5.24e-03	4.686501	1.00e+00	2.02e-04	1.00e+00	2.02e-04	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.35e+00	1.02e-02	5.35e+00	1.02e-02	1.45e+00	9.01e-03	1.52e+00	9.44e-03	0.271436	0.882133	0.284561	0.924790	1.00e+00	1.00e+00	2.02e-04	2.02e-04	6.38e+00	4.32e+00	1.66e-02	3.84e-03
chr1	852197	855072	NR_026874	0.6127	-	LOC100130417	lincRNA	1.09e-05	5.89e-03	-4.930737	4.55e+00	1.03e-02	4.55e+00	1.03e-02	1.54e+00	9.59e-03	1.62e+00	1.01e-02	3.39e-01	9.35e-01	3.56e-01	9.80e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	NaN	NaN	NaN	NaN	3.46e+00	5.64e+00	3.48e-03	1.70e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr16	22825859	22927659	NM_006043	0.4338	+	HS3ST2	protein_coding	1.22e-05	6.28e-03	3.341468	3.29e+00	9.82e-05	3.29e+00	9.82e-05	1.00e+00	6.95e-05	1.05e+00	7.28e-05	3.04e-01	7.07e-01	3.19e-01	7.41e-01	6.76e+00	1.09e-03	6.76e+00	1.09e-03	5.14e-01	3.82e-04	5.39e-01	4.01e-04	0.076055	0.351954	0.079733	0.368973	2.58e+00	4.00e+00	4.91e-05	1.47e-04	7.12e+00	6.39e+00	1.36e-03	8.15e-04
chr3	35721278	35835988	NM_001267619	0.3664	+	ARPP21	protein_coding	1.58e-05	7.44e-03	3.471306	2.29e+00	3.92e-05	2.29e+00	3.92e-05	1.00e+00	3.08e-05	1.05e+00	3.23e-05	4.36e-01	7.86e-01	4.58e-01	8.24e-01	5.93e+00	5.23e-04	5.93e+00	5.23e-04	1.00e-01	3.70e-05	1.05e-01	3.88e-05	0.016938	0.070711	0.017757	0.074130	1.58e+00	3.00e+00	1.74e-05	6.10e-05	6.00e+00	5.86e+00	5.49e-04	4.97e-04
chr8	97505881	97624037	NM_002998	0.4136	+	SDC2	protein_coding	1.63e-05	7.44e-03	-2.320146	8.62e+00	3.41e-03	8.62e+00	3.41e-03	4.70e-01	1.10e-03	4.92e-01	1.15e-03	5.45e-02	3.21e-01	5.71e-02	3.36e-01	6.34e+00	6.77e-04	6.34e+00	6.77e-04	1.26e-01	5.98e-05	1.32e-01	6.27e-05	0.019899	0.088388	0.020862	0.092662	8.95e+00	8.29e+00	4.19e-03	2.64e-03	6.25e+00	6.43e+00	6.35e-04	7.19e-04
chr5	121647763	121799914	NM_005460	0.3913	+	SNCAIP	protein_coding	1.64e-05	7.44e-03	3.300124	3.29e+00	5.92e-05	3.29e+00	5.92e-05	4.14e-01	1.86e-05	4.34e-01	1.95e-05	1.26e-01	3.14e-01	1.32e-01	3.29e-01	6.37e+00	6.41e-04	6.37e+00	6.41e-04	1.24e+00	4.97e-04	1.30e+00	5.21e-04	0.194938	0.776004	0.204364	0.813529	3.00e+00	3.58e+00	4.60e-05	7.23e-05	5.49e+00	7.25e+00	2.89e-04	9.92e-04
chr11	34172533	34379555	NM_145804	0.4792	-	ABTB2	protein_coding	1.88e-05	8.18e-03	3.090321	5.42e+00	2.10e-04	5.42e+00	2.10e-04	5.89e-01	8.54e-05	6.17e-01	8.95e-05	1.09e-01	4.06e-01	1.14e-01	4.26e-01	8.33e+00	1.83e-03	8.33e+00	1.83e-03	1.20e+00	1.37e-03	1.26e+00	1.43e-03	0.143754	0.748261	0.150705	0.784444	5.00e+00	5.83e+00	1.50e-04	2.71e-04	7.48e+00	9.18e+00	8.60e-04	2.79e-03
