Contents
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Summary
Analysis summary
Summary:
The raw bam files, one for each RNA-Seq sample, were summarized to read counts table, using the Bioconductor package GenomicRanges. In the final read counts table, each row represented each column one RNA-Seq sample and each cell, the corresponding read counts associated with each row and column.The gene counts table was normalized for inherent systematic or experimental biases (e.g. sequencing depth, gene length, GC content bias etc.) using the Bioconductor package DESeq after removing genes that had zero counts over all the RNA-Seq samples (24434 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 (5306 genes), ii) genes whose average reads per 100 bp was less than the 25th 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 (5382 genes with cutoff value 1 normalized read counts). The total number of genes excluded due to the application of gene filters was 5731. The total (unified) number of genes excluded due to the application of all filters was 33533. The resulting gene counts table was subjected to differential expression analysis for the contrasts Wt_endo versus DARE_endo, Wt_fibro versus DARE_fibro, Wt_endo versus DARECad_endo, Wt_fibro versus DARECad_fibro, Wt_endo versus DAREdd_endo, Wt_fibro versus DAREdd_fibro using the Bioconductor package DESeq. The final numbers of differentially expressed genes were (per contrast): for the contrast Wt_endo versus DARE_endo, 445 (15) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 370 (15) were up-regulated, 75 (0) 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 Wt_fibro versus DARE_fibro, 401 (31) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 328 (31) were up-regulated, 73 (0) 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 Wt_endo versus DARECad_endo, 742 (41) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 466 (35) were up-regulated, 275 (6) were down-regulated and 1 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log2 scale, for the contrast Wt_fibro versus DARECad_fibro, 567 (90) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 488 (85) were up-regulated, 79 (5) were down-regulated and 0 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log2 scale, for the contrast Wt_endo versus DAREdd_endo, 716 (37) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 419 (27) were up-regulated, 297 (10) 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 Wt_fibro versus DAREdd_fibro, 347 (29) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 267 (27) were up-regulated, 80 (2) were down-regulated and 0 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log2 scale. Literature references for all the algorithms used can be found at the end of this report.
Read counts file: imported sam/bam/bed files
Conditions: Wt_endo, Wt_fibro, DARE_endo, DARE_fibro, DARECad_endo, DARECad_fibro, DAREdd_endo, DAREdd_fibro
Samples included: wt1-endo, wt2-endo, wt3-endo, wt1-fibro, wt2-fibro, wt3-fibro, DARE1-endo, DARE2-endo, DARE3-endo, DARE1-fibro, DARE2-fibro, DARE3-fibro, DARECad1-endo, DARECad2-endo, DARECad3-endo, DARECad1-fibro, DARECad2-fibro, DARECad3-fibro, DAREdd1-endo, DAREdd2-endo, DAREdd3-endo, DAREdd1-fibro, DAREdd2-fibro, DAREdd3_fibro
Samples excluded:
none
Requested contrasts: Wt_endo_vs_DARE_endo, Wt_fibro_vs_DARE_fibro, Wt_endo_vs_DARECad_endo, Wt_fibro_vs_DARECad_fibro, Wt_endo_vs_DAREdd_endo, Wt_fibro_vs_DAREdd_fibro
Library sizes:
- wt1-endo: 1930796
- wt2-endo: 2270253
- wt3-endo: 2404123
- wt1-fibro: 2105184
- wt2-fibro: 2606595
- wt3-fibro: 2541546
- DARE1-endo: 2867003
- DARE2-endo: 1829686
- DARE3-endo: 1764576
- DARE1-fibro: 4489555
- DARE2-fibro: 3287052
- DARE3-fibro: 1883166
- DARECad1-endo: 976531
