metaseqR report

Summary

Analysis summary

Summary: 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 DESeq after removing genes that had zero counts over all the RNA-Seq samples (25671 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 (3514 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 average reads per 100 bp), iii) genes with read counts below the median read counts of the total normalized count distribution (4703 genes with cutoff value 2 normalized read counts). The total number of genes excluded due to the application of gene filters was 4155. The total (unified) number of genes excluded due to the application of all filters was 32561. The resulting gene counts table was subjected to differential expression analysis for the contrasts GFP versus TOM, GFP versus UNS, TOM versus UNS using the Bioconductor package DESeq. The final numbers of differentially expressed genes were (per contrast): for the contrast GFP versus TOM, 690 (0) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 387 were up-regulated, 303 were down-regulated and 0 were not differentially expressed according to an absolute fold change cutoff value of 1 in log₂ scale, for the contrast GFP versus UNS, 1151 (1) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 484 (0) were up-regulated, 667 (1) 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 TOM versus UNS, 464 (0) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 176 were up-regulated, 288 were down-regulated and 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 custom data frame
Conditions: GFP, TOM, UNS
Samples included: GK3R131r-GFP-DARE1, GK3R132r-GFP-DARE2, GK3R133r-GFP-DARE3, GK3R134r-TOM-DARE1, GK3R135r-TOM-DARE2, GK3R136r-TOM-DARE3, GK3R137r-UNS-DARE1, GK3R138r-UNS-DARE2, GK3R139r-UNS-DARE3, GK3R137r-UNS-DARE1-TEST1, GK3R138r-UNS-DARE2-TEST2
Samples excluded: none
Requested contrasts: GFP_vs_TOM, GFP_vs_UNS, TOM_vs_UNS
Library sizes: not available
Annotation: embedded
Organism:
Annotation source: Ensembl genomes
Count type: utr
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
- snRNA: FALSE
- protein_coding: FALSE
- antisense: FALSE
- miRNA: FALSE
- snoRNA: FALSE
- lincRNA: FALSE
- processed_transcript: FALSE
- misc_RNA: FALSE
- rRNA: TRUE
- sense_intronic: FALSE
- sense_overlapping: FALSE
- polymorphic_pseudogene: FALSE
- IG_C_gene: FALSE
- IG_J_gene: FALSE
- IG_D_gene: FALSE
- IG_LV_gene: FALSE
- IG_V_gene: FALSE
- IG_V_pseudogene: TRUE
- TR_V_gene: FALSE
- TR_V_pseudogene: TRUE
- three_prime_overlapping_ncrna: FALSE

Filter application: after normalization
Normalization algorithm: DESeq
Normalization arguments: locfunc

[[list(locfunc = function (x, na.rm = FALSE) standardGeneric("median"))locfunc

Statistical algorithm(s): DESeq
Statistical arguments for DESeq: method, sharingMode, fitType

method: blind
sharingMode: fit-only
fitType: local

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/run387/www/metaseqr_quantseq_run387_all
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
Total run time: 12 minutes 36 seconds

Filtered genes

Number of filtered genes: 32561 which is the union of

Filtered because of zero reads: 25671
Filtered because of exon filters: 0
Filtered because of gene filters: 6890 which is the union of
- length: 3514 genes with filter cutoff value 500
- avg.reads: 564 genes with filter cutoff value 0
- expression: 4703 genes further decomposed to (filter name, filtered genes, filter cutoff):
- - median: 4703 genes with filter cutoff value 2
- biotype: 76 genes with filter cutoff value rRNA, IG_V_pseudogene, TR_V_pseudogene

Differentially expressed genes

Number of differentially expressed genes per contrast:

GFP_vs_TOM: 690 (0) statistically significant genes of which 387 up regulated, 303 down regulated and 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.
GFP_vs_UNS: 1151 (1) statistically significant genes of which 484 (0) up regulated, 667 (1) 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.
TOM_vs_UNS: 464 (0) statistically significant genes of which 176 up regulated, 288 down regulated and 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