chr7	31092075	31151093	NM_001199635	0.5189	+	ADCYAP1R1	protein_coding	2.20e-05	9.22e-03	-2.632268	6.74e+00	1.82e-03	6.74e+00	1.82e-03	3.13e-01	3.95e-04	3.28e-01	4.14e-04	4.64e-02	2.17e-01	4.86e-02	2.28e-01	4.10e+00	2.80e-04	4.10e+00	2.80e-04	4.14e-01	8.39e-05	4.34e-01	8.79e-05	0.100890	0.299985	0.105768	0.314491	6.97e+00	6.52e+00	2.10e-03	1.54e-03	3.81e+00	4.39e+00	2.20e-04	3.39e-04
chr6	1610680	1614129	NM_001453	0.5333	+	FOXC1	protein_coding	2.60e-05	1.05e-02	2.253392	8.31e+00	9.22e-02	8.31e+00	9.22e-02	1.41e-01	9.02e-03	1.48e-01	9.46e-03	1.70e-02	9.78e-02	1.78e-02	1.03e-01	1.05e+01	4.41e-01	1.05e+01	4.41e-01	5.09e-01	1.53e-01	5.34e-01	1.60e-01	0.048386	0.346110	0.050726	0.362847	8.21e+00	8.41e+00	8.58e-02	9.86e-02	1.02e+01	1.09e+01	3.33e-01	5.49e-01
chr5	146770370	146889619	NM_001197294	0.4143	-	DPYSL3	protein_coding	3.00e-05	1.17e-02	2.495272	9.79e+00	7.49e-03	9.79e+00	7.49e-03	2.77e-01	1.43e-03	2.90e-01	1.50e-03	2.82e-02	1.91e-01	2.96e-02	2.00e-01	1.23e+01	4.23e-02	1.23e+01	4.23e-02	1.47e-01	4.30e-03	1.54e-01	4.51e-03	0.011946	0.101666	0.012524	0.106583	9.99e+00	9.60e+00	8.50e-03	6.48e-03	1.22e+01	1.24e+01	3.92e-02	4.53e-02
chr7	41724711	41742706	NM_002192	0.4168	-	INHBA	protein_coding	3.25e-05	1.19e-02	2.500694	4.45e+00	1.25e-03	4.45e+00	1.25e-03	7.73e-01	6.68e-04	8.10e-01	7.00e-04	1.74e-01	5.34e-01	1.82e-01	5.60e-01	7.05e+00	7.34e-03	7.05e+00	7.34e-03	2.00e-01	1.02e-03	2.10e-01	1.07e-03	0.028385	0.139279	0.029757	0.146014	5.00e+00	3.91e+00	1.72e-03	7.78e-04	6.91e+00	7.19e+00	6.61e-03	8.06e-03
chr2	136871918	136875725	NM_003467	0.5200	-	CXCR4	protein_coding	3.26e-05	1.19e-02	-2.509387	9.21e+00	1.56e-01	9.21e+00	1.56e-01	2.31e-01	2.49e-02	2.42e-01	2.61e-02	2.51e-02	1.60e-01	2.63e-02	1.67e-01	6.70e+00	2.72e-02	6.70e+00	2.72e-02	1.86e-01	3.53e-03	1.95e-01	3.70e-03	0.027755	0.129807	0.029097	0.136084	9.37e+00	9.04e+00	1.74e-01	1.38e-01	6.83e+00	6.57e+00	2.97e-02	2.47e-02
chr2	12856997	12882858	NM_021643	0.4771	+	TRIB2	protein_coding	4.50e-05	1.50e-02	2.117205	9.25e+00	2.35e-02	9.25e+00	2.35e-02	3.34e-03	5.47e-05	3.51e-03	5.73e-05	3.61e-04	2.32e-03	3.79e-04	2.43e-03	1.14e+01	1.02e-01	1.14e+01	1.02e-01	2.27e-02	1.61e-03	2.38e-02	1.69e-03	0.002000	0.015770	0.002097	0.016532	9.25e+00	9.26e+00	2.35e-02	2.36e-02	1.14e+01	1.14e+01	1.03e-01	1.01e-01