- DARECad2-endo: 1711248
- DARECad3-endo: 2962794
- DARECad1-fibro: 2199867
- DARECad2-fibro: 3182616
- DARECad3-fibro: 2758270
- DAREdd1-endo: 2053583
- DAREdd2-endo: 3232477
- DAREdd3-endo: 5835661
- DAREdd1-fibro: 3040279
- DAREdd2-fibro: 1452056
- DAREdd3_fibro: 3374114
Annotation: download
Organism: mouse ( Mus musculus), genome version alias mm10
Annotation source: Ensembl genomes
Count type: utr
Exon filters:
none applied
Gene filters:
length, avg.reads, expression, biotype - 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, boxplots, GC-content bias, transcript length bias, DEG biotype detection, volcano plot, DEG heatmap
Figure format: png, pdf
Output directory: ~/run_424_425_429_Endothelial_hisat_bam_files/metaseqr_GKlab_run424_425_429_with_hisat_bam_files
Output data: Annotation, p-value, Adjusted p-value (FDR), Fold change, Read counts
Output scale(s): Natural scale, log2 scale, Reads per Gene Model
Output values: Normalized values
Output statistics: Mean, Median, Standard deviation, Median Absolute Deviation (MAD), Coefficient of Variation, Robust Coefficient of Variation
Total run time: 38 minutes 45 seconds
Filtered genes
Number of filtered genes: 33533 which is the union of
- Filtered because of zero reads: 24434
-
Filtered because of exon filters: 0
-
Filtered because of gene filters: 9099
which is the union of
- length: 5306 genes with filter cutoff value 500
- avg.reads: 310 genes with filter cutoff value 0
- expression: 5382 genes further decomposed to (filter name, filtered genes, filter cutoff):
- median: 5382 genes with filter cutoff value 1
- biotype: 114 genes with filter cutoff value rRNA, IG_V_pseudogene, TR_V_pseudogene
Differentially expressed genes
Number of differentially expressed genes per contrast:
- Wt_endo_vs_DARE_endo: 445 (15) statistically significant genes of which 370 (15) up regulated, 75 (0) 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.
- Wt_fibro_vs_DARE_fibro: 401 (31) statistically significant genes of which 328 (31) up regulated, 73 (0) 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.
- Wt_endo_vs_DARECad_endo: 742 (41) statistically significant genes of which 466 (35) up regulated, 275 (6) down regulated and 1 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log2 scale.
- Wt_fibro_vs_DARECad_fibro: 567 (90) statistically significant genes of which 488 (85) up regulated, 79 (5) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log2 scale.
- Wt_endo_vs_DAREdd_endo: 716 (37) statistically significant genes of which 419 (27) up regulated, 297 (10) 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.
- Wt_fibro_vs_DAREdd_fibro: 347 (29) statistically significant genes of which 267 (27) up regulated, 80 (2) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log2 scale.
Run log[ 2019-09-12 17:35:53 ] INFO 2019-09-12 17:35:53: Data processing started... [ 2019-09-12 17:35:53 ] INFO Read counts file: imported sam/bam/bed files [ 2019-09-12 17:35:53 ] INFO Conditions: Wt_endo, Wt_fibro, DARE_endo, DARE_fibro, DARECad_endo, DARECad_fibro, DAREdd_endo, DAREdd_fibro [ 2019-09-12 17:35:53 ] INFO Samples to include: wt1-endo, wt2-endo, wt3-endo, wt1-fibro, wt2-fibro, wt3-fibro, DARE1-endo, DARE2-endo, DARE3-endo, DARE1-fibro, DARE2-fibro, DARE3-fibro, DARECad1-endo, DARECad2-endo, DARECad3-endo, DARECad1-fibro, DARECad2-fibro, DARECad3-fibro, DAREdd1-endo, DAREdd2-endo, DAREdd3-endo, DAREdd1-fibro, DAREdd2-fibro, DAREdd3_fibro [ 2019-09-12 17:35:53 ] INFO Samples to exclude: none [ 2019-09-12 17:35:53 ] INFO Requested contrasts: Wt_endo_vs_DARE_endo, Wt_fibro_vs_DARE_fibro, Wt_endo_vs_DARECad_endo, Wt_fibro_vs_DARECad_fibro, Wt_endo_vs_DAREdd_endo, Wt_fibro_vs_DAREdd_fibro [ 2019-09-12 17:35:53 ] INFO Annotation: download [ 2019-09-12 17:35:53 ] INFO Organism: mm10 [ 2019-09-12 17:35:53 ] INFO Reference source: ensembl [ 2019-09-12 17:35:53 ] INFO Count type: utr [ 2019-09-12 17:35:53 ] INFO Exon filters: none applied [ 2019-09-12 17:35:53 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2019-09-12 17:35:53 ] INFO length: [ 2019-09-12 17:35:53 ] INFO length: 500 [ 2019-09-12 17:35:53 ] INFO avg.reads: [ 2019-09-12 17:35:53 ] INFO average.per.bp: 100 [ 2019-09-12 17:35:53 ] INFO quantile: 0.25 [ 2019-09-12 17:35:53 ] INFO expression: [ 2019-09-12 17:35:53 ] INFO median: TRUE [ 2019-09-12 17:35:53 ] INFO mean: FALSE [ 2019-09-12 17:35:53 ] INFO quantile: NA [ 2019-09-12 17:35:53 ] INFO known: NA [ 2019-09-12 17:35:53 ] INFO custom: NA [ 2019-09-12 17:35:53 ] INFO biotype: [ 2019-09-12 17:35:53 ] INFO pseudogene: FALSE [ 2019-09-12 17:35:53 ] INFO snRNA: FALSE [ 2019-09-12 17:35:53 ] INFO protein_coding: FALSE [ 2019-09-12 17:35:53 ] INFO antisense: FALSE [ 2019-09-12 17:35:53 ] INFO miRNA: FALSE [ 2019-09-12 17:35:53 ] INFO snoRNA: FALSE [ 2019-09-12 17:35:53 ] INFO lincRNA: FALSE [ 2019-09-12 17:35:53 ] INFO processed_transcript: FALSE [ 2019-09-12 17:35:53 ] INFO misc_RNA: FALSE [ 2019-09-12 17:35:53 ] INFO rRNA: TRUE [ 2019-09-12 17:35:53 ] INFO sense_intronic: FALSE [ 2019-09-12 17:35:53 ] INFO sense_overlapping: FALSE [ 2019-09-12 17:35:53 ] INFO polymorphic_pseudogene: FALSE [ 2019-09-12 17:35:53 ] INFO IG_C_gene: FALSE [ 2019-09-12 17:35:53 ] INFO IG_J_gene: FALSE [ 2019-09-12 17:35:53 ] INFO IG_D_gene: FALSE [ 2019-09-12 17:35:53 ] INFO IG_LV_gene: FALSE [ 2019-09-12 17:35:53 ] INFO IG_V_gene: FALSE [ 2019-09-12 17:35:53 ] INFO IG_V_pseudogene: TRUE [ 2019-09-12 17:35:53 ] INFO TR_V_gene: FALSE [ 2019-09-12 17:35:53 ] INFO TR_V_pseudogene: TRUE [ 2019-09-12 17:35:53 ] INFO three_prime_overlapping_ncrna: FALSE [ 2019-09-12 17:35:53 ] INFO Filter application: postnorm [ 2019-09-12 17:35:53 ] INFO Normalization algorithm: deseq [ 2019-09-12 17:35:53 ] INFO Normalization arguments: [ 2019-09-12 17:35:53 ] INFO locfunc: [ 2019-09-12 17:35:53 ] INFO [[ [ 2019-09-12 17:35:53 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2019-09-12 17:35:53 ] INFO locfunc [ 2019-09-12 17:35:53 ] INFO Statistical algorithm: deseq [ 2019-09-12 17:35:53 ] INFO Statistical arguments: [ 2019-09-12 17:35:53 ] INFO deseq: blind, fit-only, local [ 2019-09-12 17:35:53 ] INFO Meta-analysis method: none [ 2019-09-12 17:35:53 ] INFO Multiple testing correction: BH [ 2019-09-12 17:35:53 ] INFO p-value threshold: 0.05 [ 2019-09-12 17:35:53 ] INFO Logarithmic transformation offset: 1 [ 2019-09-12 17:35:53 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, boxplot, gcbias, lengthbias, biodist, volcano, deheatmap [ 2019-09-12 17:35:53 ] INFO Figure format: png, pdf [ 2019-09-12 17:35:53 ] INFO Output directory: ~/run_424_425_429_Endothelial_hisat_bam_files/metaseqr_GKlab_run424_425_429_with_hisat_bam_files [ 2019-09-12 17:35:53 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2019-09-12 17:35:53 ] INFO Output scale(s): natural, log2, rpgm [ 2019-09-12 17:35:53 ] INFO Output values: normalized [ 2019-09-12 17:35:53 ] INFO Downloading gene annotation for mm10... [ 2019-09-12 17:36:14 ] INFO Downloading transcript annotation for mm10... [ 2019-09-12 17:38:14 ] INFO Converting annotation to GenomicRanges object... [ 2019-09-12 17:38:15 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2019-09-12 17:42:08 ] INFO Flanking merged transcript 3' UTRs per 500bp... [ 2019-09-12 17:42:12 ] INFO Reading bam file GK3R249_wt1-endo.bam for sample with name wt1-endo. This might take some time... [ 2019-09-12 17:42:12 ] INFO Reading bam file GK3R251_wt2-endo.bam for sample with name wt2-endo. This might take some time... [ 2019-09-12 