[ 2018-03-09 17:17:42 ] FATAL Condition names in sample list and contrast list do not match! Check if the contrasts follow the appropriate format (e.g. "_vs_" separating contrasting conditions...
[ 2018-03-09 17:19:22 ] FATAL Raw reads input file /data/images/proton2/run387/www/GK3R131r-GFP-DARE1.bam does not exist! Please check!
[ 2018-03-09 17:20:47 ] WARN "yes" and "no" for read strandedness have been deprecated. Please use "forward", "forward" or "no". Replacing "yes" with "forward"...
[ 2018-03-09 17:20:56 ] WARN "yes" and "no" for read strandedness have been deprecated. Please use "forward", "forward" or "no". Replacing "yes" with "forward"...
[ 2018-03-09 17:20:56 ] INFO Converting annotation to GenomicRanges object...
[ 2018-03-09 17:20:56 ] INFO Reading bam file GK3R131r-GFP-DARE1.bam for sample with name GK3R131r-GFP-DARE1. This might take some time...
[ 2018-03-09 17:20:56 ] INFO Reading bam file GK3R132r-GFP-DARE2.bam for sample with name GK3R132r-GFP-DARE2. This might take some time...
[ 2018-03-09 17:20:56 ] INFO Reading bam file GK3R133r-GFP-DARE3.bam for sample with name GK3R133r-GFP-DARE3. This might take some time...
[ 2018-03-09 17:20:56 ] INFO Reading bam file GK3R134r-TOM-DARE1.bam for sample with name GK3R134r-TOM-DARE1. This might take some time...
[ 2018-03-09 17:20:56 ] INFO Reading bam file GK3R135r-TOM-DARE2.bam for sample with name GK3R135r-TOM-DARE2. This might take some time...
[ 2018-03-09 17:20:56 ] INFO Reading bam file GK3R136r-TOM-DARE3.bam for sample with name GK3R136r-TOM-DARE3. This might take some time...
[ 2018-03-09 17:20:56 ] INFO Reading bam file GK3R137r-UNS-DARE1.bam for sample with name GK3R137r-UNS-DARE1. This might take some time...
[ 2018-03-09 17:20:56 ] INFO Reading bam file GK3R138r-UNS-DARE2.bam for sample with name GK3R138r-UNS-DARE2. This might take some time...
[ 2018-03-09 17:20:56 ] INFO Reading bam file GK3R139r-UNS-DARE3.bam for sample with name GK3R139r-UNS-DARE3. This might take some time...
[ 2018-03-09 17:20:56 ] INFO Reading bam file GK3R137r-UNS-DARE1-TEST1.bam for sample with name GK3R137r-UNS-DARE1-TEST1. This might take some time...
[ 2018-03-09 17:20:57 ] INFO Reading bam file GK3R138r-UNS-DARE2-TEST2.bam for sample with name GK3R138r-UNS-DARE2-TEST2. This might take some time...
[ 2018-03-09 17:21:00 ] INFO Counting reads overlapping with given annotation...
[ 2018-03-09 17:21:00 ] INFO ...for single-end reads...
[ 2018-03-09 17:21:00 ] INFO ...assuming forward sequenced reads...
[ 2018-03-09 17:21:01 ] INFO Counting reads overlapping with given annotation...
[ 2018-03-09 17:21:01 ] INFO ...for single-end reads...
[ 2018-03-09 17:21:01 ] INFO ...assuming forward sequenced reads...
[ 2018-03-09 17:21:02 ] INFO Counting reads overlapping with given annotation...
[ 2018-03-09 17:21:02 ] INFO ...for single-end reads...
[ 2018-03-09 17:21:02 ] INFO ...assuming forward sequenced reads...
[ 2018-03-09 17:21:02 ] INFO Counting reads overlapping with given annotation...
[ 2018-03-09 17:21:02 ] INFO ...for single-end reads...
[ 2018-03-09 17:21:02 ] INFO ...assuming forward sequenced reads...
[ 2018-03-09 17:21:03 ] INFO Counting reads overlapping with given annotation...
[ 2018-03-09 17:21:03 ] INFO ...for single-end reads...
[ 2018-03-09 17:21:03 ] INFO ...assuming forward sequenced reads...
[ 2018-03-09 17:21:04 ] INFO Counting reads overlapping with given annotation...
[ 2018-03-09 17:21:04 ] INFO ...for single-end reads...
[ 2018-03-09 17:21:04 ] INFO ...assuming forward sequenced reads...
[ 2018-03-09 17:21:05 ] INFO Counting reads overlapping with given annotation...
[ 2018-03-09 17:21:05 ] INFO ...for single-end reads...
[ 2018-03-09 17:21:05 ] INFO ...assuming forward sequenced reads...
[ 2018-03-09 17:21:05 ] INFO Counting reads overlapping with given annotation...
[ 2018-03-09 17:21:05 ] INFO ...for single-end reads...
[ 2018-03-09 17:21:05 ] INFO ...assuming forward sequenced reads...
[ 2018-03-09 17:21:06 ] INFO Counting reads overlapping with given annotation...
[ 2018-03-09 17:21:06 ] INFO ...for single-end reads...
[ 2018-03-09 17:21:06 ] INFO ...assuming forward sequenced reads...
[ 2018-03-09 17:21:08 ] INFO Counting reads overlapping with given annotation...
[ 2018-03-09 17:21:08 ] INFO ...for single-end reads...
[ 2018-03-09 17:21:08 ] INFO ...assuming forward sequenced reads...
[ 2018-03-09 17:21:09 ] INFO Counting reads overlapping with given annotation...
[ 2018-03-09 17:21:09 ] INFO ...for single-end reads...
[ 2018-03-09 17:21:09 ] INFO ...assuming forward sequenced reads...
[ 2018-03-09 17:52:48 ] INFO 2018-03-09 17:52:48: Data processing started...
[ 2018-03-09 17:52:48 ] INFO Read counts file: imported custom data frame
[ 2018-03-09 17:52:48 ] INFO Conditions: GFP, TOM, UNS
[ 2018-03-09 17:52:48 ] INFO Samples to include: GK3R131r-GFP-DARE1, GK3R132r-GFP-DARE2, GK3R133r-GFP-DARE3, GK3R134r-TOM-DARE1, GK3R135r-TOM-DARE2, GK3R136r-TOM-DARE3, GK3R137r-UNS-DARE1, GK3R138r-UNS-DARE2, GK3R139r-UNS-DARE3, GK3R137r-UNS-DARE1-TEST1, GK3R138r-UNS-DARE2-TEST2
[ 2018-03-09 17:52:48 ] INFO Samples to exclude: none
[ 2018-03-09 17:52:48 ] INFO Requested contrasts: GFP_vs_TOM, GFP_vs_UNS, TOM_vs_UNS
[ 2018-03-09 17:52:48 ] INFO Annotation: embedded
[ 2018-03-09 17:52:48 ] INFO Organism: custom
[ 2018-03-09 17:52:48 ] INFO Reference source: ensembl
[ 2018-03-09 17:52:48 ] INFO Count type: utr
[ 2018-03-09 17:52:48 ] INFO Exon filters: none applied
[ 2018-03-09 17:52:48 ] INFO Gene filters: length, avg.reads, expression, biotype
[ 2018-03-09 17:52:48 ] INFO length:
[ 2018-03-09 17:52:48 ] INFO length: 500
[ 2018-03-09 17:52:48 ] INFO avg.reads:
[ 2018-03-09 17:52:48 ] INFO average.per.bp: 100
[ 2018-03-09 17:52:48 ] INFO quantile: 0.25
[ 2018-03-09 17:52:48 ] INFO expression:
[ 2018-03-09 17:52:48 ] INFO median: TRUE
[ 2018-03-09 17:52:48 ] INFO mean: FALSE
[ 2018-03-09 17:52:48 ] INFO quantile: NA
[ 2018-03-09 17:52:48 ] INFO known: NA
[ 2018-03-09 17:52:48 ] INFO custom: NA
[ 2018-03-09 17:52:48 ] INFO biotype:
[ 2018-03-09 17:52:48 ] INFO pseudogene: FALSE
[ 2018-03-09 17:52:48 ] INFO snRNA: FALSE
[ 2018-03-09 17:52:48 ] INFO protein_coding: FALSE
[ 2018-03-09 17:52:48 ] INFO antisense: FALSE
[ 2018-03-09 17:52:48 ] INFO miRNA: FALSE
[ 2018-03-09 17:52:48 ] INFO snoRNA: FALSE
[ 2018-03-09 17:52:48 ] INFO lincRNA: FALSE
[ 2018-03-09 17:52:48 ] INFO processed_transcript: FALSE
[ 2018-03-09 17:52:48 ] INFO misc_RNA: FALSE
[ 2018-03-09 17:52:48 ] INFO rRNA: TRUE
[ 2018-03-09 17:52:48 ] INFO sense_intronic: FALSE
[ 2018-03-09 17:52:48 ] INFO sense_overlapping: FALSE
[ 2018-03-09 17:52:48 ] INFO polymorphic_pseudogene: FALSE
[ 2018-03-09 17:52:48 ] INFO IG_C_gene: FALSE
[ 2018-03-09 17:52:48 ] INFO IG_J_gene: FALSE
[ 2018-03-09 17:52:48 ] INFO IG_D_gene: FALSE
[ 2018-03-09 17:52:48 ] INFO IG_LV_gene: FALSE
[ 2018-03-09 17:52:48 ] INFO IG_V_gene: FALSE
[ 2018-03-09 17:52:48 ] INFO IG_V_pseudogene: TRUE
[ 2018-03-09 17:52:48 ] INFO TR_V_gene: FALSE
[ 2018-03-09 17:52:48 ] INFO TR_V_pseudogene: TRUE
[ 2018-03-09 17:52:48 ] INFO three_prime_overlapping_ncrna: FALSE
[ 2018-03-09 17:52:48 ] INFO Filter application: postnorm
[ 2018-03-09 17:52:48 ] INFO Normalization algorithm: deseq
[ 2018-03-09 17:52:48 ] INFO Normalization arguments:
[ 2018-03-09 17:52:48 ] INFO locfunc:
[ 2018-03-09 17:52:48 ] INFO [[
[ 2018-03-09 17:52:48 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median"))
[ 2018-03-09 17:52:48 ] INFO locfunc
[ 2018-03-09 17:52:48 ] INFO Statistical algorithm: deseq
[ 2018-03-09 17:52:48 ] INFO Statistical arguments:
[ 2018-03-09 17:52:48 ] INFO deseq: blind, fit-only, local
[ 2018-03-09 17:52:48 ] INFO Meta-analysis method: none
[ 2018-03-09 17:52:48 ] INFO Multiple testing correction: BH
[ 2018-03-09 17:52:48 ] INFO p-value threshold: 0.05
[ 2018-03-09 17:52:48 ] INFO Logarithmic transformation offset: 1
[ 2018-03-09 17:52:48 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap
[ 2018-03-09 17:52:48 ] INFO Figure format: png, pdf
[ 2018-03-09 17:52:48 ] INFO Output directory: /data/images/proton2/run387/www/metaseqr_quantseq_run387_all
[ 2018-03-09 17:52:48 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, stats, counts, flags
[ 2018-03-09 17:52:48 ] INFO Output scale(s): log2, rpgm
[ 2018-03-09 17:52:48 ] INFO Output values: normalized
[ 2018-03-09 17:52:48 ] INFO Output statistics: mean
[ 2018-03-09 17:52:48 ] INFO Reading custom external gene annotation for from /data/results/tools/rnaseq/metaseqr/mm10/gene_data_mm10.txt.gz...
[ 2018-03-09 17:52:49 ] INFO Checking chromosomes in transcript counts and gene annotation...
[ 2018-03-09 17:52:49 ] INFO Processing transcripts...
[ 2018-03-09 17:52:49 ] INFO Separating transcripts (UTR regions) per gene for GK3R131r-GFP-DARE1...
[ 2018-03-09 17:53:07 ] INFO Separating transcripts (UTR regions) per gene for GK3R132r-GFP-DARE2...
[ 2018-03-09 17:53:26 ] INFO Separating transcripts (UTR regions) per gene for GK3R133r-GFP-DARE3...
[ 2018-03-09 17:53:44 ] INFO Separating transcripts (UTR regions) per gene for GK3R134r-TOM-DARE1...
[ 2018-03-09 17:54:02 ] INFO Separating transcripts (UTR regions) per gene for GK3R135r-TOM-DARE2...
[ 2018-03-09 17:54:20 ] INFO Separating transcripts (UTR regions) per gene for GK3R136r-TOM-DARE3...
[ 2018-03-09 17:54:39 ] INFO Separating transcripts (UTR regions) per gene for GK3R137r-UNS-DARE1...
[ 2018-03-09 17:54:58 ] INFO Separating transcripts (UTR regions) per gene for GK3R138r-UNS-DARE2...
[ 2018-03-09 17:55:16 ] INFO Separating transcripts (UTR regions) per gene for GK3R139r-UNS-DARE3...
[ 2018-03-09 17:55:35 ] INFO Separating transcripts (UTR regions) per gene for GK3R137r-UNS-DARE1-TEST1...