chr11	30431617	30602040	NM_001584	0.3944	-	MPPED2	protein_coding	4.54e-05	1.50e-02	2.136502	6.03e+00	3.78e-04	6.03e+00	3.78e-04	7.79e-02	2.07e-05	8.17e-02	2.17e-05	1.29e-02	5.48e-02	1.35e-02	5.75e-02	8.15e+00	1.68e-03	8.15e+00	1.68e-03	3.29e-01	3.82e-04	3.45e-01	4.00e-04	0.040324	0.226668	0.042274	0.237629	6.09e+00	5.98e+00	3.93e-04	3.64e-04	7.92e+00	8.38e+00	1.41e-03	1.95e-03
chr5	172741725	172756506	NM_003714	0.5093	-	STC2	protein_coding	4.72e-05	1.50e-02	-3.823657	7.79e+00	2.10e-02	7.79e+00	2.10e-02	1.79e+00	2.10e-02	1.87e+00	2.20e-02	2.30e-01	1.00e+00	2.41e-01	1.05e+00	4.46e+00	1.42e-03	4.46e+00	1.42e-03	9.28e-02	9.57e-05	9.73e-02	1.00e-04	0.020818	0.067344	0.021824	0.070600	6.52e+00	9.05e+00	6.16e-03	3.59e-02	4.52e+00	4.39e+00	1.49e-03	1.35e-03
chr7	120628750	120937498	NM_024913	0.3660	+	CPED1	protein_coding	4.73e-05	1.50e-02	2.180572	5.90e+00	1.91e-04	5.90e+00	1.91e-04	2.39e-01	3.21e-05	2.51e-01	3.36e-05	4.05e-02	1.68e-01	4.25e-02	1.76e-01	8.06e+00	8.78e-04	8.06e+00	8.78e-04	3.64e-01	2.20e-04	3.81e-01	2.30e-04	0.045118	0.250488	0.047299	0.262601	5.73e+00	6.07e+00	1.68e-04	2.14e-04	8.32e+00	7.81e+00	1.03e-03	7.22e-04
chr2	21224300	21266945	NM_000384	0.4297	-	APOB	protein_coding	4.79e-05	1.50e-02	-5.321928	4.12e+00	9.15e-04	4.12e+00	9.15e-04	3.00e+00	1.19e-03	3.15e+00	1.25e-03	7.28e-01	1.31e+00	7.64e-01	1.37e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	NaN	NaN	NaN	NaN	6.25e+00	2.00e+00	1.76e-03	7.03e-05	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr7	1654105	1656328	NR_001288	0.3885	+	TFAMP1	processed_pseudogene	4.89e-05	1.50e-02	4.485427	1.29e+00	6.75e-04	1.29e+00	6.75e-04	4.14e-01	3.18e-04	4.34e-01	3.33e-04	3.20e-01	4.71e-01	3.36e-01	4.94e-01	5.36e+00	2.47e-02	5.36e+00	2.47e-02	1.69e+00	2.42e-02	1.77e+00	2.53e-02	0.314459	0.977093	0.329666	1.024342	1.58e+00	1.00e+00	9.00e-04	4.50e-04	4.17e+00	6.55e+00	7.65e-03	4.18e-02
chr2	45169036	45173216	NM_005413	0.5721	+	SIX3	protein_coding	5.12e-05	1.53e-02	-2.153805	9.79e+00	2.13e-01	9.79e+00	2.13e-01	1.26e-01	1.86e-02	1.32e-01	1.95e-02	1.29e-02	8.75e-02	1.35e-02	9.17e-02	7.61e+00	4.76e-02	7.61e+00	4.76e-02	4.14e-01	1.35e-02	4.34e-01	1.42e-02	0.054322	0.284264	0.056949	0.298010	9.88e+00	9.71e+00	2.26e-01	2.00e-01	7.32e+00	7.91e+00	3.80e-02	5.72e-02