17:42:12 ] INFO Reading bam file GK3R253_wt3-endo.bam for sample with name wt3-endo. This might take some time... [ 2019-09-12 17:42:12 ] INFO Reading bam file GK3R250_wt1-fibro.bam for sample with name wt1-fibro. This might take some time... [ 2019-09-12 17:42:12 ] INFO Reading bam file GK3R252_wt2-fibro.bam for sample with name wt2-fibro. This might take some time... [ 2019-09-12 17:42:12 ] INFO Reading bam file GK3R254_wt3-fibro.bam for sample with name wt3-fibro. This might take some time... [ 2019-09-12 17:42:12 ] INFO Reading bam file GK3R255_DARE1-endo.bam for sample with name DARE1-endo. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R257_DARE2-endo.bam for sample with name DARE2-endo. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R259_DARE3-endo.bam for sample with name DARE3-endo. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R256_DARE1-fibro.bam for sample with name DARE1-fibro. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R258_DARE2-fibro.bam for sample with name DARE2-fibro. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R260_DARE3-fibro.bam for sample with name DARE3-fibro. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R261_DARECad1-endo.bam for sample with name DARECad1-endo. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R263_DARECad2-endo.bam for sample with name DARECad2-endo. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R265_DARECad3-endo.bam for sample with name DARECad3-endo. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R262_DARECad1-fibro.bam for sample with name DARECad1-fibro. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R264_DARECad2-fibro.bam for sample with name DARECad2-fibro. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R266_DARECad3-fibro.bam for sample with name DARECad3-fibro. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R267_DAREdd1-endo.bam for sample with name DAREdd1-endo. This might take some time... [ 2019-09-12 17:42:13 ] INFO Reading bam file GK3R269_DAREdd2-endo.bam for sample with name DAREdd2-endo. This might take some time... [ 2019-09-12 17:42:14 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:14 ] INFO ...for single-end reads... [ 2019-09-12 17:42:14 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:15 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:15 ] INFO ...for single-end reads... [ 2019-09-12 17:42:15 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:15 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:15 ] INFO ...for single-end reads... [ 2019-09-12 17:42:15 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:16 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:16 ] INFO ...for single-end reads... [ 2019-09-12 17:42:16 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:16 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:16 ] INFO ...for single-end reads... [ 2019-09-12 17:42:16 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:16 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:16 ] INFO ...for single-end reads... [ 2019-09-12 17:42:16 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:16 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:16 ] INFO ...for single-end reads... [ 2019-09-12 17:42:16 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:16 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:16 ] INFO ...for single-end reads... [ 2019-09-12 17:42:16 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:16 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:16 ] INFO ...for single-end reads... [ 2019-09-12 17:42:16 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:16 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:16 ] INFO ...for single-end reads... [ 2019-09-12 17:42:16 