[ 2018-03-09 17:55:54 ] INFO Separating transcripts (UTR regions) per gene for GK3R138r-UNS-DARE2-TEST2...
[ 2018-03-09 17:56:13 ] INFO Saving gene model to /data/images/proton2/run387/www/metaseqr_quantseq_run387_all/data/gene_model.RData
[ 2018-03-09 17:56:16 ] INFO Summarizing count data...
[ 2018-03-09 17:56:44 ] INFO Removing genes with zero counts in all samples...
[ 2018-03-09 17:56:44 ] INFO Normalizing with: deseq
[ 2018-03-09 17:56:45 ] INFO Applying gene filter length...
[ 2018-03-09 17:56:45 ] INFO Threshold below which ignored: 500
[ 2018-03-09 17:56:45 ] INFO Applying gene filter avg.reads...
[ 2018-03-09 17:56:45 ] INFO Threshold below which ignored: 0
[ 2018-03-09 17:56:45 ] INFO Applying gene filter expression...
[ 2018-03-09 17:56:45 ] INFO Threshold below which ignored: 2
[ 2018-03-09 17:56:45 ] INFO Applying gene filter biotype...
[ 2018-03-09 17:56:45 ] INFO Biotypes ignored: rRNA, IG_V_pseudogene, TR_V_pseudogene
[ 2018-03-09 17:56:45 ] INFO 32561 genes filtered out
[ 2018-03-09 17:56:45 ] INFO 16987 genes remain after filtering
[ 2018-03-09 17:56:45 ] INFO Running statistical tests with: deseq
[ 2018-03-09 17:56:45 ] INFO Contrast: GFP_vs_TOM
[ 2018-03-09 17:57:04 ] INFO Contrast: GFP_vs_UNS
[ 2018-03-09 17:57:21 ] INFO Contrast: TOM_vs_UNS
[ 2018-03-09 17:57:39 ] INFO Contrast GFP_vs_TOM: found 690 genes
[ 2018-03-09 17:57:39 ] INFO Contrast GFP_vs_UNS: found 1151 genes
[ 2018-03-09 17:57:39 ] INFO Contrast TOM_vs_UNS: found 464 genes
[ 2018-03-09 17:57:40 ] INFO Building output files...
[ 2018-03-09 17:57:42 ] INFO Contrast: GFP_vs_TOM
[ 2018-03-09 17:57:42 ] INFO Adding non-filtered data...
[ 2018-03-09 17:57:42 ] INFO binding annotation...
[ 2018-03-09 17:57:43 ] INFO binding p-values...
[ 2018-03-09 17:57:44 ] INFO binding FDRs...
[ 2018-03-09 17:57:45 ] INFO binding log2 normalized fold changes...
[ 2018-03-09 17:57:45 ] INFO binding normalized mean counts...
[ 2018-03-09 17:57:45 ] INFO binding normalized mean counts...
[ 2018-03-09 17:57:46 ] INFO binding all normalized counts for GFP...
[ 2018-03-09 17:57:46 ] INFO binding all normalized counts for TOM...
[ 2018-03-09 17:57:47 ] INFO binding filtering flags...
[ 2018-03-09 17:57:47 ] INFO Writing output...
[ 2018-03-09 17:57:47 ] INFO Adding filtered data...
[ 2018-03-09 17:57:47 ] INFO binding annotation...
[ 2018-03-09 17:57:47 ] INFO binding p-values...
[ 2018-03-09 17:57:47 ] INFO binding FDRs...
[ 2018-03-09 17:57:48 ] INFO binding log2 normalized fold changes...
[ 2018-03-09 17:57:48 ] INFO binding normalized mean counts...
[ 2018-03-09 17:57:48 ] INFO binding normalized mean counts...
[ 2018-03-09 17:57:49 ] INFO binding all normalized counts for GFP...
[ 2018-03-09 17:57:49 ] INFO binding all normalized counts for TOM...
[ 2018-03-09 17:57:49 ] INFO binding filtering flags...
[ 2018-03-09 17:57:50 ] INFO Writing output...
[ 2018-03-09 17:57:52 ] INFO Contrast: GFP_vs_UNS
[ 2018-03-09 17:57:52 ] INFO Adding non-filtered data...
[ 2018-03-09 17:57:52 ] INFO binding annotation...
[ 2018-03-09 17:57:52 ] INFO binding p-values...
[ 2018-03-09 17:57:53 ] INFO binding FDRs...
[ 2018-03-09 17:57:53 ] INFO binding log2 normalized fold changes...
[ 2018-03-09 17:57:53 ] INFO binding normalized mean counts...
[ 2018-03-09 17:57:53 ] INFO binding normalized mean counts...
[ 2018-03-09 17:57:54 ] INFO binding all normalized counts for GFP...
[ 2018-03-09 17:57:55 ] INFO binding all normalized counts for UNS...
[ 2018-03-09 17:57:56 ] INFO binding filtering flags...
[ 2018-03-09 17:57:56 ] INFO Writing output...
[ 2018-03-09 17:57:56 ] INFO Adding filtered data...
[ 2018-03-09 17:57:56 ] INFO binding annotation...
[ 2018-03-09 17:57:56 ] INFO binding p-values...
[ 2018-03-09 17:57:56 ] INFO binding FDRs...
[ 2018-03-09 17:57:57 ] INFO binding log2 normalized fold changes...
[ 2018-03-09 17:57:57 ] INFO binding normalized mean counts...
[ 2018-03-09 17:57:57 ] INFO binding normalized mean counts...
[ 2018-03-09 17:57:58 ] INFO binding all normalized counts for GFP...
[ 2018-03-09 17:57:58 ] INFO binding all normalized counts for UNS...
[ 2018-03-09 17:57:58 ] INFO binding filtering flags...
[ 2018-03-09 17:57:59 ] INFO Writing output...
[ 2018-03-09 17:58:01 ] INFO Contrast: TOM_vs_UNS
[ 2018-03-09 17:58:01 ] INFO Adding non-filtered data...
[ 2018-03-09 17:58:01 ] INFO binding annotation...
[ 2018-03-09 17:58:02 ] INFO binding p-values...
[ 2018-03-09 17:58:02 ] INFO binding FDRs...
[ 2018-03-09 17:58:03 ] INFO binding log2 normalized fold changes...
[ 2018-03-09 17:58:03 ] INFO binding normalized mean counts...
[ 2018-03-09 17:58:03 ] INFO binding normalized mean counts...
[ 2018-03-09 17:58:04 ] INFO binding all normalized counts for TOM...
[ 2018-03-09 17:58:05 ] INFO binding all normalized counts for UNS...
[ 2018-03-09 17:58:06 ] INFO binding filtering flags...
[ 2018-03-09 17:58:06 ] INFO Writing output...
[ 2018-03-09 17:58:07 ] INFO Adding filtered data...
[ 2018-03-09 17:58:07 ] INFO binding annotation...
[ 2018-03-09 17:58:07 ] INFO binding p-values...
[ 2018-03-09 17:58:07 ] INFO binding FDRs...
[ 2018-03-09 17:58:07 ] INFO binding log2 normalized fold changes...
[ 2018-03-09 17:58:07 ] INFO binding normalized mean counts...
[ 2018-03-09 17:58:08 ] INFO binding normalized mean counts...
[ 2018-03-09 17:58:08 ] INFO binding all normalized counts for TOM...
[ 2018-03-09 17:58:08 ] INFO binding all normalized counts for UNS...
[ 2018-03-09 17:58:08 ] INFO binding filtering flags...
[ 2018-03-09 17:58:09 ] INFO Writing output...
[ 2018-03-09 17:58:12 ] INFO Creating quality control graphs...
[ 2018-03-09 17:58:12 ] INFO Plotting in png format...
[ 2018-03-09 17:58:12 ] INFO Plotting mds...
[ 2018-03-09 17:58:12 ] INFO Plotting biodetection...
[ 2018-03-09 17:58:13 ] INFO Plotting countsbio...
[ 2018-03-09 17:58:15 ] INFO Plotting saturation...
[ 2018-03-09 17:58:23 ] INFO Plotting readnoise...
[ 2018-03-09 17:58:25 ] INFO Plotting correl...
[ 2018-03-09 17:58:26 ] INFO Plotting pairwise...
[ 2018-03-09 17:59:02 ] INFO Plotting boxplot...
[ 2018-03-09 17:59:02 ] INFO Plotting gcbias...
[ 2018-03-09 17:59:03 ] INFO Plotting lengthbias...
[ 2018-03-09 17:59:04 ] INFO Plotting meandiff...
[ 2018-03-09 17:59:06 ] INFO Plotting meanvar...
[ 2018-03-09 17:59:21 ] INFO Plotting boxplot...
[ 2018-03-09 17:59:21 ] INFO Plotting gcbias...
[ 2018-03-09 17:59:22 ] INFO Plotting lengthbias...
[ 2018-03-09 17:59:23 ] INFO Plotting meandiff...
[ 2018-03-09 17:59:25 ] INFO Plotting meanvar...
[ 2018-03-09 17:59:40 ] INFO Plotting biodist...
[ 2018-03-09 17:59:40 ] INFO Contrast: GFP_vs_TOM
[ 2018-03-09 17:59:41 ] INFO Contrast: GFP_vs_UNS
[ 2018-03-09 17:59:41 ] INFO Contrast: TOM_vs_UNS
[ 2018-03-09 17:59:41 ] INFO Plotting volcano...
[ 2018-03-09 17:59:41 ] INFO Contrast: GFP_vs_TOM
[ 2018-03-09 17:59:42 ] INFO Contrast: GFP_vs_UNS
[ 2018-03-09 17:59:42 ] INFO Contrast: TOM_vs_UNS
[ 2018-03-09 17:59:43 ] INFO Plotting deheatmap...
[ 2018-03-09 17:59:43 ] INFO Contrast: GFP_vs_TOM
[ 2018-03-09 18:00:25 ] INFO Contrast: GFP_vs_UNS
[ 2018-03-09 18:01:08 ] INFO Contrast: TOM_vs_UNS
[ 2018-03-09 18:01:50 ] INFO Plotting filtered...
[ 2018-03-09 18:01:51 ] INFO Plotting in pdf format...
[ 2018-03-09 18:01:51 ] INFO Plotting mds...
[ 2018-03-09 18:01:51 ] INFO Plotting biodetection...
[ 2018-03-09 18:01:52 ] INFO Plotting countsbio...
[ 2018-03-09 18:01:54 ] INFO Plotting saturation...
[ 2018-03-09 18:02:00 ] INFO Plotting readnoise...
[ 2018-03-09 18:02:03 ] INFO Plotting correl...
[ 2018-03-09 18:02:03 ] INFO Plotting pairwise...
[ 2018-03-09 18:02:23 ] INFO Plotting boxplot...
[ 2018-03-09 18:02:23 ] INFO Plotting gcbias...
[ 2018-03-09 18:02:24 ] INFO Plotting lengthbias...
[ 2018-03-09 18:02:26 ] INFO Plotting meandiff...
[ 2018-03-09 18:02:29 ] INFO Plotting meanvar...
[ 2018-03-09 18:02:43 ] INFO Plotting boxplot...
[ 2018-03-09 18:02:43 ] INFO Plotting gcbias...
[ 2018-03-09 18:02:45 ] INFO Plotting lengthbias...
[ 2018-03-09 18:02:46 ] INFO Plotting meandiff...
[ 2018-03-09 18:02:49 ] INFO Plotting meanvar...
[ 2018-03-09 18:03:04 ] INFO Plotting biodist...
[ 2018-03-09 18:03:04 ] INFO Contrast: GFP_vs_TOM
[ 2018-03-09 18:03:05 ] INFO Contrast: GFP_vs_UNS
[ 2018-03-09 18:03:05 ] INFO Contrast: TOM_vs_UNS
[ 2018-03-09 18:03:05 ] INFO Plotting volcano...
[ 2018-03-09 18:03:05 ] INFO Contrast: GFP_vs_TOM
[ 2018-03-09 18:03:05 ] INFO Contrast: GFP_vs_UNS
[ 2018-03-09 18:03:06 ] INFO Contrast: TOM_vs_UNS
[ 2018-03-09 18:03:06 ] INFO Plotting deheatmap...
[ 2018-03-09 18:03:06 ] INFO Contrast: GFP_vs_TOM
[ 2018-03-09 18:03:52 ] INFO Contrast: GFP_vs_UNS
[ 2018-03-09 18:04:37 ] INFO Contrast: TOM_vs_UNS
[ 2018-03-09 18:05:23 ] INFO Plotting filtered...
[ 2018-03-09 18:05:23 ] INFO Creating HTML report...
[ 2018-03-09 18:05:23 ] 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 GFP

Mean-difference plots for the replicates of TOM

Mean-difference plots for the replicates of UNS

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 GFP

Mean-variance plots for the replicates of TOM

Mean-variance plots for the replicates of UNS

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 GFP_vs_TOM

Volcano plot for the contrast GFP_vs_UNS

Volcano plot for the contrast TOM_vs_UNS

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 GFP_vs_TOM

DEG heatmap for the contrast GFP_vs_UNS

DEG heatmap for the contrast TOM_vs_UNS

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 GFP_vs_TOM

Biotype distribution in DEG for the contrast GFP_vs_UNS

Biotype distribution in DEG for the contrast TOM_vs_UNS

Get all the figures in png, pdf format.