chr14	96343108	96391908	NR_038861	0.4713	+	TUNAR	lincRNA	5.38e-05	1.56e-02	-3.013806	5.68e+00	1.06e-03	5.68e+00	1.06e-03	4.14e-01	3.04e-04	4.34e-01	3.19e-04	7.28e-02	2.88e-01	7.63e-02	3.02e-01	2.70e+00	1.13e-04	2.70e+00	1.13e-04	1.57e-01	1.45e-05	1.65e-01	1.52e-05	0.058326	0.128565	0.061146	0.134782	5.98e+00	5.39e+00	1.27e-03	8.40e-04	2.81e+00	2.58e+00	1.23e-04	1.02e-04
chr10	120789227	120793244	NM_199461	0.5087	+	NANOS1	protein_coding	5.64e-05	1.60e-02	2.162450	6.38e+00	2.12e-02	6.38e+00	2.12e-02	5.08e-01	7.39e-03	5.33e-01	7.75e-03	7.97e-02	3.49e-01	8.35e-02	3.66e-01	8.59e+00	9.56e-02	8.59e+00	9.56e-02	4.77e-02	3.17e-03	5.00e-02	3.32e-03	0.005554	0.033146	0.005823	0.034748	6.02e+00	6.74e+00	1.59e-02	2.64e-02	8.55e+00	8.62e+00	9.34e-02	9.78e-02
chr17	64298925	64806862	NM_002737	0.4385	+	PRKCA	protein_coding	6.74e-05	1.86e-02	-2.218170	1.04e+01	2.80e-03	1.04e+01	2.80e-03	4.12e-01	7.89e-04	4.32e-01	8.27e-04	3.95e-02	2.82e-01	4.14e-02	2.96e-01	8.19e+00	5.99e-04	8.19e+00	5.99e-04	6.30e-01	2.55e-04	6.61e-01	2.67e-04	0.076999	0.424961	0.080722	0.445510	1.02e+01	1.07e+01	2.24e-03	3.35e-03	8.63e+00	7.74e+00	7.80e-04	4.19e-04
chr2	30945637	31030311	NM_144575	0.4603	-	CAPN13	protein_coding	7.17e-05	1.93e-02	3.662965	1.50e+00	2.36e-05	1.50e+00	2.36e-05	7.07e-01	1.67e-05	7.41e-01	1.75e-05	4.71e-01	7.07e-01	4.94e-01	7.41e-01	4.92e+00	4.37e-04	4.92e+00	4.37e-04	1.43e+00	3.84e-04	1.50e+00	4.03e-04	0.290939	0.879106	0.305008	0.921616	1.00e+00	2.00e+00	1.18e-05	3.54e-05	3.91e+00	5.93e+00	1.65e-04	7.09e-04
chr21	22370613	22915648	NM_004540	0.3403	+	NCAM2	protein_coding	7.35e-05	1.94e-02	3.088683	7.12e+00	2.53e-04	7.12e+00	2.53e-04	7.34e-02	1.30e-05	7.70e-02	1.36e-05	1.03e-02	5.12e-02	1.08e-02	5.37e-02	1.01e+01	2.17e-03	1.01e+01	2.17e-03	6.48e-01	9.43e-04	6.79e-01	9.89e-04	0.063944	0.435097	0.067036	0.456136	7.07e+00	7.17e+00	2.44e-04	2.62e-04	9.68e+00	1.06e+01	1.50e-03	2.83e-03
chr7	12610202	12693228	NM_001112706	0.3855	+	SCIN	protein_coding	9.06e-05	2.33e-02	4.769387	2.29e+00	5.42e-05	2.29e+00	5.42e-05	1.00e+00	4.26e-05	1.05e+00	4.46e-05	4.36e-01	7.86e-01	4.58e-01	8.24e-01	5.98e+00	1.79e-03	5.98e+00	1.79e-03	3.08e+00	2.32e-03	3.23e+00	2.43e-03	0.514354	1.290826	0.539226	1.353246	1.58e+00	3.00e+00	2.41e-05	8.43e-05	8.16e+00	3.81e+00	3.43e-03	1.57e-04