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:17 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:17 ] INFO ...for single-end reads... [ 2019-09-12 17:42:17 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:17 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:17 ] INFO ...for single-end reads... [ 2019-09-12 17:42:17 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:17 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:17 ] INFO ...for single-end reads... [ 2019-09-12 17:42:17 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:17 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:17 ] INFO ...for single-end reads... [ 2019-09-12 17:42:17 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:17 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:17 ] INFO ...for single-end reads... [ 2019-09-12 17:42:17 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:17 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:17 ] INFO ...for single-end reads... [ 2019-09-12 17:42:17 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:17 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:17 ] INFO ...for single-end reads... [ 2019-09-12 17:42:17 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:18 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:18 ] INFO ...for single-end reads... [ 2019-09-12 17:42:18 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:18 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:18 ] INFO ...for single-end reads... [ 2019-09-12 17:42:18 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:19 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:19 ] INFO ...for single-end reads... [ 2019-09-12 17:42:19 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:28 ] INFO Reading bam file GK3R271_DAREdd3-endo.bam for sample with name DAREdd3-endo. This might take some time... [ 2019-09-12 17:42:29 ] INFO Reading bam file GK3R272_DAREdd3_fibro.bam for sample with name DAREdd3_fibro. This might take some time... [ 2019-09-12 17:42:32 ] INFO Reading bam file GK3R268_DAREdd1-fibro.bam for sample with name DAREdd1-fibro. This might take some time... [ 2019-09-12 17:42:34 ] INFO Reading bam file GK3R270_DAREdd2-fibro.bam for sample with name DAREdd2-fibro. This might take some time... [ 2019-09-12 17:42:35 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:35 ] INFO ...for single-end reads... [ 2019-09-12 17:42:35 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:36 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:36 ] INFO ...for single-end reads... [ 2019-09-12 17:42:36 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:37 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:37 ] INFO ...for single-end reads... [ 2019-09-12 17:42:37 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:42:38 ] INFO Counting reads overlapping with given annotation... [ 2019-09-12 17:42:38 ] INFO ...for single-end reads... [ 2019-09-12 17:42:38 ] INFO ...assuming forward sequenced reads... [ 2019-09-12 17:43:13 ] INFO Exporting raw read counts table to ~/run_424_425_429_Endothelial_hisat_bam_files/metaseqr_GKlab_run424_425_429_with_hisat_bam_files/lists/raw_counts_table.txt.gz [ 2019-09-12 17:43:17 ] INFO Checking chromosomes in transcript counts and gene annotation... [ 2019-09-12 17:43:17 ] INFO Processing transcripts... [ 2019-09-12 17:43:17 ] INFO Separating transcripts (UTR regions) per gene for wt1-endo... [ 2019-09-12 17:43:48 ] INFO Separating transcripts (UTR regions) per gene for wt2-endo... [ 2019-09-12 17:44:20 ] INFO Separating transcripts (UTR regions) per gene for wt3-endo... [ 2019-09-12 17:44:51 ] INFO Separating transcripts (UTR regions) per gene for wt1-fibro... [ 2019-09-12 17:45:24 ] INFO Separating transcripts (UTR