Results

DEG table for the contrast GFP_vs_TOM

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 GFP_vs_TOM. 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_deseq	FDR_deseq	log2_normalized_fold_change_GFP_vs_TOM	log2_normalized_mean_counts_GFP	rpgm_normalized_mean_counts_GFP	log2_normalized_mean_counts_TOM	rpgm_normalized_mean_counts_TOM	log2_normalized_counts_GK3R131r-GFP-DARE1	log2_normalized_counts_GK3R132r-GFP-DARE2	log2_normalized_counts_GK3R133r-GFP-DARE3	rpgm_normalized_counts_GK3R131r-GFP-DARE1	rpgm_normalized_counts_GK3R132r-GFP-DARE2	rpgm_normalized_counts_GK3R133r-GFP-DARE3	log2_normalized_counts_GK3R134r-TOM-DARE1	log2_normalized_counts_GK3R135r-TOM-DARE2	log2_normalized_counts_GK3R136r-TOM-DARE3	rpgm_normalized_counts_GK3R134r-TOM-DARE1	rpgm_normalized_counts_GK3R135r-TOM-DARE2	rpgm_normalized_counts_GK3R136r-TOM-DARE3
chr17	32815449	32830261	ENSMUSG00000095253	0.4142	-	Zfp799	protein_coding	2.80e-05	0.240	-6.50779	2.69e+00	1.09e-02	0.00e+00	0.00e+00	0.00e+00	8.08e+00	0.00e+00	0.00e+00	3.27e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr3	63963633	63968659	ENSMUSG00000097724	0.4307	+	Gm26850	antisense	2.83e-05	0.240	-6.82867	2.80e+00	4.49e-02	0.00e+00	0.00e+00	0.00e+00	8.41e+00	0.00e+00	0.00e+00	1.35e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr15	103562762	103565078	ENSMUSG00000022491	0.4368	-	Glycam1	protein_coding	7.48e-05	0.278	-6.72338	6.38e+00	7.61e-02	0.00e+00	0.00e+00	6.58e+00	7.56e+00	5.00e+00	6.90e-02	1.37e-01	2.25e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr16	48842552	48844461	ENSMUSG00000061100	0.4288	+	Retnla	protein_coding	8.00e-05	0.278	-6.10852	5.87e+00	4.81e-02	0.00e+00	0.00e+00	5.78e+00	6.93e+00	4.91e+00	3.82e-02	8.56e-02	2.05e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr9	58063788	58153996	ENSMUSG00000032327	0.5069	+	Stra6	protein_coding	8.66e-05	0.278	-6.84130	6.71e+00	1.54e-02	0.00e+00	0.00e+00	6.83e+00	7.43e+00	5.86e+00	1.53e-02	2.32e-02	7.74e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr13	96924689	96950912	ENSMUSG00000091387	0.4717	+	Gcnt4	protein_coding	9.82e-05	0.278	-6.14975	3.23e+00	1.52e-02	0.00e+00	0.00e+00	2.00e+00	7.70e+00	0.00e+00	6.52e-04	4.50e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr4	124700701	124708611	ENSMUSG00000032643	0.5434	+	Fhl3	protein_coding	1.47e-04	0.356	-5.57743	3.99e+00	1.94e-02	3.33e-01	1.03e-04	0.00e+00	7.38e+00	4.58e+00	0.00e+00	5.11e-02	7.12e-03	0.00e+00	1.00e+00	0.00e+00	0.00e+00	3.10e-04	0.00e+00
chr19	36731737	36736653	ENSMUSG00000067279	0.4364	-	Ppp1r3c	protein_coding	2.23e-04	0.457	-5.44846	5.27e+00	1.46e-02	0.00e+00	0.00e+00	4.46e+00	6.21e+00	5.13e+00	7.16e-03	2.49e-02	1.16e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr11	52154722	52168159	ENSMUSG00000108218	0.4730	-	Olfr1372-ps1	transcribed_unprocessed_pseudogene	2.46e-04	0.457	-5.58496	5.19e+00	1.87e-02	0.00e+00	0.00e+00	5.93e+00	6.17e+00	3.46e+00	2.39e-02	2.83e-02	3.99e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr8	121054882	121083110	ENSMUSG00000097336	0.5216	-	Fendrr	processed_transcript	2.69e-04	0.457	-5.58496	5.51e+00	1.25e-02	0.00e+00	0.00e+00	5.52e+00	6.09e+00	4.91e+00	1.20e-02	1.78e-02	7.71e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr15	9111985	9155425	ENSMUSG00000054115	0.4269	-	Skp2	protein_coding	3.76e-04	0.534	-6.62936	3.66e+00	1.14e-02	0.00e+00	0.00e+00	0.00e+00	2.81e+00	8.17e+00	0.00e+00	6.95e-04	3.34e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chrX	166390033	166440704	ENSMUSG00000040586	0.4016	-	Ofd1	protein_coding	4.03e-04	0.534	-6.70506	3.42e+00	4.62e-02	0.00e+00	0.00e+00	0.00e+00	2.00e+00	8.27e+00	0.00e+00	1.34e-03	1.37e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr7	44225360	44229618	ENSMUSG00000063903	0.5196	+	Klk1	protein_coding	6.95e-04	0.534	-3.96963	1.83e+00	5.68e-03	0.00e+00	0.00e+00	0.00e+00	5.49e+00	0.00e+00	0.00e+00	1.70e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr18	43728069	43737237	ENSMUSG00000024503	0.3967	-	Spink1	protein_coding	6.96e-04	0.534	5.79874	0.00e+00	0.00e+00	2.46e+00	4.06e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.37e+00	0.00e+00	0.00e+00	1.22e-01
chr9	105989454	106096783	ENSMUSG00000032572	0.4494	-	Col6a4	protein_coding	7.04e-04	0.534	-5.24793	5.20e+00	9.11e-03	0.00e+00	0.00e+00	5.64e+00	5.21e+00	4.75e+00	1.21e-02	8.86e-03	6.40e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr10	127289696	127290788	ENSMUSG00000092384	0.5572	-	Gm4189	processed_transcript	7.86e-04	0.534	5.65344	0.00e+00	0.00e+00	2.41e+00	3.93e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.22e+00	0.00e+00	0.00e+00	1.18e-01
chr2	114047282	114053548	ENSMUSG00000068614	0.4686	-	Actc1	protein_coding	7.90e-04	0.534	-5.38082	3.83e+00	1.51e-02	0.00e+00	0.00e+00	6.54e+00	4.95e+00	0.00e+00	3.42e-02	1.11e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr11	5106265	5152257	ENSMUSG00000034164	0.5125	-	Emid1	protein_coding	8.06e-04	0.534	-4.62936	4.31e+00	4.12e-03	3.33e-01	4.30e-05	3.46e+00	6.30e+00	3.17e+00	1.29e-03	1.01e-02	1.03e-03	0.00e+00	1.00e+00	0.00e+00	0.00e+00	1.29e-04	0.00e+00
chr14	61598226	61605946	ENSMUSG00000035235	0.4293	+	Trim13	protein_coding	8.17e-04	0.534	7.19967	0.00e+00	0.00e+00	4.11e+00	1.01e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	8.76e+00	1.00e+00	2.58e+00	3.00e-01	6.94e-04	3.47e-03
chr10	127705170	127720887	ENSMUSG00000025401	0.5285	+	Myo1a	protein_coding	8.28e-04	0.534	5.56478	0.00e+00	0.00e+00	4.34e+00	3.26e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	2.58e+00	3.46e+00	6.97e+00	3.52e-03	7.03e-03	8.72e-02
chr7	102702215	102712064	ENSMUSG00000070423	0.4185	+	Olfr558	protein_coding	9.25e-04	0.534	-4.87447	4.06e+00	9.13e-03	0.00e+00	0.00e+00	1.58e+00	5.88e+00	4.70e+00	6.44e-04	1.87e-02	8.05e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr11	76902159	76916587	ENSMUSG00000020839	0.4327	+	Tmigd1	protein_coding	9.87e-04	0.534	5.38082	0.00e+00	0.00e+00	2.31e+00	1.33e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.94e+00	0.00e+00	0.00e+00	3.98e-02
chr3	146852367	146984009	ENSMUSG00000036745	0.4182	+	Ttll7	protein_coding	1.00e-03	0.534	-7.63481	3.88e+00	3.03e-02	3.33e-01	3.83e-05	0.00e+00	9.63e+00	2.00e+00	0.00e+00	9.06e-02	3.45e-04	0.00e+00	1.00e+00	0.00e+00	0.00e+00	1.15e-04	0.00e+00
chr2	164805098	164822130	ENSMUSG00000045822	0.4676	+	Zswim3	protein_coding	1.04e-03	0.534	-6.95884	3.09e+00	1.22e-01	5.28e-01	3.93e-04	0.00e+00	9.28e+00	0.00e+00	0.00e+00	3.65e-01	0.00e+00	0.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	1.18e-03
chr16	36792884	36875003	ENSMUSG00000022838	0.3725	-	Eaf2	protein_coding	1.05e-03	0.534	5.80735	0.00e+00	0.00e+00	5.58e+00	1.21e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.64e+00	4.70e+00	5.39e+00	2.17e-02	5.48e-03	8.99e-03
chr3	144910921	144932529	ENSMUSG00000074195	0.3951	-	Clca4b	protein_coding	1.07e-03	0.534	5.35755	0.00e+00	0.00e+00	4.31e+00	2.77e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.91e+00	2.32e+00	6.69e+00	9.70e-03	2.77e-03	7.07e-02
chr9	62419492	62537044	ENSMUSG00000041729	0.5044	-	Coro2b	protein_coding	1.12e-03	0.534	5.80735	0.00e+00	0.00e+00	3.31e+00	5.17e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.35e+00	1.00e+00	1.58e+00	1.52e-02	9.40e-05	1.88e-04
chr12	80518990	80603896	ENSMUSG00000021130	0.4821	+	Galnt16	protein_coding	1.15e-03	0.534	-5.91716	4.82e+00	4.22e-02	1.00e+00	4.02e-04	2.00e+00	8.66e+00	3.81e+00	9.04e-04	1.22e-01	3.92e-03	0.00e+00	1.00e+00	2.00e+00	0.00e+00	3.01e-04	9.04e-04
chr1	105615742	105616358	ENSMUSG00000101656	0.4943	+	Gm8004	processed_pseudogene	1.28e-03	0.534	-6.44294	2.67e+00	6.86e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	8.02e+00	0.00e+00	0.00e+00	2.06e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr4	127311421	127314039	ENSMUSG00000050234	0.5697	-	Gja4	protein_coding	1.33e-03	0.534	-4.87447	4.79e+00	1.57e-02	0.00e+00	0.00e+00	4.32e+00	5.46e+00	4.58e+00	1.06e-02	2.39e-02	1.28e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr17	34597862	34600936	ENSMUSG00000015452	0.5626	+	Ager	protein_coding	1.37e-03	0.534	-4.75489	4.39e+00	1.00e-02	0.00e+00	0.00e+00	4.52e+00	5.64e+00	3.00e+00	8.49e-03	1.89e-02	2.70e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr1	85604085	85611896	ENSMUSG00000073628	0.4278	-	Gm10552	antisense	1.37e-03	0.534	5.47032	0.00e+00	0.00e+00	5.22e+00	1.73e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.95e+00	3.91e+00	5.81e+00	2.43e-02	5.58e-03	2.19e-02
chr9	22332012	22389188	ENSMUSG00000036777	0.4174	-	Anln	protein_coding	1.44e-03	0.534	-6.82655	2.94e+00	2.02e-02	3.33e-01	4.47e-05	0.00e+00	0.00e+00	8.82e+00	0.00e+00	0.00e+00	6.05e-02	1.00e+00	0.00e+00	0.00e+00	1.34e-04	0.00e+00	0.00e+00
chr16	11313812	11320074	ENSMUSG00000022496	0.4669	+	Tnfrsf17	protein_coding	1.49e-03	0.534	5.72792	0.00e+00	0.00e+00	5.64e+00	3.80e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.32e+00	5.17e+00	5.43e+00	5.77e-02	2.55e-02	3.07e-02
chr1	60887000	60915832	ENSMUSG00000026011	0.4160	+	Ctla4	protein_coding	1.53e-03	0.534	6.57491	0.00e+00	0.00e+00	6.27e+00	2.58e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.51e+00	6.02e+00	5.29e+00	4.95e-02	1.75e-02	1.04e-02
chr2	172868012	172940321	ENSMUSG00000008999	0.5207	-	Bmp7	protein_coding	1.53e-03	0.534	-5.01495	4.73e+00	6.76e-03	0.00e+00	0.00e+00	3.81e+00	4.46e+00	5.93e+00	2.81e-03	4.53e-03	1.30e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr8	114439655	115352708	ENSMUSG00000004637	0.4583	+	Wwox	protein_coding	1.56e-03	0.534	-4.98489	4.67e+00	2.20e-03	0.00e+00	0.00e+00	3.81e+00	5.95e+00	4.25e+00	9.34e-04	4.38e-03	1.29e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr15	75108158	75111970	ENSMUSG00000022584	0.4881	-	Ly6c2	protein_coding	1.57e-03	0.534	5.77259	0.00e+00	0.00e+00	5.65e+00	3.27e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.09e+00	4.75e+00	6.11e+00	4.09e-02	1.59e-02	4.15e-02
chrX	33505661	33507010	ENSMUSG00000079297	0.4407	+	Gm2223	processed_pseudogene	1.62e-03	0.534	-6.99152	3.00e+00	1.35e-01	3.33e-01	2.66e-04	8.99e+00	0.00e+00	0.00e+00	4.04e-01	0.00e+00	0.00e+00	1.00e+00	0.00e+00	0.00e+00	7.97e-04	0.00e+00	0.00e+00
chr15	60822271	60831793	ENSMUSG00000097493	0.4820	+	9930014A18Rik	processed_transcript	1.65e-03	0.534	6.70506	0.00e+00	0.00e+00	3.29e+00	2.06e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	8.27e+00	1.58e+00	0.00e+00	6.14e-02	3.99e-04
chr7	28179469	28187294	ENSMUSG00000002409	0.5819	+	Dyrk1b	protein_coding	1.66e-03	0.534	6.54432	0.00e+00	0.00e+00	2.71e+00	5.68e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	8.12e+00	0.00e+00	0.00e+00	1.70e-01	0.00e+00
chr2	84980461	84983632	ENSMUSG00000027073	0.4864	+	Prg2	protein_coding	1.73e-03	0.534	6.07325	0.00e+00	0.00e+00	5.72e+00	4.85e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.07e+00	6.86e+00	4.25e+00	4.82e-02	8.41e-02	1.32e-02
chr2	121357714	121363737	ENSMUSG00000000308	0.4809	+	Ckmt1	protein_coding	1.76e-03	0.534	5.10154	0.00e+00	0.00e+00	3.24e+00	5.43e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.17e+00	0.00e+00	6.54e+00	1.30e-03	0.00e+00	1.50e-02
chr12	5077472	5375682	ENSMUSG00000020627	0.4760	-	Klhl29	protein_coding	1.79e-03	0.534	-5.63227	5.32e+00	1.66e-02	6.67e-01	1.35e-04	3.91e+00	4.32e+00	7.73e+00	2.84e-03	3.85e-03	4.30e-02	1.00e+00	1.00e+00	0.00e+00	2.03e-04	2.03e-04	0.00e+00
chr11	9118103	9136170	ENSMUSG00000020407	0.4606	+	Upp1	protein_coding	1.80e-03	0.534	5.12928	0.00e+00	0.00e+00	4.96e+00	6.54e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	4.86e+00	4.17e+00	5.86e+00	5.39e-03	3.27e-03	1.10e-02
chr16	23113943	23127737	ENSMUSG00000022881	0.4038	-	Rfc4	protein_coding	1.83e-03	0.534	-4.08746	2.80e+00	1.91e-03	0.00e+00	0.00e+00	0.00e+00	5.39e+00	3.00e+00	0.00e+00	4.90e-03	8.36e-04	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr17	32120820	32166880	ENSMUSG00000038146	0.4988	-	Notch3	protein_coding	1.86e-03	0.534	-6.10014	5.09e+00	1.01e-01	1.00e+00	1.04e-03	0.00e+00	9.28e+00	5.98e+00	0.00e+00	2.76e-01	2.75e-02	0.00e+00	3.00e+00	0.00e+00	0.00e+00	3.11e-03	0.00e+00
chr5	138264921	138272840	ENSMUSG00000075593	0.4822	-	Gal3st4	protein_coding	1.87e-03	0.534	7.19640	0.00e+00	0.00e+00	3.92e+00	5.06e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.00e+00	8.75e+00	0.00e+00	2.43e-03	1.49e-01	0.00e+00
chr11	21683308	21684056	ENSMUSG00000083761	0.5541	-	Pgam1-ps1	processed_pseudogene	1.87e-03	0.534	-5.97728	4.04e+00	1.33e-01	1.19e+00	1.33e-03	1.58e+00	8.96e+00	1.58e+00	1.59e-03	3.96e-01	1.59e-03	2.00e+00	0.00e+00	1.58e+00	2.39e-03	0.00e+00	1.59e-03
chr11	106311341	106314762	ENSMUSG00000040592	0.5406	-	Cd79b	protein_coding	1.89e-03	0.534	5.54432	0.00e+00	0.00e+00	5.45e+00	2.66e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.13e+00	5.36e+00	4.86e+00	4.01e-02	2.33e-02	1.63e-02
chr2	24367580	24414954	ENSMUSG00000026979	0.4684	+	Psd4	protein_coding	1.91e-03	0.534	5.16993	0.00e+00	0.00e+00	5.05e+00	2.12e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.55e+00	4.17e+00	5.43e+00	2.79e-03	1.03e-03	2.55e-03
chr14	51129068	51131122	ENSMUSG00000021880	0.4409	+	Rnase6	protein_coding	1.94e-03	0.534	5.26053	0.00e+00	0.00e+00	5.01e+00	2.12e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.15e+00	4.17e+00	4.70e+00	3.97e-02	9.65e-03	1.42e-02
chr5	65861213	65896700	ENSMUSG00000029204	0.4495	+	Rhoh	protein_coding	1.97e-03	0.534	5.18322	0.00e+00	0.00e+00	4.87e+00	4.71e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.09e+00	3.70e+00	4.81e+00	8.94e-03	1.60e-03	3.60e-03
chr9	103423578	103461260	ENSMUSG00000086236	0.4566	+	5830418P13Rik	antisense	1.98e-03	0.534	5.19640	0.00e+00	0.00e+00	3.83e+00	7.11e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.02e+00	0.00e+00	5.46e+00	1.28e-02	0.00e+00	8.57e-03
chr13	48261427	48264036	ENSMUSG00000021379	0.5345	+	Id4	protein_coding	1.98e-03	0.534	-4.54432	3.24e+00	6.65e-03	0.00e+00	0.00e+00	0.00e+00	5.73e+00	4.00e+00	0.00e+00	1.55e-02	4.47e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr12	32173473	32208659	ENSMUSG00000020573	0.4237	-	Pik3cg	protein_coding	2.02e-03	0.534	5.42626	0.00e+00	0.00e+00	5.26e+00	7.48e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.95e+00	5.58e+00	4.25e+00	1.09e-02	8.37e-03	3.21e-03
chr11	62820231	62850808	ENSMUSG00000047821	0.4558	+	Trim16	protein_coding	2.06e-03	0.534	-6.89280	3.16e+00	3.99e-02	8.62e-01	1.69e-04	0.00e+00	9.47e+00	0.00e+00	0.00e+00	1.20e-01	0.00e+00	1.58e+00	0.00e+00	1.00e+00	3.37e-04	0.00e+00	1.69e-04
chr6	69814631	69815154	ENSMUSG00000096422	0.4447	-	Igkv12-44	IG_V_gene	2.09e-03	0.534	5.15650	0.00e+00	0.00e+00	4.58e+00	2.76e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.27e+00	3.00e+00	4.46e+00	6.06e-02	5.58e-03	1.67e-02
chr17	25958364	25985796	ENSMUSG00000037326	0.5112	-	Capn15	protein_coding	2.10e-03	0.534	-4.56817	3.77e+00	1.55e-02	1.33e+00	5.50e-04	2.58e+00	8.71e+00	0.00e+00	5.50e-04	4.61e-02	0.00e+00	0.00e+00	4.00e+00	0.00e+00	0.00e+00	1.65e-03	0.00e+00
chr3	110250015	110253706	ENSMUSG00000105509	0.4791	+	C130013H08Rik	antisense	2.11e-03	0.534	5.41504	0.00e+00	0.00e+00	4.66e+00	3.32e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.69e+00	3.58e+00	3.70e+00	8.13e-02	8.77e-03	9.57e-03
chr7	139978932	139992562	ENSMUSG00000025473	0.5169	-	Adam8	protein_coding	2.14e-03	0.534	5.49185	0.00e+00	0.00e+00	5.32e+00	5.74e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.86e+00	5.86e+00	4.25e+00	7.43e-03	7.43e-03	2.35e-03
chr11	70156197	70170834	ENSMUSG00000000318	0.4728	+	Clec10a	protein_coding	2.23e-03	0.534	5.35755	0.00e+00	0.00e+00	4.96e+00	6.81e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.81e+00	4.70e+00	6.38e+00	2.21e-03	4.25e-03	1.40e-02
chr15	10717144	10722471	ENSMUSG00000096971	0.4531	+	4930556M19Rik	lincRNA	2.28e-03	0.534	-5.93074	2.50e+00	4.78e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.50e+00	0.00e+00	0.00e+00	1.44e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr4	4133531	4138819	ENSMUSG00000045573	0.4386	-	Penk	protein_coding	2.29e-03	0.534	5.57491	0.00e+00	0.00e+00	5.00e+00	1.66e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.70e+00	6.73e+00	4.58e+00	4.26e-03	3.73e-02	8.17e-03
chr11	6506548	6520965	ENSMUSG00000020437	0.5216	-	Myo1g	protein_coding	2.29e-03	0.534	7.02237	0.00e+00	0.00e+00	7.01e+00	5.12e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.82e+00	6.98e+00	7.24e+00	4.45e-03	4.97e-03	5.96e-03
chr9	45253837	45269149	ENSMUSG00000032089	0.5000	-	Il10ra	protein_coding	2.34e-03	0.534	5.49185	0.00e+00	0.00e+00	5.30e+00	6.03e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.75e+00	4.17e+00	5.98e+00	7.27e-03	2.33e-03	8.50e-03
chr8	11007850	11054541	ENSMUSG00000096938	0.4671	+	9530052E02Rik	processed_transcript	2.39e-03	0.534	-4.66297	4.63e+00	1.93e-02	0.00e+00	0.00e+00	4.70e+00	4.95e+00	4.25e+00	1.99e-02	2.38e-02	1.43e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr2	117279993	117343001	ENSMUSG00000027347	0.4395	-	Rasgrp1	protein_coding	2.40e-03	0.534	4.75489	0.00e+00	0.00e+00	4.25e+00	2.97e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.17e+00	3.70e+00	5.88e+00	9.15e-04	1.37e-03	6.63e-03
chr14	66044988	66045877	ENSMUSG00000068165	0.5034	+	Gm10233	processed_pseudogene	2.41e-03	0.534	-4.12470	3.47e+00	4.09e-02	1.53e+00	1.59e-03	1.58e+00	7.24e+00	1.58e+00	1.59e-03	1.20e-01	1.59e-03	1.00e+00	2.00e+00	1.58e+00	7.97e-04	2.39e-03	1.59e-03