chr5	59783758	59822245	NR_028509	0.3980	+	PART1	lincRNA	1.13e-04	2.78e-02	3.614710	1.00e+00	2.60e-05	1.00e+00	2.60e-05	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	4.54e+00	6.11e-04	4.54e+00	6.11e-04	6.45e-01	2.76e-04	6.76e-01	2.89e-04	0.142011	0.451345	0.148878	0.473170	1.00e+00	1.00e+00	2.60e-05	2.60e-05	5.00e+00	4.09e+00	8.05e-04	4.16e-04
chr11	83166055	85338314	NM_001142699	0.3701	-	DLG2	protein_coding	1.15e-04	2.78e-02	2.375973	8.73e+00	2.01e-04	8.73e+00	2.01e-04	4.97e-01	6.80e-05	5.21e-01	7.13e-05	5.69e-02	3.39e-01	5.97e-02	3.55e-01	1.11e+01	1.04e-03	1.11e+01	1.04e-03	4.99e-01	3.55e-04	5.24e-01	3.72e-04	0.044963	0.339536	0.047137	0.355955	8.38e+00	9.08e+00	1.53e-04	2.49e-04	1.08e+01	1.15e+01	7.94e-04	1.30e-03
chr7	1748797	1787590	NM_001128636	0.5744	+	ELFN1	protein_coding	1.15e-04	2.78e-02	3.483083	2.29e+00	1.16e-04	2.29e+00	1.16e-04	1.00e+00	9.11e-05	1.05e+00	9.55e-05	4.36e-01	7.86e-01	4.58e-01	8.24e-01	5.93e+00	1.56e-03	5.93e+00	1.56e-03	2.50e-01	2.73e-04	2.62e-01	2.87e-04	0.042156	0.175316	0.044195	0.183793	1.58e+00	3.00e+00	5.16e-05	1.80e-04	6.11e+00	5.75e+00	1.75e-03	1.37e-03
chr5	174151574	174157902	NM_002449	0.4690	+	MSX2	protein_coding	1.23e-04	2.87e-02	-3.222392	5.75e+00	8.69e-03	5.75e+00	8.69e-03	6.00e-01	3.58e-03	6.29e-01	3.75e-03	1.04e-01	4.11e-01	1.09e-01	4.31e-01	2.56e+00	7.90e-04	2.56e+00	7.90e-04	3.43e-01	2.23e-04	3.60e-01	2.34e-04	0.133839	0.282843	0.140311	0.296520	5.32e+00	6.17e+00	6.16e-03	1.12e-02	2.81e+00	2.32e+00	9.48e-04	6.32e-04
chr5	82767492	82878122	NM_004385	0.3717	+	VCAN	protein_coding	1.24e-04	2.87e-02	2.511134	6.12e+00	6.55e-04	6.12e+00	6.55e-04	6.76e-01	3.00e-04	7.09e-01	3.15e-04	1.10e-01	4.58e-01	1.16e-01	4.81e-01	8.50e+00	3.78e-03	8.50e+00	3.78e-03	1.12e+00	2.68e-03	1.18e+00	2.81e-03	0.132200	0.710490	0.138593	0.744847	6.60e+00	5.64e+00	8.68e-04	4.43e-04	7.71e+00	9.30e+00	1.88e-03	5.68e-03
chrX	119392504	119445391	NM_017938	0.4318	-	TMEM255A	protein_coding	1.29e-04	2.93e-02	-5.115477	5.62e+00	2.93e-03	5.62e+00	2.93e-03	3.71e+00	3.96e-03	3.89e+00	4.15e-03	6.60e-01	1.35e+00	6.92e-01	1.42e+00	2.16e+00	6.62e-05	2.16e+00	6.62e-05	2.28e-01	1.34e-05	2.39e-01	1.40e-05	0.105341	0.202031	0.110435	0.211800	8.25e+00	3.00e+00	5.73e-03	1.32e-04	2.00e+00	2.32e+00	5.67e-05	7.56e-05
chr5	52084135	52249485	NM_181501	0.3674	+	ITGA1	protein_coding	1.37e-04	3.04e-02	2.019778	6.32e+00	4.87e-04	6.32e+00	4.87e-04	4.19e-01	1.41e-04	4.39e-01	1.48e-04	6.63e-02	2.90e-01	6.95e-02	3.04e-01	8.34e+00	1.99e-03	8.34e+00	1.99e-03	3.71e-01	5.09e-04	3.89e-01	5.34e-04	0.044502	0.255374	0.046654	0.267723	6.61e+00	6.02e+00	5.87e-04	3.87e-04	8.08e+00	8.61e+00	1.63e-03	2.35e-03