regions) per gene for wt2-fibro... [ 2019-09-12 17:45:57 ] INFO Separating transcripts (UTR regions) per gene for wt3-fibro... [ 2019-09-12 17:46:28 ] INFO Separating transcripts (UTR regions) per gene for DARE1-endo... [ 2019-09-12 17:47:00 ] INFO Separating transcripts (UTR regions) per gene for DARE2-endo... [ 2019-09-12 17:47:37 ] INFO Separating transcripts (UTR regions) per gene for DARE3-endo... [ 2019-09-12 17:48:17 ] INFO Separating transcripts (UTR regions) per gene for DARE1-fibro... [ 2019-09-12 17:48:48 ] INFO Separating transcripts (UTR regions) per gene for DARE2-fibro... [ 2019-09-12 17:49:23 ] INFO Separating transcripts (UTR regions) per gene for DARE3-fibro... [ 2019-09-12 17:49:55 ] INFO Separating transcripts (UTR regions) per gene for DARECad1-endo... [ 2019-09-12 17:50:28 ] INFO Separating transcripts (UTR regions) per gene for DARECad2-endo... [ 2019-09-12 17:50:59 ] INFO Separating transcripts (UTR regions) per gene for DARECad3-endo... [ 2019-09-12 17:51:30 ] INFO Separating transcripts (UTR regions) per gene for DARECad1-fibro... [ 2019-09-12 17:52:05 ] INFO Separating transcripts (UTR regions) per gene for DARECad2-fibro... [ 2019-09-12 17:52:35 ] INFO Separating transcripts (UTR regions) per gene for DARECad3-fibro... [ 2019-09-12 17:53:05 ] INFO Separating transcripts (UTR regions) per gene for DAREdd1-endo... [ 2019-09-12 17:53:36 ] INFO Separating transcripts (UTR regions) per gene for DAREdd2-endo... [ 2019-09-12 17:54:07 ] INFO Separating transcripts (UTR regions) per gene for DAREdd3-endo... [ 2019-09-12 17:54:37 ] INFO Separating transcripts (UTR regions) per gene for DAREdd1-fibro... [ 2019-09-12 17:55:10 ] INFO Separating transcripts (UTR regions) per gene for DAREdd2-fibro... [ 2019-09-12 17:55:42 ] INFO Separating transcripts (UTR regions) per gene for DAREdd3_fibro... [ 2019-09-12 17:56:18 ] INFO Saving gene model to ~/run_424_425_429_Endothelial_hisat_bam_files/metaseqr_GKlab_run424_425_429_with_hisat_bam_files/data/gene_model.RData [ 2019-09-12 17:56:25 ] INFO Summarizing count data... [ 2019-09-12 17:56:59 ] INFO Removing genes with zero counts in all samples... [ 2019-09-12 17:57:01 ] INFO Normalizing with: deseq [ 2019-09-12 17:57:02 ] INFO Applying gene filter length... [ 2019-09-12 17:57:02 ] INFO Threshold below which ignored: 500 [ 2019-09-12 17:57:02 ] INFO Applying gene filter avg.reads... [ 2019-09-12 17:57:02 ] INFO Threshold below which ignored: 0 [ 2019-09-12 17:57:02 ] INFO Applying gene filter expression... [ 2019-09-12 17:57:02 ] INFO Threshold below which ignored: 1 [ 2019-09-12 17:57:02 ] INFO Applying gene filter biotype... [ 2019-09-12 17:57:02 ] INFO Biotypes ignored: rRNA, IG_V_pseudogene, TR_V_pseudogene [ 2019-09-12 17:57:02 ] INFO 33533 genes filtered out [ 2019-09-12 17:57:02 ] INFO 21917 genes remain after filtering [ 2019-09-12 17:57:02 ] INFO Running statistical tests with: deseq [ 2019-09-12 17:57:03 ] INFO Contrast: Wt_endo_vs_DARE_endo [ 2019-09-12 17:57:12 ] INFO Contrast: Wt_fibro_vs_DARE_fibro [ 2019-09-12 17:57:24 ] INFO Contrast: Wt_endo_vs_DARECad_endo [ 2019-09-12 17:57:32 ] INFO Contrast: Wt_fibro_vs_DARECad_fibro [ 2019-09-12 17:57:43 ] INFO Contrast: Wt_endo_vs_DAREdd_endo [ 2019-09-12 17:57:55 ] INFO Contrast: Wt_fibro_vs_DAREdd_fibro [ 2019-09-12 17:58:06 ] INFO Contrast Wt_endo_vs_DARE_endo: found 445 genes [ 2019-09-12 17:58:06 ] INFO Contrast Wt_fibro_vs_DARE_fibro: found 401 genes [ 2019-09-12 17:58:06 ] INFO Contrast Wt_endo_vs_DARECad_endo: found 742 genes [ 2019-09-12 17:58:06 ] INFO Contrast Wt_fibro_vs_DARECad_fibro: found 567 genes [ 2019-09-12 17:58:06 ] INFO Contrast Wt_endo_vs_DAREdd_endo: found 716 genes [ 2019-09-12 17:58:06 ] INFO Contrast Wt_fibro_vs_DAREdd_fibro: found 347 genes [ 2019-09-12 