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

DEG table for the contrast GFP_vs_UNS

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 GFP_vs_UNS. 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_deseq	FDR_deseq	log2_normalized_fold_change_GFP_vs_UNS	log2_normalized_mean_counts_GFP	rpgm_normalized_mean_counts_GFP	log2_normalized_mean_counts_UNS	rpgm_normalized_mean_counts_UNS	log2_normalized_counts_GK3R131r-GFP-DARE1	log2_normalized_counts_GK3R132r-GFP-DARE2	log2_normalized_counts_GK3R133r-GFP-DARE3	rpgm_normalized_counts_GK3R131r-GFP-DARE1	rpgm_normalized_counts_GK3R132r-GFP-DARE2	rpgm_normalized_counts_GK3R133r-GFP-DARE3	log2_normalized_counts_GK3R137r-UNS-DARE1	log2_normalized_counts_GK3R138r-UNS-DARE2	log2_normalized_counts_GK3R139r-UNS-DARE3	log2_normalized_counts_GK3R137r-UNS-DARE1-TEST1	log2_normalized_counts_GK3R138r-UNS-DARE2-TEST2	rpgm_normalized_counts_GK3R137r-UNS-DARE1	rpgm_normalized_counts_GK3R138r-UNS-DARE2	rpgm_normalized_counts_GK3R139r-UNS-DARE3	rpgm_normalized_counts_GK3R137r-UNS-DARE1-TEST1	rpgm_normalized_counts_GK3R138r-UNS-DARE2-TEST2
chr3	63963633	63968659	ENSMUSG00000097724	0.4307	+	Gm26850	antisense	2.17e-06	0.0368	-6.82867	2.80e+00	4.49e-02	0.00e+00	0.00e+00	0.00e+00	8.41e+00	0.00e+00	0.00e+00	1.35e-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	0.00e+00	0.00e+00	0.00e+00
chr6	142564837	142571614	ENSMUSG00000030247	0.4574	-	Kcnj8	protein_coding	1.02e-05	0.0863	-5.81592	5.51e+00	1.92e-02	0.00e+00	0.00e+00	4.64e+00	6.77e+00	5.13e+00	8.34e-03	3.75e-02	1.18e-02	0.00e+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	0.00e+00
chr11	52154722	52168159	ENSMUSG00000108218	0.4730	-	Olfr1372-ps1	transcribed_unprocessed_pseudogene	2.51e-05	0.1150	-5.58496	5.19e+00	1.87e-02	0.00e+00	0.00e+00	5.93e+00	6.17e+00	3.46e+00	2.39e-02	2.83e-02	3.99e-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	0.00e+00	0.00e+00
chr8	121054882	121083110	ENSMUSG00000097336	0.5216	-	Fendrr	processed_transcript	2.71e-05	0.1150	-5.58496	5.51e+00	1.25e-02	0.00e+00	0.00e+00	5.52e+00	6.09e+00	4.91e+00	1.20e-02	1.78e-02	7.71e-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	0.00e+00	0.00e+00
chr12	80518990	80603896	ENSMUSG00000021130	0.4821	+	Galnt16	protein_coding	4.51e-05	0.1441	-6.65412	4.82e+00	4.22e-02	3.17e-01	1.21e-04	2.00e+00	8.66e+00	3.81e+00	9.04e-04	1.22e-01	3.92e-03	1.58e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.03e-04	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr13	96924689	96950912	ENSMUSG00000091387	0.4717	+	Gcnt4	protein_coding	6.23e-05	0.1441	-4.88671	3.23e+00	1.52e-02	8.34e-01	3.04e-04	2.00e+00	7.70e+00	0.00e+00	6.52e-04	4.50e-02	0.00e+00	0.00e+00	1.58e+00	2.58e+00	0.00e+00	0.00e+00	0.00e+00	4.35e-04	1.09e-03	0.00e+00	0.00e+00
chr5	14025276	14256689	ENSMUSG00000063531	0.3715	+	Sema3e	protein_coding	7.98e-05	0.1441	-6.75933	2.94e+00	2.35e-02	3.17e-01	6.24e-05	8.82e+00	0.00e+00	0.00e+00	7.05e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.12e-04	0.00e+00	0.00e+00
chr2	114047282	114053548	ENSMUSG00000068614	0.4686	-	Actc1	protein_coding	8.24e-05	0.1441	-5.38082	3.83e+00	1.51e-02	0.00e+00	0.00e+00	6.54e+00	4.95e+00	0.00e+00	3.42e-02	1.11e-02	0.00e+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	0.00e+00	0.00e+00
chr1	105615742	105616358	ENSMUSG00000101656	0.4943	+	Gm8004	processed_pseudogene	8.33e-05	0.1441	-6.17991	2.67e+00	6.86e-02	2.00e-01	1.59e-04	0.00e+00	0.00e+00	8.02e+00	0.00e+00	0.00e+00	2.06e-01	1.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.97e-04	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr7	30291728	30308367	ENSMUSG00000013921	0.5248	+	Clip3	protein_coding	8.48e-05	0.1441	-5.79998	4.75e+00	1.14e-02	3.17e-01	5.91e-05	3.17e+00	3.32e+00	7.75e+00	1.18e-03	1.33e-03	3.16e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	2.96e-04
chr16	48842552	48844461	ENSMUSG00000061100	0.4288	+	Retnla	protein_coding	1.06e-04	0.1450	-4.97102	5.87e+00	4.81e-02	5.61e-01	8.49e-04	5.78e+00	6.93e+00	4.91e+00	3.82e-02	8.56e-02	2.05e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	2.81e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	4.24e-03
chr1	162874317	162898726	ENSMUSG00000040170	0.4156	-	Fmo2	protein_coding	1.16e-04	0.1450	-5.24793	5.00e+00	4.26e-03	0.00e+00	0.00e+00	4.46e+00	4.39e+00	6.15e+00	2.42e-03	2.30e-03	8.06e-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	0.00e+00	0.00e+00
chr9	65398506	65414853	ENSMUSG00000041696	0.4965	+	Rasl12	protein_coding	1.26e-04	0.1450	-4.93860	3.78e+00	2.50e-03	0.00e+00	0.00e+00	3.46e+00	6.29e+00	1.58e+00	8.44e-04	6.50e-03	1.69e-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	0.00e+00	0.00e+00
chr10	41914990	42018442	ENSMUSG00000071324	0.4565	-	Armc2	protein_coding	1.29e-04	0.1450	-5.79586	4.65e+00	2.99e-03	2.00e-01	9.11e-06	3.46e+00	3.00e+00	7.50e+00	4.56e-04	3.19e-04	8.20e-03	1.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	4.56e-05	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr3	146852367	146984009	ENSMUSG00000036745	0.4182	+	Ttll7	protein_coding	1.32e-04	0.1450	-7.37178	3.88e+00	3.03e-02	4.00e-01	6.89e-05	0.00e+00	9.63e+00	2.00e+00	0.00e+00	9.06e-02	3.45e-04	0.00e+00	2.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.45e-04	0.00e+00	0.00e+00	0.00e+00
chr15	9111985	9155425	ENSMUSG00000054115	0.4269	-	Skp2	protein_coding	1.49e-04	0.1450	-5.95128	3.66e+00	1.14e-02	5.17e-01	6.95e-05	0.00e+00	2.81e+00	8.17e+00	0.00e+00	6.95e-04	3.34e-02	1.00e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	1.16e-04	2.32e-04	0.00e+00	0.00e+00	0.00e+00
chr9	56865033	56899870	ENSMUSG00000032911	0.5484	+	Cspg4	protein_coding	1.59e-04	0.1450	-5.01309	5.45e+00	1.07e-02	5.17e-01	1.27e-04	4.17e+00	6.27e+00	5.91e+00	3.58e-03	1.60e-02	1.24e-02	1.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	2.11e-04	0.00e+00	4.22e-04	0.00e+00	0.00e+00
chr4	124700701	124708611	ENSMUSG00000032643	0.5434	+	Fhl3	protein_coding	1.61e-04	0.1450	-5.14447	3.99e+00	1.94e-02	7.17e-01	2.48e-04	0.00e+00	7.38e+00	4.58e+00	0.00e+00	5.11e-02	7.12e-03	1.00e+00	1.58e+00	0.00e+00	1.00e+00	0.00e+00	3.10e-04	6.19e-04	0.00e+00	3.10e-04	0.00e+00
chr3	87971078	87980451	ENSMUSG00000004891	0.5470	+	Nes	protein_coding	1.62e-04	0.1450	-4.77259	2.11e+00	8.99e-03	0.00e+00	0.00e+00	0.00e+00	6.32e+00	0.00e+00	0.00e+00	2.70e-02	0.00e+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	0.00e+00	0.00e+00
chr11	101330605	101341938	ENSMUSG00000019326	0.5094	+	Aoc3	protein_coding	1.78e-04	0.1457	-4.56478	3.35e+00	5.10e-03	0.00e+00	0.00e+00	0.00e+00	5.58e+00	4.46e+00	0.00e+00	1.06e-02	4.72e-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	0.00e+00	0.00e+00
chr14	32856756	32939487	ENSMUSG00000050666	0.4559	+	Vstm4	protein_coding	1.81e-04	0.1457	-5.77039	6.22e+00	3.00e-02	5.17e-01	2.08e-04	5.61e+00	7.33e+00	5.70e+00	1.67e-02	5.56e-02	1.77e-02	1.58e+00	0.00e+00	0.00e+00	1.00e+00	0.00e+00	6.95e-04	0.00e+00	0.00e+00	3.47e-04	0.00e+00
chr15	10717144	10722471	ENSMUSG00000096971	0.4531	+	4930556M19Rik	lincRNA	2.03e-04	0.1457	-5.66770	2.50e+00	4.78e-02	2.00e-01	1.59e-04	0.00e+00	0.00e+00	7.50e+00	0.00e+00	0.00e+00	1.44e-01	1.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.97e-04	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr5	146384985	146473615	ENSMUSG00000029636	0.4549	+	Wasf3	protein_coding	2.11e-04	0.1457	-5.56986	6.14e+00	1.67e-02	5.17e-01	1.34e-04	5.70e+00	5.83e+00	6.89e+00	1.14e-02	1.25e-02	2.63e-02	1.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	2.23e-04	0.00e+00	4.45e-04	0.00e+00	0.00e+00
chr11	28853204	28926743	ENSMUSG00000020467	0.3874	+	Efemp1	protein_coding	2.14e-04	0.1457	-5.02647	5.76e+00	1.97e-02	6.34e-01	2.73e-04	5.55e+00	5.21e+00	6.52e+00	1.57e-02	1.23e-02	3.10e-02	0.00e+00	1.58e+00	0.00e+00	0.00e+00	1.58e+00	0.00e+00	6.82e-04	0.00e+00	0.00e+00	6.82e-04
chr17	32815449	32830261	ENSMUSG00000095253	0.4142	-	Zfp799	protein_coding	2.14e-04	0.1457	-4.65980	2.69e+00	1.09e-02	1.46e+00	3.15e-04	0.00e+00	8.08e+00	0.00e+00	0.00e+00	3.27e-02	0.00e+00	1.00e+00	0.00e+00	3.00e+00	1.00e+00	2.32e+00	1.21e-04	0.00e+00	8.47e-04	1.21e-04	4.84e-04
chr1	189207930	189402273	ENSMUSG00000037624	0.4335	-	Kcnk2	protein_coding	2.41e-04	0.1494	-5.14296	4.65e+00	4.26e-03	0.00e+00	0.00e+00	4.81e+00	3.00e+00	6.13e+00	3.35e-03	8.69e-04	8.56e-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	0.00e+00	0.00e+00
chr4	127311421	127314039	ENSMUSG00000050234	0.5697	-	Gja4	protein_coding	2.41e-04	0.1494	-4.87447	4.79e+00	1.57e-02	0.00e+00	0.00e+00	4.32e+00	5.46e+00	4.58e+00	1.06e-02	2.39e-02	1.28e-02	0.00e+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	0.00e+00
chr14	34143992	34152489	ENSMUSG00000048337	0.4906	-	Npy4r	protein_coding	2.46e-04	0.1494	5.50462	0.00e+00	0.00e+00	2.37e+00	1.28e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.69e+00	0.00e+00	4.17e+00	0.00e+00	0.00e+00	5.92e-02	0.00e+00	4.91e-03	0.00e+00	0.00e+00
chr5	12669155	12670728	ENSMUSG00000105237	0.5210	-	Gm42580	processed_pseudogene	2.73e-04	0.1576	5.37851	0.00e+00	0.00e+00	2.31e+00	3.24e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.56e+00	0.00e+00	0.00e+00	0.00e+00	4.00e+00	1.50e-01	0.00e+00	0.00e+00	0.00e+00	1.20e-02
chrX	133908426	133932446	ENSMUSG00000031253	0.4268	+	Srpx2	protein_coding	2.78e-04	0.1576	-5.11944	5.51e+00	2.13e-02	3.17e-01	1.79e-04	4.81e+00	5.58e+00	6.13e+00	1.21e-02	2.10e-02	3.09e-02	0.00e+00	0.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	8.95e-04	0.00e+00
chr11	12936834	12937938	ENSMUSG00000083859	0.5231	-	Gm12003	processed_pseudogene	2.88e-04	0.1576	5.78660	0.00e+00	0.00e+00	3.47e+00	4.32e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.77e+00	0.00e+00	4.64e+00	0.00e+00	4.95e+00	1.73e-01	0.00e+00	1.91e-02	0.00e+00	2.39e-02
chr11	62820231	62850808	ENSMUSG00000047821	0.4558	+	Trim16	protein_coding	3.07e-04	0.1597	-6.40737	3.16e+00	3.99e-02	1.15e+00	3.03e-04	0.00e+00	9.47e+00	0.00e+00	0.00e+00	1.20e-01	0.00e+00	0.00e+00	2.58e+00	1.58e+00	0.00e+00	1.58e+00	0.00e+00	8.43e-04	3.37e-04	0.00e+00	3.37e-04
chr8	20385782	20424814	ENSMUSG00000071793	0.4108	-	2610005L07Rik	transcribed_unprocessed_pseudogene	3.10e-04	0.1597	-5.52704	3.86e+00	3.27e-02	6.34e-01	3.19e-04	7.88e+00	3.70e+00	0.00e+00	9.33e-02	4.78e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.58e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	7.97e-04	7.97e-04
chr9	97444395	98033181	ENSMUSG00000032452	0.4348	-	Clstn2	protein_coding	3.40e-04	0.1685	-4.75489	4.68e+00	5.15e-03	0.00e+00	0.00e+00	4.09e+00	5.21e+00	4.75e+00	3.17e-03	7.13e-03	5.15e-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	0.00e+00	0.00e+00
chr2	69821944	69836651	ENSMUSG00000042155	0.4500	+	Klhl23	protein_coding	3.47e-04	0.1685	-4.52838	5.46e+00	9.18e-03	1.27e+00	2.49e-04	4.46e+00	7.00e+00	4.91e+00	3.27e-03	1.98e-02	4.51e-03	0.00e+00	1.58e+00	1.58e+00	1.58e+00	1.58e+00	0.00e+00	3.11e-04	3.11e-04	3.11e-04	3.11e-04
chrX	161717069	161779496	ENSMUSG00000043518	0.4352	+	Rai2	protein_coding	3.57e-04	0.1686	-5.10620	5.70e+00	3.79e-02	6.34e-01	4.98e-04	4.91e+00	5.36e+00	6.85e+00	1.80e-02	2.49e-02	7.09e-02	0.00e+00	1.58e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	1.24e-03	0.00e+00	1.24e-03	0.00e+00