chr12	117645946	117799607	NM_001204218	0.4739	-	NOS1	protein_coding	1.46e-04	3.18e-02	2.659624	5.43e+00	2.90e-04	5.43e+00	2.90e-04	6.74e-01	1.33e-04	7.06e-01	1.40e-04	1.24e-01	4.61e-01	1.30e-01	4.83e-01	8.00e+00	1.86e-03	8.00e+00	1.86e-03	9.90e-01	1.19e-03	1.04e+00	1.25e-03	0.123695	0.639234	0.129677	0.670146	4.95e+00	5.91e+00	1.95e-04	3.84e-04	7.30e+00	8.70e+00	1.02e-03	2.71e-03
chr11	110447758	110583451	NM_020809	0.3666	-	ARHGAP20	protein_coding	1.58e-04	3.38e-02	3.006919	3.63e+00	8.84e-05	3.63e+00	8.84e-05	6.49e-01	4.17e-05	6.80e-01	4.37e-05	1.79e-01	4.71e-01	1.87e-01	4.94e-01	6.52e+00	7.63e-04	6.52e+00	7.63e-04	1.05e+00	5.16e-04	1.10e+00	5.41e-04	0.160997	0.676363	0.168782	0.709070	3.17e+00	4.09e+00	5.90e-05	1.18e-04	7.27e+00	5.78e+00	1.13e-03	3.98e-04
chr2	206547223	206662857	NM_201266	0.4578	+	NRP2	protein_coding	1.79e-04	3.76e-02	2.344828	4.64e+00	2.08e-04	4.64e+00	2.08e-04	8.17e-02	1.22e-05	8.56e-02	1.28e-05	1.76e-02	5.89e-02	1.84e-02	6.18e-02	6.91e+00	1.09e-03	6.91e+00	1.09e-03	7.01e-01	5.14e-04	7.35e-01	5.39e-04	0.101531	0.471405	0.106441	0.494200	4.70e+00	4.58e+00	2.16e-04	1.99e-04	7.40e+00	6.41e+00	1.45e-03	7.26e-04
chr2	238768186	238820759	NM_005855	0.5227	+	RAMP1	protein_coding	2.05e-04	4.22e-02	2.052140	6.61e+00	1.85e-03	6.61e+00	1.85e-03	2.39e-01	3.09e-04	2.51e-01	3.24e-04	3.62e-02	1.67e-01	3.79e-02	1.75e-01	8.65e+00	7.75e-03	8.65e+00	7.75e-03	3.56e-01	1.90e-03	3.73e-01	1.99e-03	0.041107	0.244668	0.043095	0.256499	6.44e+00	6.78e+00	1.64e-03	2.07e-03	8.90e+00	8.40e+00	9.09e-03	6.41e-03
chr10	21068902	21186531	NM_006393	0.3712	-	NEBL	protein_coding	2.34e-04	4.74e-02	1.899237	6.56e+00	7.95e-04	6.56e+00	7.95e-04	1.84e-01	1.02e-04	1.93e-01	1.07e-04	2.81e-02	1.29e-01	2.94e-02	1.35e-01	8.46e+00	2.99e-03	8.46e+00	2.99e-03	8.98e-02	1.86e-04	9.41e-02	1.95e-04	0.010611	0.062362	0.011124	0.065378	6.69e+00	6.43e+00	8.67e-04	7.23e-04	8.40e+00	8.52e+00	2.86e-03	3.12e-03
chr12	15033797	15038996	NM_001190839	0.3790	-	MGP	protein_coding	2.49e-04	4.96e-02	3.858770	4.63e+00	5.87e-03	4.63e+00	5.87e-03	1.48e+00	5.30e-03	1.55e+00	5.56e-03	3.19e-01	9.04e-01	3.34e-01	9.48e-01	8.83e+00	8.77e-02	8.83e+00	8.77e-02	1.21e-01	7.34e-03	1.27e-01	7.70e-03	0.013662	0.083736	0.014322	0.087786	5.67e+00	3.58e+00	9.62e-03	2.12e-03	8.75e+00	8.92e+00	8.25e-02	9.29e-02