17:58:06 ] INFO Exporting and compressing normalized read counts table to ~/run_424_425_429_Endothelial_hisat_bam_files/metaseqr_GKlab_run424_425_429_with_hisat_bam_files/lists/normalized_counts_table.txt [ 2019-09-12 17:58:08 ] INFO Building output files... [ 2019-09-12 17:58:11 ] INFO Contrast: Wt_endo_vs_DARE_endo [ 2019-09-12 17:58:11 ] INFO Adding non-filtered data... [ 2019-09-12 17:58:11 ] INFO binding annotation... [ 2019-09-12 17:58:12 ] INFO binding p-values... [ 2019-09-12 17:58:13 ] INFO binding FDRs... [ 2019-09-12 17:58:15 ] INFO binding natural normalized fold changes... [ 2019-09-12 17:58:15 ] INFO binding log2 normalized fold changes... [ 2019-09-12 17:58:15 ] INFO binding all normalized counts for Wt_endo... [ 2019-09-12 17:58:16 ] INFO binding all normalized counts for DARE_endo... [ 2019-09-12 17:58:17 ] INFO binding filtering flags... [ 2019-09-12 17:58:18 ] INFO Writing output... [ 2019-09-12 17:58:18 ] INFO Adding filtered data... [ 2019-09-12 17:58:18 ] INFO binding annotation... [ 2019-09-12 17:58:18 ] INFO binding p-values... [ 2019-09-12 17:58:18 ] INFO binding FDRs... [ 2019-09-12 17:58:19 ] INFO binding natural normalized fold changes... [ 2019-09-12 17:58:19 ] INFO binding log2 normalized fold changes... [ 2019-09-12 17:58:19 ] INFO binding all normalized counts for Wt_endo... [ 2019-09-12 17:58:19 ] INFO binding all normalized counts for DARE_endo... [ 2019-09-12 17:58:19 ] INFO binding filtering flags... [ 2019-09-12 17:58:20 ] INFO Writing output... [ 2019-09-12 17:58:22 ] INFO Contrast: Wt_fibro_vs_DARE_fibro [ 2019-09-12 17:58:22 ] INFO Adding non-filtered data... [ 2019-09-12 17:58:22 ] INFO binding annotation... [ 2019-09-12 17:58:25 ] INFO binding p-values... [ 2019-09-12 17:58:25 ] INFO binding FDRs... [ 2019-09-12 17:58:25 ] INFO binding natural normalized fold changes... [ 2019-09-12 17:58:25 ] INFO binding log2 normalized fold changes... [ 2019-09-12 17:58:25 ] INFO binding all normalized counts for Wt_fibro... [ 2019-09-12 17:58:26 ] INFO binding all normalized counts for DARE_fibro... [ 2019-09-12 17:58:27 ] INFO binding filtering flags... [ 2019-09-12 17:58:28 ] INFO Writing output... [ 2019-09-12 17:58:28 ] INFO Adding filtered data... [ 2019-09-12 17:58:28 ] INFO binding annotation... [ 2019-09-12 17:58:28 ] INFO binding p-values... [ 2019-09-12 17:58:28 ] INFO binding FDRs... [ 2019-09-12 17:58:29 ] INFO binding natural normalized fold changes... [ 2019-09-12 17:58:29 ] INFO binding log2 normalized fold changes... [ 2019-09-12 17:58:29 ] INFO binding all normalized counts for Wt_fibro... [ 2019-09-12 17:58:29 ] INFO binding all normalized counts for DARE_fibro... [ 2019-09-12 17:58:29 ] INFO binding filtering flags... [ 2019-09-12 17:58:30 ] INFO Writing output... [ 2019-09-12 17:58:32 ] INFO Contrast: Wt_endo_vs_DARECad_endo [ 2019-09-12 17:58:32 ] INFO Adding non-filtered data... [ 2019-09-12 17:58:32 ] INFO binding annotation... [ 2019-09-12 17:58:33 ] INFO binding p-values... [ 2019-09-12 17:58:33 ] INFO binding FDRs... [ 2019-09-12 17:58:34 ] INFO binding natural normalized fold changes... [ 2019-09-12 17:58:34 ] INFO binding log2 normalized fold changes... [ 2019-09-12 17:58:34 ] INFO binding all normalized counts for Wt_endo... [ 2019-09-12 17:58:35 ] INFO binding all normalized counts for DARECad_endo... [ 2019-09-12 17:58:36 ] INFO binding filtering flags... [ 2019-09-12 17:58:37 ] INFO Writing output... [ 2019-09-12 17:58:37 ] INFO Adding filtered data... [ 2019-09-12 17:58:37 ] INFO binding annotation... [ 2019-09-12 17:58:37 ] INFO binding p-values... [ 2019-09-12 17:58:37 ] INFO binding FDRs... [ 2019-09-12 17:58:38 ] INFO binding natural normalized fold changes... [ 2019-09-12 17:58:38 ] INFO binding log2 normalized fold