chr2	163466379	163472629	ENSMUSG00000048486	0.4967	-	Fitm2	protein_coding	3.75e-04	0.1722	-4.38082	4.08e+00	9.29e-03	7.17e-01	2.28e-04	2.00e+00	6.78e+00	3.46e+00	6.85e-04	2.49e-02	2.28e-03	0.00e+00	2.00e+00	0.00e+00	0.00e+00	1.58e+00	0.00e+00	6.85e-04	0.00e+00	0.00e+00	4.57e-04
chr18	61649625	61665537	ENSMUSG00000097324	0.5202	-	Carmn	lincRNA	4.36e-04	0.1753	-4.45744	4.97e+00	1.89e-02	7.81e-01	4.78e-04	3.46e+00	6.75e+00	4.70e+00	3.99e-03	4.27e-02	9.97e-03	0.00e+00	0.00e+00	0.00e+00	1.58e+00	2.32e+00	0.00e+00	0.00e+00	0.00e+00	7.97e-04	1.59e-03
chr3	104945272	104961921	ENSMUSG00000027840	0.4931	-	Wnt2b	protein_coding	4.46e-04	0.1753	-4.92019	4.97e+00	8.40e-03	2.00e-01	4.75e-05	5.09e+00	3.91e+00	5.91e+00	7.84e-03	3.33e-03	1.40e-02	1.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	2.38e-04	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr12	105603085	105605428	ENSMUSG00000041347	0.5205	+	Bdkrb1	protein_coding	4.49e-04	0.1753	-4.69890	5.96e+00	3.81e-02	9.81e-01	8.69e-04	6.02e+00	5.93e+00	5.93e+00	3.97e-02	3.72e-02	3.72e-02	0.00e+00	1.58e+00	0.00e+00	1.00e+00	2.32e+00	0.00e+00	1.24e-03	0.00e+00	6.21e-04	2.48e-03
chr2	74703248	74716130	ENSMUSG00000052371	0.4983	-	Hoxd3os1	antisense	4.61e-04	0.1753	-4.73697	5.35e+00	1.07e-02	5.17e-01	1.53e-04	5.04e+00	5.09e+00	5.93e+00	8.18e-03	8.44e-03	1.53e-02	0.00e+00	0.00e+00	0.00e+00	1.00e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	2.56e-04	5.11e-04
chr11	43474276	43491525	ENSMUSG00000046491	0.4809	+	C1qtnf2	protein_coding	4.64e-04	0.1753	-4.74389	6.05e+00	2.55e-02	6.34e-01	5.93e-04	6.39e+00	5.39e+00	6.38e+00	3.08e-02	1.52e-02	3.04e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.17e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	2.97e-03
chr11	90859767	90861348	ENSMUSG00000083764	0.4583	-	Gm11516	processed_pseudogene	4.64e-04	0.1753	-5.63582	3.25e+00	4.68e-02	2.00e-01	1.59e-04	0.00e+00	2.32e+00	7.43e+00	0.00e+00	3.19e-03	1.37e-01	1.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.97e-04	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr5	142852616	142853199	ENSMUSG00000082308	0.5788	-	Gm15770	processed_pseudogene	4.66e-04	0.1753	-5.10154	3.24e+00	2.66e-02	0.00e+00	0.00e+00	6.54e+00	0.00e+00	3.17e+00	7.34e-02	0.00e+00	6.38e-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	0.00e+00	0.00e+00
chr13	51408618	51422797	ENSMUSG00000067586	0.5034	+	S1pr3	protein_coding	4.71e-04	0.1753	-4.71882	5.68e+00	1.25e-02	6.64e-01	2.42e-04	6.15e+00	5.32e+00	5.55e+00	1.69e-02	9.44e-03	1.11e-02	1.00e+00	0.00e+00	0.00e+00	0.00e+00	2.32e+00	2.42e-04	0.00e+00	0.00e+00	0.00e+00	9.69e-04
chr12	86056744	86079041	ENSMUSG00000021253	0.4898	-	Tgfb3	protein_coding	4.75e-04	0.1753	-6.22239	5.37e+00	6.48e-02	7.17e-01	4.37e-04	8.67e+00	2.32e+00	5.13e+00	1.78e-01	1.75e-03	1.48e-02	0.00e+00	2.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	1.31e-03	0.00e+00	8.73e-04	0.00e+00
chr2	31314415	31460738	ENSMUSG00000055632	0.5208	+	Hmcn2	protein_coding	4.91e-04	0.1754	-5.35755	6.13e+00	1.97e-02	8.34e-01	2.44e-04	5.61e+00	5.52e+00	7.24e+00	1.17e-02	1.10e-02	3.65e-02	1.00e+00	0.00e+00	0.00e+00	1.58e+00	1.58e+00	2.44e-04	0.00e+00	0.00e+00	4.87e-04	4.87e-04
chr9	22332012	22389188	ENSMUSG00000036777	0.4174	-	Anln	protein_coding	5.04e-04	0.1754	-5.75616	2.94e+00	2.02e-02	9.17e-01	2.41e-04	0.00e+00	0.00e+00	8.82e+00	0.00e+00	0.00e+00	6.05e-02	0.00e+00	0.00e+00	3.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	9.38e-04	0.00e+00	2.68e-04
chr13	4228700	4248681	ENSMUSG00000071551	0.3759	+	Akr1c19	protein_coding	5.06e-04	0.1754	-4.16993	3.12e+00	6.19e-03	0.00e+00	0.00e+00	5.04e+00	4.32e+00	0.00e+00	1.16e-02	6.91e-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	0.00e+00	0.00e+00	0.00e+00
chr9	60712989	60738801	ENSMUSG00000034839	0.4716	+	Larp6	protein_coding	5.27e-04	0.1790	-4.45438	5.58e+00	2.80e-02	6.34e-01	8.01e-04	4.52e+00	6.64e+00	5.58e+00	1.10e-02	4.95e-02	2.35e-02	0.00e+00	3.17e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	4.00e-03	0.00e+00	0.00e+00	0.00e+00
chr5	91074622	91093646	ENSMUSG00000029377	0.3961	+	Ereg	protein_coding	5.40e-04	0.1799	-4.82443	4.54e+00	5.75e-03	0.00e+00	0.00e+00	5.70e+00	3.46e+00	4.46e+00	1.07e-02	2.10e-03	4.42e-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	0.00e+00	0.00e+00
chr10	26980036	27619758	ENSMUSG00000019899	0.3766	-	Lama2	protein_coding	5.58e-04	0.1823	-4.55714	5.23e+00	3.99e-03	4.00e-01	6.53e-05	5.09e+00	5.21e+00	5.39e+00	3.59e-03	3.92e-03	4.47e-03	0.00e+00	2.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.27e-04	0.00e+00	0.00e+00	0.00e+00
chr15	6813577	6874969	ENSMUSG00000022146	0.4311	-	Osmr	protein_coding	5.76e-04	0.1845	-4.64386	5.65e+00	6.70e-03	9.17e-01	1.49e-04	5.39e+00	6.48e+00	5.09e+00	5.08e-03	1.09e-02	4.09e-03	1.00e+00	2.00e+00	0.00e+00	1.58e+00	0.00e+00	1.24e-04	3.72e-04	0.00e+00	2.48e-04	0.00e+00
chr2	85162334	85196699	ENSMUSG00000075224	0.4360	-	Lrrc55	protein_coding	5.98e-04	0.1880	-4.71882	5.71e+00	7.79e-03	7.17e-01	1.51e-04	5.73e+00	5.86e+00	5.55e+00	7.84e-03	8.60e-03	6.94e-03	0.00e+00	2.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	4.52e-04	0.00e+00	3.02e-04	0.00e+00
chr5	43662346	43740972	ENSMUSG00000039765	0.4323	+	Cc2d2a	protein_coding	6.19e-04	0.1881	-5.21809	4.43e+00	1.29e-02	6.00e-01	1.56e-04	2.58e+00	3.17e+00	7.54e+00	9.74e-04	1.56e-03	3.60e-02	1.00e+00	2.00e+00	0.00e+00	0.00e+00	0.00e+00	1.95e-04	5.84e-04	0.00e+00	0.00e+00	0.00e+00
chr9	7502352	7510240	ENSMUSG00000047562	0.4035	+	Mmp10	protein_coding	6.20e-04	0.1881	-5.10154	6.55e+00	6.79e-02	1.38e+00	1.33e-03	7.16e+00	6.86e+00	5.64e+00	9.45e-02	7.65e-02	3.26e-02	1.00e+00	2.00e+00	0.00e+00	2.32e+00	1.58e+00	6.65e-04	2.00e-03	0.00e+00	2.66e-03	1.33e-03
chr10	76595762	76623630	ENSMUSG00000020241	0.5044	-	Col6a2	protein_coding	6.44e-04	0.1919	-5.83048	7.31e+00	2.65e-02	1.18e+00	3.01e-04	7.22e+00	7.41e+00	7.31e+00	2.48e-02	2.83e-02	2.64e-02	0.00e+00	2.00e+00	0.00e+00	1.58e+00	2.32e+00	0.00e+00	5.02e-04	0.00e+00	3.35e-04	6.69e-04
chr19	5068078	5070637	ENSMUSG00000056481	0.6137	+	Cd248	protein_coding	6.66e-04	0.1920	-4.47393	4.44e+00	2.12e-02	2.00e-01	1.65e-04	5.29e+00	5.04e+00	3.00e+00	3.13e-02	2.64e-02	5.77e-03	1.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	8.24e-04	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr11	59505662	59513647	ENSMUSG00000072893	0.5080	+	4933439C10Rik	processed_transcript	6.67e-04	0.1920	-4.43741	3.95e+00	4.08e-03	0.00e+00	0.00e+00	2.00e+00	4.86e+00	5.00e+00	5.92e-04	5.52e-03	6.12e-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	0.00e+00	0.00e+00
chr11	55158470	55185077	ENSMUSG00000020264	0.4722	-	Slc36a2	protein_coding	6.84e-04	0.1937	-5.07800	6.59e+00	2.97e-02	9.51e-01	5.91e-04	7.09e+00	6.71e+00	5.98e+00	3.99e-02	3.08e-02	1.83e-02	0.00e+00	0.00e+00	0.00e+00	3.17e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	2.37e-03	5.91e-04
chr8	116921730	116941507	ENSMUSG00000031756	0.4807	+	Cenpn	protein_coding	7.11e-04	0.1953	-9.07771	3.55e+00	1.17e-01	0.00e+00	0.00e+00	1.07e+01	0.00e+00	0.00e+00	3.50e-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	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr4	108014791	108096445	ENSMUSG00000028600	0.4651	-	Podn	protein_coding	7.13e-04	0.1953	-4.90689	6.54e+00	1.96e-02	1.08e+00	4.54e-04	6.21e+00	6.36e+00	7.04e+00	1.51e-02	1.67e-02	2.70e-02	0.00e+00	2.58e+00	0.00e+00	0.00e+00	2.81e+00	0.00e+00	1.03e-03	0.00e+00	0.00e+00	1.24e-03
chr12	5077472	5375682	ENSMUSG00000020627	0.4760	-	Klhl29	protein_coding	7.36e-04	0.1975	-5.52124	5.32e+00	1.66e-02	6.34e-01	1.62e-04	3.91e+00	4.32e+00	7.73e+00	2.84e-03	3.85e-03	4.30e-02	1.58e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	4.05e-04	4.05e-04	0.00e+00	0.00e+00	0.00e+00
chr5	33198184	33218455	ENSMUSG00000037379	0.4873	-	Spon2	protein_coding	7.48e-04	0.1975	-5.20457	5.70e+00	1.35e-02	5.17e-01	1.39e-04	5.39e+00	5.04e+00	6.67e+00	9.53e-03	7.44e-03	2.35e-02	1.58e+00	0.00e+00	0.00e+00	1.00e+00	0.00e+00	4.65e-04	0.00e+00	0.00e+00	2.32e-04	0.00e+00
chr2	119373042	119477687	ENSMUSG00000034154	0.4088	-	Ino80	protein_coding	7.63e-04	0.1975	-6.04985	4.78e+00	2.98e-02	9.81e-01	2.64e-04	3.17e+00	2.32e+00	8.85e+00	1.51e-03	7.54e-04	8.70e-02	1.00e+00	0.00e+00	0.00e+00	1.58e+00	2.32e+00	1.88e-04	0.00e+00	0.00e+00	3.77e-04	7.54e-04
chr13	43370710	43395202	ENSMUSG00000054021	0.4539	+	Sirt5	protein_coding	7.67e-04	0.1975	-7.07459	3.64e+00	1.31e-01	5.17e-01	3.65e-04	1.58e+00	0.00e+00	9.33e+00	1.22e-03	0.00e+00	3.91e-01	1.58e+00	0.00e+00	0.00e+00	1.00e+00	0.00e+00	1.22e-03	0.00e+00	0.00e+00	6.08e-04	0.00e+00
chr4	148098437	148130698	ENSMUSG00000029005	0.5062	-	Draxin	protein_coding	7.82e-04	0.1984	-4.12163	4.05e+00	5.74e-03	6.34e-01	1.51e-04	4.46e+00	6.11e+00	1.58e+00	3.97e-03	1.29e-02	3.78e-04	0.00e+00	0.00e+00	1.58e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	3.78e-04	0.00e+00	3.78e-04
chr8	77663031	77724464	ENSMUSG00000031616	0.4362	-	Ednra	protein_coding	8.16e-04	0.2039	-4.65980	5.74e+00	1.34e-02	1.15e+00	3.14e-04	4.95e+00	5.55e+00	6.70e+00	6.74e-03	1.03e-02	2.31e-02	1.00e+00	1.58e+00	0.00e+00	1.58e+00	1.58e+00	2.25e-04	4.49e-04	0.00e+00	4.49e-04	4.49e-04
chr2	164805098	164822130	ENSMUSG00000045822	0.4676	+	Zswim3	protein_coding	8.39e-04	0.2059	-5.55830	3.09e+00	1.22e-01	1.36e+00	2.01e-03	0.00e+00	9.28e+00	0.00e+00	0.00e+00	3.65e-01	0.00e+00	1.00e+00	0.00e+00	0.00e+00	2.00e+00	3.81e+00	5.90e-04	0.00e+00	0.00e+00	1.77e-03	7.67e-03
chr2	173020498	173034734	ENSMUSG00000027510	0.5623	+	Rbm38	protein_coding	8.49e-04	0.2059	5.11270	0.00e+00	0.00e+00	4.24e+00	7.26e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.49e+00	2.00e+00	4.17e+00	5.75e+00	2.81e+00	1.92e-02	6.48e-04	3.67e-03	1.14e-02	1.30e-03
chr14	7964533	7994573	ENSMUSG00000025279	0.4684	-	Dnase1l3	protein_coding	9.28e-04	0.2086	5.71149	0.00e+00	0.00e+00	5.23e+00	8.96e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.38e+00	3.70e+00	3.70e+00	6.63e+00	5.75e+00	1.43e-02	2.09e-03	2.09e-03	1.71e-02	9.24e-03
chr16	10420557	10447362	ENSMUSG00000050908	0.4797	-	Tvp23a	protein_coding	9.34e-04	0.2086	-4.27302	3.80e+00	1.84e-03	0.00e+00	0.00e+00	2.58e+00	5.36e+00	3.46e+00	5.02e-04	4.01e-03	1.00e-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	0.00e+00	0.00e+00
chr3	106759921	106790149	ENSMUSG00000040747	0.3689	-	Cd53	protein_coding	9.51e-04	0.2086	5.14568	0.00e+00	0.00e+00	4.80e+00	1.61e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.51e+00	4.39e+00	3.70e+00	4.81e+00	4.58e+00	4.21e-02	9.36e-03	5.62e-03	1.26e-02	1.08e-02
chr1	172341210	172374085	ENSMUSG00000044708	0.4888	+	Kcnj10	protein_coding	9.60e-04	0.2086	-4.60779	4.46e+00	2.48e-02	2.20e+00	8.33e-04	2.81e+00	8.58e+00	2.00e+00	1.14e-03	7.26e-02	5.68e-04	1.58e+00	1.58e+00	3.46e+00	1.58e+00	2.81e+00	3.79e-04	3.79e-04	1.89e-03	3.79e-04	1.14e-03
chr17	25958364	25985796	ENSMUSG00000037326	0.5112	-	Capn15	protein_coding	9.67e-04	0.2086	-4.89010	3.77e+00	1.55e-02	1.95e+00	4.18e-04	2.58e+00	8.71e+00	0.00e+00	5.50e-04	4.61e-02	0.00e+00	1.58e+00	3.00e+00	2.58e+00	2.58e+00	0.00e+00	2.20e-04	7.69e-04	5.50e-04	5.50e-04	0.00e+00
chr9	115909455	116076176	ENSMUSG00000056880	0.4482	+	Gadl1	protein_coding	9.88e-04	0.2086	-4.87447	2.14e+00	5.92e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.43e+00	0.00e+00	0.00e+00	1.78e-02	0.00e+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	0.00e+00