chr19	47123724	47128354	NM_000960	0.5902	-	PTGIR	protein_coding	2.69e-04	5.25e-02	2.383704	3.79e+00	3.24e-03	3.79e+00	3.24e-03	1.12e+00	2.44e-03	1.17e+00	2.56e-03	2.96e-01	7.54e-01	3.10e-01	7.91e-01	6.38e+00	1.78e-02	6.38e+00	1.78e-02	1.84e-01	2.29e-03	1.93e-01	2.40e-03	0.028811	0.128565	0.030204	0.134782	4.58e+00	3.00e+00	4.97e-03	1.51e-03	6.25e+00	6.51e+00	1.62e-02	1.94e-02
chr3	170714136	170744768	NM_000340	0.3698	-	SLC2A2	protein_coding	2.73e-04	5.25e-02	3.906891	1.00e+00	3.26e-05	1.00e+00	3.26e-05	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	4.27e+00	9.47e-04	4.27e+00	9.47e-04	2.07e+00	1.06e-03	2.17e+00	1.11e-03	0.483910	1.121618	0.507310	1.175855	1.00e+00	1.00e+00	3.26e-05	3.26e-05	5.73e+00	2.81e+00	1.70e-03	1.96e-04
chr5	16067414	16179897	NM_001102562	0.3921	-	MARCH11	protein_coding	3.08e-04	5.77e-02	-1.988002	9.87e+00	8.51e-03	9.87e+00	8.51e-03	4.73e-01	2.74e-03	4.95e-01	2.87e-03	4.79e-02	3.22e-01	5.02e-02	3.38e-01	7.88e+00	2.14e-03	7.88e+00	2.14e-03	4.42e-01	6.47e-04	4.63e-01	6.79e-04	0.056059	0.302836	0.058770	0.317480	1.02e+01	9.53e+00	1.04e-02	6.57e-03	7.57e+00	8.19e+00	1.68e-03	2.60e-03
chr20	36755788	36793831	NM_004613	0.5262	-	TGM2	protein_coding	3.11e-04	5.77e-02	2.860597	3.23e+00	2.23e-04	3.23e+00	2.23e-04	3.25e-01	5.58e-05	3.41e-01	5.85e-05	1.01e-01	2.50e-01	1.05e-01	2.62e-01	6.06e+00	1.79e-03	6.06e+00	1.79e-03	5.45e-01	6.69e-04	5.71e-01	7.01e-04	0.089942	0.374351	0.094291	0.392453	3.00e+00	3.46e+00	1.84e-04	2.63e-04	5.67e+00	6.44e+00	1.31e-03	2.26e-03
chr11	15133969	15268756	NM_001031853	0.4370	+	INSC	protein_coding	3.28e-04	5.99e-02	-4.410522	5.98e+00	1.18e-03	5.98e+00	1.18e-03	3.22e+00	1.54e-03	3.38e+00	1.61e-03	5.39e-01	1.31e+00	5.65e-01	1.37e+00	2.73e+00	4.82e-05	2.73e+00	4.82e-05	1.03e+00	3.67e-05	1.08e+00	3.85e-05	0.378052	0.761500	0.396333	0.798323	3.70e+00	8.26e+00	8.90e-05	2.26e-03	3.46e+00	2.00e+00	7.42e-05	2.23e-05
chr10	111705316	111768139	NR_038943	0.4156	-	ADD3-AS1	protein_coding	4.00e-04	7.19e-02	3.169925	2.00e+00	4.78e-05	2.00e+00	4.78e-05	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.16e+00	5.57e-04	5.16e+00	5.57e-04	2.85e-01	1.13e-04	2.99e-01	1.18e-04	0.055319	0.202031	0.057994	0.211800	2.00e+00	2.00e+00	4.78e-05	4.78e-05	4.95e+00	5.36e+00	4.78e-04	6.37e-04