chr5	36017180	36398139	ENSMUSG00000029093	0.5086	-	Sorcs2	protein_coding	1.02e-03	0.2086	-4.31389	5.85e+00	6.93e-03	1.18e+00	2.36e-04	5.36e+00	5.98e+00	6.23e+00	4.73e-03	7.33e-03	8.75e-03	0.00e+00	2.58e+00	0.00e+00	1.00e+00	2.32e+00	0.00e+00	5.91e-04	0.00e+00	1.18e-04	4.73e-04
chr3	18054174	18057517	ENSMUSG00000025128	0.5167	+	Bhlhe22	protein_coding	1.02e-03	0.2086	-4.60733	5.24e+00	1.43e-02	5.17e-01	2.25e-04	4.70e+00	5.61e+00	5.39e+00	9.39e-03	1.80e-02	1.54e-02	1.00e+00	0.00e+00	0.00e+00	1.58e+00	0.00e+00	3.76e-04	0.00e+00	0.00e+00	7.52e-04	0.00e+00
chr2	144142488	144143373	ENSMUSG00000082480	0.5756	-	Gm11687	processed_pseudogene	1.03e-03	0.2086	5.94953	0.00e+00	0.00e+00	4.11e+00	4.85e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.65e+00	0.00e+00	5.29e+00	1.58e+00	6.02e+00	1.59e-01	0.00e+00	3.03e-02	1.59e-03	5.10e-02
chr12	101746565	101819055	ENSMUSG00000021186	0.4545	-	Fbln5	protein_coding	1.03e-03	0.2086	-5.80408	6.48e+00	4.30e-02	1.00e+00	5.89e-04	4.70e+00	9.31e+00	5.43e+00	4.60e-03	1.17e-01	7.73e-03	0.00e+00	0.00e+00	0.00e+00	1.00e+00	4.00e+00	0.00e+00	0.00e+00	0.00e+00	1.84e-04	2.76e-03
chr9	123962124	123968692	ENSMUSG00000025804	0.3978	-	Ccr1	protein_coding	1.05e-03	0.2086	5.16993	0.00e+00	0.00e+00	4.89e+00	1.37e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.30e+00	5.36e+00	3.91e+00	4.86e+00	4.00e+00	3.05e-02	1.57e-02	5.48e-03	1.10e-02	5.87e-03
chr17	32120820	32166880	ENSMUSG00000038146	0.4988	-	Notch3	protein_coding	1.06e-03	0.2086	-5.69960	5.09e+00	1.01e-01	1.61e+00	1.51e-03	0.00e+00	9.28e+00	5.98e+00	0.00e+00	2.76e-01	2.75e-02	1.00e+00	3.46e+00	2.58e+00	1.00e+00	0.00e+00	4.44e-04	4.44e-03	2.22e-03	4.44e-04	0.00e+00
chr8	31187331	31261738	ENSMUSG00000046152	0.4421	+	Fut10	protein_coding	1.07e-03	0.2086	-4.08746	4.03e+00	2.34e-03	0.00e+00	0.00e+00	4.17e+00	4.46e+00	3.46e+00	2.49e-03	3.07e-03	1.46e-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	0.00e+00	0.00e+00
chr12	79130777	79156301	ENSMUSG00000021125	0.4294	+	Arg2	protein_coding	1.07e-03	0.2086	5.24793	0.00e+00	0.00e+00	5.00e+00	2.43e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.32e+00	4.17e+00	5.21e+00	5.29e+00	4.00e+00	5.18e-02	1.12e-02	2.36e-02	2.49e-02	9.84e-03
chr8	70184340	70212305	ENSMUSG00000002346	0.5079	-	Slc25a42	protein_coding	1.08e-03	0.2086	-7.84941	3.90e+00	6.25e-02	4.00e-01	1.02e-04	1.01e+01	0.00e+00	1.58e+00	1.87e-01	0.00e+00	3.40e-04	0.00e+00	2.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.09e-04	0.00e+00	0.00e+00	0.00e+00
chr17	34143307	34151553	ENSMUSG00000037548	0.4964	+	H2-DMb2	protein_coding	1.08e-03	0.2086	5.59096	0.00e+00	0.00e+00	5.48e+00	1.59e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.32e+00	5.36e+00	4.52e+00	5.55e+00	5.64e+00	2.66e-02	1.35e-02	7.42e-03	1.55e-02	1.65e-02
chr6	86195223	86275719	ENSMUSG00000029999	0.4789	+	Tgfa	protein_coding	1.11e-03	0.2086	5.91767	3.33e-01	5.31e-05	3.27e+00	1.27e-02	0.00e+00	1.00e+00	0.00e+00	0.00e+00	1.59e-04	0.00e+00	8.57e+00	0.00e+00	1.58e+00	2.58e+00	3.58e+00	6.06e-02	0.00e+00	3.19e-04	7.97e-04	1.75e-03
chr12	38779380	38868215	ENSMUSG00000004151	0.3851	+	Etv1	protein_coding	1.14e-03	0.2086	-4.58782	5.03e+00	4.30e-03	4.00e-01	5.26e-05	5.52e+00	4.86e+00	4.70e+00	5.92e-03	3.68e-03	3.29e-03	1.00e+00	0.00e+00	0.00e+00	1.00e+00	0.00e+00	1.32e-04	0.00e+00	0.00e+00	1.32e-04	0.00e+00
chr9	33728247	33728850	ENSMUSG00000079884	0.5215	+	Gm10698	processed_pseudogene	1.14e-03	0.2086	4.82273	6.67e-01	7.97e-04	3.53e+00	4.43e-02	0.00e+00	0.00e+00	2.00e+00	0.00e+00	0.00e+00	2.39e-03	7.97e+00	0.00e+00	4.17e+00	3.17e+00	2.32e+00	1.99e-01	0.00e+00	1.36e-02	6.38e-03	3.19e-03
chr5	25100983	25110109	ENSMUSG00000043833	0.4836	+	2900005J15Rik	processed_transcript	1.14e-03	0.2086	-4.69779	3.42e+00	1.41e-02	3.17e-01	1.59e-04	1.58e+00	2.00e+00	6.67e+00	7.97e-04	1.20e-03	4.03e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.97e-04
chr4	43631935	43651244	ENSMUSG00000028469	0.5023	+	Npr2	protein_coding	1.16e-03	0.2086	-3.76939	4.46e+00	3.65e-03	7.17e-01	1.51e-04	3.58e+00	6.00e+00	3.81e+00	1.38e-03	7.93e-03	1.64e-03	0.00e+00	0.00e+00	2.58e+00	1.00e+00	0.00e+00	0.00e+00	0.00e+00	6.29e-04	1.26e-04	0.00e+00
chr10	121033960	121100650	ENSMUSG00000020218	0.4349	+	Wif1	protein_coding	1.16e-03	0.2086	-4.45943	4.34e+00	1.04e-02	0.00e+00	0.00e+00	3.46e+00	4.64e+00	4.91e+00	4.94e-03	1.19e-02	1.43e-02	0.00e+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	0.00e+00
chr17	71781947	71858351	ENSMUSG00000024059	0.4347	+	Clip4	protein_coding	1.18e-03	0.2086	-4.36632	5.02e+00	1.05e-02	5.17e-01	1.96e-04	4.81e+00	4.86e+00	5.39e+00	8.84e-03	9.16e-03	1.34e-02	0.00e+00	0.00e+00	0.00e+00	1.00e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	3.27e-04	6.54e-04
chr11	114996721	115001880	ENSMUSG00000044811	0.5008	-	Cd300c2	protein_coding	1.19e-03	0.2086	4.87774	0.00e+00	0.00e+00	4.35e+00	7.19e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.15e+00	4.64e+00	3.00e+00	5.17e+00	2.81e+00	1.77e-02	6.07e-03	1.77e-03	8.86e-03	1.52e-03
chr4	65124174	65357509	ENSMUSG00000028370	0.4086	+	Pappa	protein_coding	1.19e-03	0.2086	-4.50250	4.41e+00	3.08e-03	0.00e+00	0.00e+00	4.95e+00	3.70e+00	4.58e+00	4.26e-03	1.71e-03	3.27e-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	0.00e+00	0.00e+00
chr3	59096448	59101821	ENSMUSG00000050075	0.3967	-	Gpr171	protein_coding	1.23e-03	0.2086	4.83794	0.00e+00	0.00e+00	4.24e+00	1.26e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.13e+00	4.39e+00	2.58e+00	5.29e+00	2.81e+00	3.14e-02	9.10e-03	2.27e-03	1.73e-02	2.73e-03
chr6	41546730	41548352	ENSMUSG00000076498	0.4750	+	Trbc2	TR_C_gene	1.23e-03	0.2086	6.05311	0.00e+00	0.00e+00	5.98e+00	4.59e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.55e+00	6.32e+00	5.13e+00	5.95e+00	5.93e+00	6.53e-02	5.54e-02	2.39e-02	4.28e-02	4.21e-02
chr19	11443553	11463549	ENSMUSG00000056290	0.3871	+	Ms4a4b	protein_coding	1.24e-03	0.2086	5.65535	0.00e+00	0.00e+00	5.60e+00	1.17e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.70e+00	5.13e+00	5.88e+00	6.15e+00	5.13e+00	1.21e-02	8.04e-03	1.37e-02	1.66e-02	8.04e-03
chr15	18818947	19014236	ENSMUSG00000022321	0.3655	+	Cdh10	protein_coding	1.24e-03	0.2086	-7.81698	4.46e+00	5.43e-02	7.17e-01	1.21e-04	0.00e+00	1.04e+01	3.00e+00	0.00e+00	1.62e-01	8.45e-04	0.00e+00	0.00e+00	1.58e+00	2.00e+00	0.00e+00	0.00e+00	0.00e+00	2.41e-04	3.62e-04	0.00e+00
chr11	100228845	100232078	ENSMUSG00000084257	0.4858	-	Gm11597	unprocessed_pseudogene	1.25e-03	0.2086	5.64962	0.00e+00	0.00e+00	4.15e+00	3.92e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.11e+00	2.00e+00	5.67e+00	0.00e+00	6.98e+00	5.42e-02	2.39e-03	3.99e-02	0.00e+00	9.97e-02
chr17	7738569	7827302	ENSMUSG00000071984	0.4497	-	Fndc1	protein_coding	1.25e-03	0.2086	-6.38402	5.71e+00	4.33e-02	7.61e-01	3.76e-04	3.91e+00	9.77e+00	3.46e+00	2.02e-03	1.27e-01	1.45e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.81e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.88e-03
chr15	84324026	84342978	ENSMUSG00000022439	0.5140	+	Parvg	protein_coding	1.26e-03	0.2086	5.50462	0.00e+00	0.00e+00	5.32e+00	6.66e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.29e+00	5.32e+00	4.32e+00	5.98e+00	4.70e+00	1.15e-02	5.85e-03	2.85e-03	9.30e-03	3.75e-03
chr9	75775364	75900310	ENSMUSG00000032179	0.3803	+	Bmp5	protein_coding	1.28e-03	0.2086	-4.60486	6.53e+00	2.27e-02	1.78e+00	7.08e-04	6.73e+00	5.86e+00	7.00e+00	2.48e-02	1.35e-02	3.00e-02	0.00e+00	2.00e+00	2.58e+00	2.00e+00	2.32e+00	0.00e+00	7.08e-04	1.18e-03	7.08e-04	9.44e-04
chr15	102998257	103011881	ENSMUSG00000001661	0.4924	+	Hoxc6	protein_coding	1.28e-03	0.2086	-4.21643	5.42e+00	1.03e-02	8.78e-01	3.48e-04	5.17e+00	4.70e+00	6.38e+00	7.61e-03	5.43e-03	1.78e-02	0.00e+00	0.00e+00	1.58e+00	0.00e+00	2.81e+00	0.00e+00	0.00e+00	4.35e-04	0.00e+00	1.30e-03
chr7	29953621	29965711	ENSMUSG00000063623	0.4614	+	C230062I16Rik	processed_transcript	1.29e-03	0.2086	-4.34577	4.14e+00	5.06e-03	0.00e+00	0.00e+00	4.91e+00	4.52e+00	3.00e+00	7.59e-03	5.76e-03	1.83e-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	0.00e+00	0.00e+00
chr3	88364584	88368541	ENSMUSG00000041423	0.5599	+	Paqr6	protein_coding	1.33e-03	0.2122	-4.52356	4.22e+00	5.07e-03	0.00e+00	0.00e+00	3.58e+00	3.58e+00	5.49e+00	2.53e-03	2.53e-03	1.01e-02	0.00e+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	0.00e+00
chr5	91051871	91074773	ENSMUSG00000107350	0.3953	-	Gm42532	antisense	1.36e-03	0.2122	-4.47032	5.30e+00	3.46e-02	7.17e-01	7.97e-04	5.83e+00	4.25e+00	5.83e+00	4.47e-02	1.44e-02	4.47e-02	0.00e+00	2.00e+00	0.00e+00	0.00e+00	1.58e+00	0.00e+00	2.39e-03	0.00e+00	0.00e+00	1.59e-03
chr17	32183770	32189549	ENSMUSG00000037577	0.4799	-	Ephx3	protein_coding	1.38e-03	0.2122	-5.93664	6.46e+00	1.03e-01	1.91e+00	1.26e-03	4.17e+00	9.37e+00	5.83e+00	7.14e-03	2.77e-01	2.35e-02	1.58e+00	2.00e+00	1.58e+00	1.58e+00	2.81e+00	8.40e-04	1.26e-03	8.40e-04	8.40e-04	2.52e-03
chr16	32142785	32165594	ENSMUSG00000052384	0.4701	-	Nrros	protein_coding	1.38e-03	0.2122	5.72792	0.00e+00	0.00e+00	5.52e+00	1.24e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.95e+00	4.91e+00	4.52e+00	6.70e+00	5.52e+00	1.45e-02	6.90e-03	5.24e-03	2.45e-02	1.07e-02
chr9	30942562	30963838	ENSMUSG00000031994	0.4955	+	Adamts8	protein_coding	1.39e-03	0.2122	-4.35588	4.25e+00	2.94e-03	3.17e-01	4.25e-05	5.93e+00	4.25e+00	2.58e+00	6.38e-03	1.91e-03	5.32e-04	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	2.13e-04
chr8	68356781	68735146	ENSMUSG00000036356	0.4094	-	Csgalnact1	protein_coding	1.39e-03	0.2122	6.00720	5.28e-01	8.07e-05	3.87e+00	1.29e-02	1.58e+00	0.00e+00	0.00e+00	2.42e-04	0.00e+00	0.00e+00	8.84e+00	5.36e+00	5.13e+00	0.00e+00	0.00e+00	5.54e-02	4.84e-03	4.12e-03	0.00e+00	0.00e+00
chr6	6351304	6352267	ENSMUSG00000097900	0.4782	-	Gm8652	processed_pseudogene	1.41e-03	0.2122	4.92735	1.06e+00	1.06e-03	2.78e+00	5.58e-02	1.58e+00	0.00e+00	1.58e+00	1.59e-03	0.00e+00	1.59e-03	8.42e+00	1.58e+00	0.00e+00	2.32e+00	1.58e+00	2.73e-01	1.59e-03	0.00e+00	3.19e-03	1.59e-03
chr12	113418558	113422730	ENSMUSG00000076617	0.4992	-	Ighm	IG_C_gene	1.43e-03	0.2122	5.92600	0.00e+00	0.00e+00	5.87e+00	2.06e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.39e+00	5.36e+00	5.46e+00	6.17e+00	5.98e+00	2.86e-02	1.38e-02	1.48e-02	2.45e-02	2.14e-02
chr3	152153447	152154116	ENSMUSG00000084343	0.5194	+	Gm16198	processed_pseudogene	1.44e-03	0.2122	7.27798	0.00e+00	0.00e+00	4.37e+00	1.23e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	9.43e+00	2.00e+00	6.09e+00	1.00e+00	3.32e+00	5.51e-01	2.39e-03	5.34e-02	7.97e-04	7.18e-03
chr7	30818348	30823775	ENSMUSG00000051314	0.5228	-	Ffar2	protein_coding	1.44e-03	0.2122	5.64386	0.00e+00	0.00e+00	5.50e+00	1.43e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	5.55e+00	6.07e+00	4.52e+00	6.32e+00	5.04e+00	1.34e-02	1.93e-02	6.42e-03	2.31e-02	9.34e-03
chr9	95637601	95698096	ENSMUSG00000015354	0.4438	+	Pcolce2	protein_coding	1.46e-03	0.2122	-4.41504	2.93e+00	3.69e-03	0.00e+00	0.00e+00	5.78e+00	0.00e+00	3.00e+00	9.80e-03	0.00e+00	1.27e-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	0.00e+00	0.00e+00

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

DEG table for the contrast TOM_vs_UNS

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 TOM_vs_UNS. 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_deseq	FDR_deseq	log2_normalized_fold_change_TOM_vs_UNS	log2_normalized_mean_counts_TOM	rpgm_normalized_mean_counts_TOM	log2_normalized_mean_counts_UNS	rpgm_normalized_mean_counts_UNS	log2_normalized_counts_GK3R134r-TOM-DARE1	log2_normalized_counts_GK3R135r-TOM-DARE2	log2_normalized_counts_GK3R136r-TOM-DARE3	rpgm_normalized_counts_GK3R134r-TOM-DARE1	rpgm_normalized_counts_GK3R135r-TOM-DARE2	rpgm_normalized_counts_GK3R136r-TOM-DARE3	log2_normalized_counts_GK3R137r-UNS-DARE1	log2_normalized_counts_GK3R138r-UNS-DARE2	log2_normalized_counts_GK3R139r-UNS-DARE3	log2_normalized_counts_GK3R137r-UNS-DARE1-TEST1	log2_normalized_counts_GK3R138r-UNS-DARE2-TEST2	rpgm_normalized_counts_GK3R137r-UNS-DARE1	rpgm_normalized_counts_GK3R138r-UNS-DARE2	rpgm_normalized_counts_GK3R139r-UNS-DARE3	rpgm_normalized_counts_GK3R137r-UNS-DARE1-TEST1	rpgm_normalized_counts_GK3R138r-UNS-DARE2-TEST2
chr10	127289696	127290788	ENSMUSG00000092384	0.5572	-	Gm4189	processed_transcript	2.14e-05	0.178	-5.65344	2.41e+00	3.93e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.22e+00	0.00e+00	0.00e+00	1.18e-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	0.00e+00	0.00e+00
chr1	162874317	162898726	ENSMUSG00000040170	0.4156	-	Fmo2	protein_coding	2.93e-05	0.178	-5.85798	5.54e+00	6.57e-03	0.00e+00	0.00e+00	4.17e+00	6.63e+00	5.83e+00	1.96e-03	1.13e-02	6.45e-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	0.00e+00	0.00e+00
chr14	34143992	34152489	ENSMUSG00000048337	0.4906	-	Npy4r	protein_coding	3.73e-05	0.178	5.50462	0.00e+00	0.00e+00	2.37e+00	1.28e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.69e+00	0.00e+00	4.17e+00	0.00e+00	0.00e+00	5.92e-02	0.00e+00	4.91e-03	0.00e+00	0.00e+00
chr5	12669155	12670728	ENSMUSG00000105237	0.5210	-	Gm42580	processed_pseudogene	4.19e-05	0.178	5.37851	0.00e+00	0.00e+00	2.31e+00	3.24e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.56e+00	0.00e+00	0.00e+00	0.00e+00	4.00e+00	1.50e-01	0.00e+00	0.00e+00	0.00e+00	1.20e-02
chrX	41400854	41678601	ENSMUSG00000001986	0.3876	+	Gria3	protein_coding	6.31e-05	0.184	-5.81592	3.71e+00	4.98e-03	0.00e+00	0.00e+00	1.00e+00	7.32e+00	2.81e+00	9.00e-05	1.43e-02	5.40e-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	0.00e+00	0.00e+00
chr5	138264921	138272840	ENSMUSG00000075593	0.4822	-	Gal3st4	protein_coding	8.27e-05	0.184	-6.71097	3.92e+00	5.06e-02	3.17e-01	1.39e-04	3.00e+00	8.75e+00	0.00e+00	2.43e-03	1.49e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.94e-04
chr13	4228700	4248681	ENSMUSG00000071551	0.3759	+	Akr1c19	protein_coding	8.65e-05	0.184	-5.10154	3.77e+00	1.21e-02	0.00e+00	0.00e+00	0.00e+00	5.49e+00	5.83e+00	0.00e+00	1.60e-02	2.04e-02	0.00e+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	0.00e+00
chr7	28179469	28187294	ENSMUSG00000002409	0.5819	+	Dyrk1b	protein_coding	8.67e-05	0.184	-6.28129	2.71e+00	5.68e-02	2.00e-01	1.23e-04	0.00e+00	8.12e+00	0.00e+00	0.00e+00	1.70e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.15e-04	0.00e+00
chr7	73375509	73419899	ENSMUSG00000070509	0.5051	+	Rgma	protein_coding	1.46e-04	0.276	-7.43145	4.90e+00	4.28e-02	3.17e-01	7.11e-05	9.46e+00	4.25e+00	1.00e+00	1.25e-01	3.20e-03	1.78e-04	0.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	3.55e-04	0.00e+00	0.00e+00
chr17	17843328	17855188	ENSMUSG00000003665	0.4484	-	Has1	protein_coding	2.13e-04	0.336	-5.40939	5.62e+00	4.32e-02	5.17e-01	3.87e-04	5.46e+00	7.14e+00	4.25e+00	2.77e-02	9.03e-02	1.16e-02	1.00e+00	0.00e+00	0.00e+00	0.00e+00	1.58e+00	6.45e-04	0.00e+00	0.00e+00	0.00e+00	1.29e-03
chr11	51059257	51072799	ENSMUSG00000020364	0.4503	+	Zfp354a	protein_coding	2.18e-04	0.336	-5.44846	2.34e+00	9.23e-03	0.00e+00	0.00e+00	0.00e+00	7.01e+00	0.00e+00	0.00e+00	2.77e-02	0.00e+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	0.00e+00	0.00e+00
chr5	32789820	32854256	ENSMUSG00000054280	0.4374	-	Prr14l	protein_coding	2.78e-04	0.377	4.90111	6.67e-01	8.81e-05	2.73e+00	6.45e-03	1.00e+00	1.00e+00	0.00e+00	1.32e-04	1.32e-04	0.00e+00	7.88e+00	1.58e+00	0.00e+00	2.58e+00	1.58e+00	3.10e-02	2.64e-04	0.00e+00	6.60e-04	2.64e-04
chr11	100228845	100232078	ENSMUSG00000084257	0.4858	-	Gm11597	unprocessed_pseudogene	3.16e-04	0.377	5.64962	0.00e+00	0.00e+00	4.15e+00	3.92e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.11e+00	2.00e+00	5.67e+00	0.00e+00	6.98e+00	5.42e-02	2.39e-03	3.99e-02	0.00e+00	9.97e-02
chr17	62604184	62881317	ENSMUSG00000048915	0.4169	-	Efna5	protein_coding	3.38e-04	0.377	-6.02545	5.46e+00	3.52e-02	8.34e-01	3.17e-04	8.78e+00	3.58e+00	4.00e+00	9.97e-02	2.49e-03	3.40e-03	0.00e+00	2.58e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	1.13e-03	0.00e+00	4.53e-04	0.00e+00
chr3	152153447	152154116	ENSMUSG00000084343	0.5194	+	Gm16198	processed_pseudogene	3.43e-04	0.377	7.27798	0.00e+00	0.00e+00	4.37e+00	1.23e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	9.43e+00	2.00e+00	6.09e+00	1.00e+00	3.32e+00	5.51e-01	2.39e-03	5.34e-02	7.97e-04	7.18e-03
chr16	38362209	38378216	ENSMUSG00000022803	0.4954	+	Popdc2	protein_coding	3.66e-04	0.377	-4.87350	4.79e+00	3.16e-02	1.01e+00	7.68e-04	4.25e+00	2.00e+00	8.11e+00	5.76e-03	9.59e-04	8.79e-02	0.00e+00	0.00e+00	3.46e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	3.20e-03	6.40e-04	0.00e+00
chr7	4983483	4996158	ENSMUSG00000051550	0.5073	-	Zfp579	protein_coding	3.79e-04	0.377	-5.24793	2.27e+00	6.87e-03	0.00e+00	0.00e+00	0.00e+00	6.81e+00	0.00e+00	0.00e+00	2.06e-02	0.00e+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	0.00e+00	0.00e+00
chr11	33963013	33973641	ENSMUSG00000020155	0.4801	+	Kcnmb1	protein_coding	3.99e-04	0.377	-6.88301	3.20e+00	5.71e-02	7.81e-01	2.65e-04	9.60e+00	0.00e+00	0.00e+00	1.71e-01	0.00e+00	0.00e+00	0.00e+00	1.58e+00	0.00e+00	0.00e+00	2.32e+00	0.00e+00	4.41e-04	0.00e+00	0.00e+00	8.83e-04
chr16	26581704	26730117	ENSMUSG00000022514	0.3951	+	Il1rap	protein_coding	7.14e-04	0.602	-6.31942	5.06e+00	1.18e-02	7.61e-01	8.70e-05	3.46e+00	9.12e+00	2.58e+00	6.21e-04	3.46e-02	3.11e-04	0.00e+00	0.00e+00	0.00e+00	1.00e+00	2.81e+00	0.00e+00	0.00e+00	0.00e+00	6.21e-05	3.73e-04
chr2	129129700	129134134	ENSMUSG00000037938	0.4933	+	Chchd5	protein_coding	7.69e-04	0.602	5.26946	1.00e+00	6.38e-04	3.17e+00	4.26e-02	1.00e+00	2.00e+00	0.00e+00	4.78e-04	1.44e-03	0.00e+00	8.75e+00	1.58e+00	0.00e+00	2.32e+00	3.17e+00	2.06e-01	9.57e-04	0.00e+00	1.91e-03	3.83e-03
chr4	116708509	116751206	ENSMUSG00000028689	0.4310	+	Ccdc163	protein_coding	7.85e-04	0.602	6.04002	0.00e+00	0.00e+00	2.44e+00	5.64e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.58e+00	8.32e+00	0.00e+00	0.00e+00	2.32e+00	1.74e-04	2.77e-02	0.00e+00	0.00e+00	3.48e-04
chr5	138264952	138279958	ENSMUSG00000106247	0.5004	-	Gm43720	protein_coding	7.90e-04	0.602	-6.34840	3.92e+00	1.15e-02	6.34e-01	6.29e-05	3.00e+00	8.75e+00	0.00e+00	5.51e-04	3.38e-02	0.00e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	1.58e+00	1.57e-04	0.00e+00	0.00e+00	0.00e+00	1.57e-04
chr9	95637601	95698096	ENSMUSG00000015354	0.4438	+	Pcolce2	protein_coding	8.15e-04	0.602	-4.16993	3.85e+00	3.09e-03	0.00e+00	0.00e+00	2.32e+00	4.70e+00	4.52e+00	7.26e-04	4.54e-03	3.99e-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	0.00e+00	0.00e+00
chr3	66562805	66563551	ENSMUSG00000103600	0.4270	-	Gm17952	processed_pseudogene	8.68e-04	0.614	6.23649	0.00e+00	0.00e+00	2.22e+00	5.93e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	2.58e+00	0.00e+00	0.00e+00	0.00e+00	8.52e+00	3.99e-03	0.00e+00	0.00e+00	0.00e+00	2.93e-01
chr17	7170115	7303313	ENSMUSG00000023809	0.4888	+	Rps6ka2	protein_coding	9.61e-04	0.615	-4.69539	2.80e+00	1.33e-02	7.81e-01	2.84e-04	7.39e+00	1.00e+00	0.00e+00	3.95e-02	2.37e-04	0.00e+00	0.00e+00	1.58e+00	0.00e+00	2.32e+00	0.00e+00	0.00e+00	4.73e-04	0.00e+00	9.47e-04	0.00e+00
chr6	6351304	6352267	ENSMUSG00000097900	0.4782	-	Gm8652	processed_pseudogene	9.88e-04	0.615	4.92735	1.00e+00	1.06e-03	2.78e+00	5.58e-02	2.00e+00	0.00e+00	1.00e+00	2.39e-03	0.00e+00	7.97e-04	8.42e+00	1.58e+00	0.00e+00	2.32e+00	1.58e+00	2.73e-01	1.59e-03	0.00e+00	3.19e-03	1.59e-03
chr3	110250015	110253706	ENSMUSG00000105509	0.4791	+	C130013H08Rik	antisense	1.01e-03	0.615	-4.41504	4.66e+00	3.32e-02	6.64e-01	7.97e-04	6.69e+00	3.58e+00	3.70e+00	8.13e-02	8.77e-03	9.57e-03	0.00e+00	0.00e+00	0.00e+00	1.00e+00	2.32e+00	0.00e+00	0.00e+00	0.00e+00	7.97e-04	3.19e-03
chr17	22424222	22456689	ENSMUSG00000071266	0.3742	+	Zfp946	protein_coding	1.02e-03	0.615	6.44294	0.00e+00	0.00e+00	2.58e+00	2.56e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.00e+00	1.58e+00	1.58e+00	0.00e+00	8.73e+00	2.98e-04	5.95e-04	5.95e-04	0.00e+00	1.27e-01
chr14	61598226	61605946	ENSMUSG00000035235	0.4293	+	Trim13	protein_coding	1.09e-03	0.615	-5.82116	4.11e+00	1.01e-01	1.12e+00	1.11e-03	8.76e+00	1.00e+00	2.58e+00	3.00e-01	6.94e-04	3.47e-03	2.00e+00	0.00e+00	0.00e+00	2.00e+00	1.58e+00	2.08e-03	0.00e+00	0.00e+00	2.08e-03	1.39e-03
chr11	12936834	12937938	ENSMUSG00000083859	0.5231	-	Gm12003	processed_pseudogene	1.10e-03	0.615	4.78660	8.62e-01	7.97e-04	3.47e+00	4.32e-02	1.00e+00	0.00e+00	1.58e+00	7.97e-04	0.00e+00	1.59e-03	7.77e+00	0.00e+00	4.64e+00	0.00e+00	4.95e+00	1.73e-01	0.00e+00	1.91e-02	0.00e+00	2.39e-02
chr7	131457012	131457516	ENSMUSG00000108964	0.5109	+	Gm18600	processed_pseudogene	1.22e-03	0.615	5.52356	0.00e+00	0.00e+00	1.56e+00	3.59e-02	0.00e+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	0.00e+00	7.82e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.79e-01
chr11	105292643	105351139	ENSMUSG00000020695	0.4958	+	Mrc2	protein_coding	1.24e-03	0.615	-5.38082	4.99e+00	1.09e-02	7.17e-01	1.33e-04	3.46e+00	7.82e+00	3.70e+00	1.33e-03	2.98e-02	1.59e-03	1.58e+00	2.00e+00	0.00e+00	0.00e+00	0.00e+00	2.65e-04	3.98e-04	0.00e+00	0.00e+00	0.00e+00
chr9	108358202	108359069	ENSMUSG00000104280	0.5703	-	Rps2-ps11	processed_pseudogene	1.24e-03	0.615	4.91409	3.33e-01	2.66e-04	3.98e+00	3.13e-02	0.00e+00	0.00e+00	1.00e+00	0.00e+00	0.00e+00	7.97e-04	6.55e+00	2.58e+00	6.29e+00	0.00e+00	4.46e+00	7.42e-02	3.99e-03	6.14e-02	0.00e+00	1.67e-02
chr15	60822271	60831793	ENSMUSG00000097493	0.4820	+	9930014A18Rik	processed_transcript	1.26e-03	0.615	-4.85706	3.29e+00	2.06e-02	1.21e+00	5.18e-04	0.00e+00	8.27e+00	1.58e+00	0.00e+00	6.14e-02	3.99e-04	1.00e+00	1.58e+00	3.46e+00	0.00e+00	0.00e+00	1.99e-04	3.99e-04	1.99e-03	0.00e+00	0.00e+00
chr3	104945272	104961921	ENSMUSG00000027840	0.4931	-	Wnt2b	protein_coding	1.27e-03	0.615	-4.69116	3.00e+00	7.13e-03	2.00e-01	4.75e-05	0.00e+00	6.43e+00	2.58e+00	0.00e+00	2.02e-02	1.19e-03	1.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	2.38e-04	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr7	128016442	128017220	ENSMUSG00000108696	0.4608	-	Gm5738	processed_pseudogene	1.31e-03	0.619	4.21723	0.00e+00	0.00e+00	1.30e+00	1.40e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	6.48e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	7.02e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr11	101330605	101341938	ENSMUSG00000019326	0.5094	+	Aoc3	protein_coding	1.37e-03	0.620	-4.08746	3.82e+00	3.60e-03	0.00e+00	0.00e+00	3.70e+00	4.95e+00	2.81e+00	2.70e-03	6.74e-03	1.35e-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	0.00e+00	0.00e+00
chr15	85205949	85286535	ENSMUSG00000006369	0.5036	+	Fbln1	protein_coding	1.40e-03	0.620	-4.55897	5.94e+00	1.25e-02	9.81e-01	3.46e-04	5.25e+00	6.61e+00	5.95e+00	7.11e-03	1.86e-02	1.17e-02	0.00e+00	2.58e+00	0.00e+00	0.00e+00	2.32e+00	0.00e+00	9.61e-04	0.00e+00	0.00e+00	7.69e-04
chr1	63730614	63754655	ENSMUSG00000025962	0.3994	+	Fastkd2	protein_coding	1.45e-03	0.620	6.24031	0.00e+00	0.00e+00	3.67e+00	1.03e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.00e+00	2.58e+00	8.43e+00	2.00e+00	4.32e+00	1.38e-04	6.88e-04	4.75e-02	4.13e-04	2.61e-03
chr9	62419492	62537044	ENSMUSG00000041729	0.5044	-	Coro2b	protein_coding	1.46e-03	0.620	-4.54432	3.31e+00	5.17e-03	8.34e-01	1.32e-04	7.35e+00	1.00e+00	1.58e+00	1.52e-02	9.40e-05	1.88e-04	0.00e+00	0.00e+00	0.00e+00	2.58e+00	1.58e+00	0.00e+00	0.00e+00	0.00e+00	4.70e-04	1.88e-04
chr2	32236590	32255005	ENSMUSG00000039254	0.5047	+	Pomt1	protein_coding	1.55e-03	0.636	5.13750	0.00e+00	0.00e+00	2.85e+00	1.81e-03	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.00e+00	7.33e+00	2.58e+00	1.00e+00	2.32e+00	5.29e-05	8.46e-03	2.64e-04	5.29e-05	2.11e-04
chr4	124986430	125009099	ENSMUSG00000028871	0.5235	+	Rspo1	protein_coding	1.57e-03	0.636	-4.22239	4.08e+00	9.66e-03	0.00e+00	0.00e+00	3.32e+00	4.00e+00	4.91e+00	4.92e-03	8.21e-03	1.59e-02	0.00e+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	0.00e+00
chr3	81036416	81214040	ENSMUSG00000028019	0.3820	+	Pdgfc	protein_coding	1.74e-03	0.686	-4.55714	2.78e+00	3.53e-03	4.00e-01	5.77e-05	6.77e+00	0.00e+00	1.58e+00	1.04e-02	0.00e+00	1.92e-04	0.00e+00	0.00e+00	0.00e+00	2.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	2.89e-04	0.00e+00
chr6	86195223	86275719	ENSMUSG00000029999	0.4789	+	Tgfa	protein_coding	1.83e-03	0.693	4.59574	1.39e+00	3.72e-04	3.27e+00	1.27e-02	2.58e+00	0.00e+00	1.58e+00	7.97e-04	0.00e+00	3.19e-04	8.57e+00	0.00e+00	1.58e+00	2.58e+00	3.58e+00	6.06e-02	0.00e+00	3.19e-04	7.97e-04	1.75e-03
chr7	19282624	19296160	ENSMUSG00000030401	0.5013	+	Rtn2	protein_coding	1.84e-03	0.693	3.72247	3.33e-01	1.16e-04	1.28e+00	5.78e-03	0.00e+00	0.00e+00	1.00e+00	0.00e+00	0.00e+00	3.48e-04	6.39e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	2.89e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00
chr2	156632825	156633468	ENSMUSG00000083498	0.4612	-	Gm14172	processed_pseudogene	1.92e-03	0.710	5.17792	0.00e+00	0.00e+00	1.49e+00	2.81e-02	0.00e+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	0.00e+00	7.47e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.40e-01
chr6	90403479	90428797	ENSMUSG00000048794	0.5029	-	Cfap100	protein_coding	2.05e-03	0.734	8.17592	0.00e+00	0.00e+00	2.10e+00	2.10e-02	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.05e+01	0.00e+00	0.00e+00	0.00e+00	0.00e+00	1.05e-01	0.00e+00	0.00e+00	0.00e+00	0.00e+00

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

References

Anders, S., and Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biol 11, R106.
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.