chr3	158787040	159615155	NM_001197113	0.3906	+	IQCJ-SCHIP1	protein_coding	4.38e-04	7.75e-02	1.942203	9.40e+00	8.18e-04	9.40e+00	8.18e-04	1.36e-01	7.68e-05	1.42e-01	8.06e-05	1.44e-02	9.40e-02	1.51e-02	9.85e-02	1.13e+01	3.15e-03	1.13e+01	3.15e-03	6.99e-01	1.47e-03	7.33e-01	1.54e-03	0.062072	0.466699	0.065073	0.489267	9.50e+00	9.31e+00	8.72e-04	7.63e-04	1.08e+01	1.18e+01	2.11e-03	4.18e-03
chr1	215796235	216596738	NM_206933	0.3636	-	USH2A	protein_coding	4.49e-04	7.82e-02	2.540326	5.49e+00	5.68e-05	5.49e+00	5.68e-05	5.62e-01	2.21e-05	5.89e-01	2.32e-05	1.03e-01	3.89e-01	1.07e-01	4.07e-01	7.68e+00	3.37e-04	7.68e+00	3.37e-04	1.59e+00	3.12e-04	1.67e+00	3.27e-04	0.207135	0.926192	0.217152	0.970979	5.09e+00	5.88e+00	4.12e-05	7.25e-05	8.80e+00	6.55e+00	5.57e-04	1.16e-04
chrX	21392415	21672813	NM_014927	0.3498	+	CNKSR2	protein_coding	4.58e-04	7.86e-02	2.444590	6.24e+00	2.66e-04	6.24e+00	2.66e-04	1.35e-02	2.52e-06	1.42e-02	2.64e-06	2.17e-03	9.49e-03	2.27e-03	9.95e-03	8.50e+00	1.46e-03	8.50e+00	1.46e-03	1.06e+00	9.89e-04	1.11e+00	1.04e-03	0.124610	0.676063	0.130635	0.708755	6.23e+00	6.25e+00	2.64e-04	2.67e-04	7.75e+00	9.25e+00	7.63e-04	2.16e-03

Download the DEG result list for Prol_vs_D8plus.
Download the whole result list for Prol_vs_D8plus.

Download the raw read counts table for the experiment.
Download the normalized read counts table for the experiment.

References

Statham, A.L., Strbenac, D., Coolen, M.W., Stirzaker, C., Clark, S.J., Robinson, M.D. (2010). Repitools: an R package for the analysis of enrichment-based epigenomic data. Bioinformatics 26(13), 1662-1663.
Robinson, M.D., McCarthy, D.J., and Smyth, G.K. (2010). edgeR: a Bioconductor package for differential expression analysis of digital gene expression data. Bioinformatics 26, 139-140.
Planet, E., Attolini, C.S., Reina, O., Flores, O., and Rossell, D. (2012). htSeqTools: high-throughput sequencing quality control, processing and visualization in R. Bioinformatics 28, 589-590.
Tarazona, S., Garcia-Alcalde, F., Dopazo, J., Ferrer, A., and Conesa, A. (2011). Differential expression in RNA-seq: a matter of depth. Genome Res 21, 2213-2223.
Risso, D., Schwartz, K., Sherlock, G., and Dudoit, S. (2011). GC-content normalization for RNA-Seq data. BMC Bioinformatics 12, 480.
Benjamini, Y., and Hochberg, Y. (1995). Controlling the False Discovery Rate: A Practical and Powerful Approach to Multiple Testing. Journal of the Royal Statistical Society Series B (Methodological) 57, 289-300.