changes... [ 2019-09-12 17:58:38 ] INFO binding all normalized counts for Wt_endo... [ 2019-09-12 17:58:38 ] INFO binding all normalized counts for DARECad_endo... [ 2019-09-12 17:58:38 ] INFO binding filtering flags... [ 2019-09-12 17:58:39 ] INFO Writing output... [ 2019-09-12 17:58:41 ] INFO Contrast: Wt_fibro_vs_DARECad_fibro [ 2019-09-12 17:58:41 ] INFO Adding non-filtered data... [ 2019-09-12 17:58:41 ] INFO binding annotation... [ 2019-09-12 17:58:42 ] INFO binding p-values... [ 2019-09-12 17:58:42 ] INFO binding FDRs... [ 2019-09-12 17:58:43 ] INFO binding natural normalized fold changes... [ 2019-09-12 17:58:43 ] INFO binding log2 normalized fold changes... [ 2019-09-12 17:58:43 ] INFO binding all normalized counts for Wt_fibro... [ 2019-09-12 17:58:44 ] INFO binding all normalized counts for DARECad_fibro... [ 2019-09-12 17:58:45 ] INFO binding filtering flags... [ 2019-09-12 17:58:46 ] INFO Writing output... [ 2019-09-12 17:58:47 ] INFO Adding filtered data... [ 2019-09-12 17:58:47 ] INFO binding annotation... [ 2019-09-12 17:58:47 ] INFO binding p-values... [ 2019-09-12 17:58:47 ] INFO binding FDRs... [ 2019-09-12 17:58:47 ] INFO binding natural normalized fold changes... [ 2019-09-12 17:58:47 ] INFO binding log2 normalized fold changes... [ 2019-09-12 17:58:47 ] INFO binding all normalized counts for Wt_fibro... [ 2019-09-12 17:58:47 ] INFO binding all normalized counts for DARECad_fibro... [ 2019-09-12 17:58:47 ] INFO binding filtering flags... [ 2019-09-12 17:58:50 ] INFO Writing output... [ 2019-09-12 17:58:52 ] INFO Contrast: Wt_endo_vs_DAREdd_endo [ 2019-09-12 17:58:52 ] INFO Adding non-filtered data... [ 2019-09-12 17:58:52 ] INFO binding annotation... [ 2019-09-12 17:58:53 ] INFO binding p-values... [ 2019-09-12 17:58:53 ] INFO binding FDRs... [ 2019-09-12 17:58:53 ] INFO binding natural normalized fold changes... [ 2019-09-12 17:58:54 ] INFO binding log2 normalized fold changes... [ 2019-09-12 17:58:54 ] INFO binding all normalized counts for Wt_endo... [ 2019-09-12 17:58:55 ] INFO binding all normalized counts for DAREdd_endo... [ 2019-09-12 17:58:56 ] INFO binding filtering flags... [ 2019-09-12 17:58:57 ] INFO Writing output... [ 2019-09-12 17:58:57 ] INFO Adding filtered data... [ 2019-09-12 17:58:57 ] INFO binding annotation... [ 2019-09-12 17:58:57 ] INFO binding p-values... [ 2019-09-12 17:58:57 ] INFO binding FDRs... [ 2019-09-12 17:58:57 ] INFO binding natural normalized fold changes... [ 2019-09-12 17:58:57 ] INFO binding log2 normalized fold changes... [ 2019-09-12 17:58:57 ] INFO binding all normalized counts for Wt_endo... [ 2019-09-12 17:58:57 ] INFO binding all normalized counts for DAREdd_endo... [ 2019-09-12 17:58:57 ] INFO binding filtering flags... [ 2019-09-12 17:58:58 ] INFO Writing output... [ 2019-09-12 17:59:01 ] INFO Contrast: Wt_fibro_vs_DAREdd_fibro [ 2019-09-12 17:59:01 ] INFO Adding non-filtered data... [ 2019-09-12 17:59:01 ] INFO binding annotation... [ 2019-09-12 17:59:02 ] INFO binding p-values... [ 2019-09-12 17:59:02 ] INFO binding FDRs... [ 2019-09-12 17:59:02 ] INFO binding natural normalized fold changes... [ 2019-09-12 17:59:02 ] INFO binding log2 normalized fold changes... [ 2019-09-12 17:59:02 ] INFO binding all normalized counts for Wt_fibro... [ 2019-09-12 17:59:04 ] INFO binding all normalized counts for DAREdd_fibro... [ 2019-09-12 17:59:06 ] INFO binding filtering flags... [ 2019-09-12 17:59:07 ] INFO Writing output... [ 2019-09-12 17:59:07 ] INFO Adding filtered data... [ 2019-09-12 17:59:07 ] INFO binding annotation... [ 2019-09-12 17:59:07 ] INFO binding p-values... [ 2019-09-12 17:59:07 ] INFO binding FDRs... [ 2019-09-12 17:59:08 ] INFO binding natural normalized fold changes... [ 2019-09-12 17:59:08 ] INFO binding log2 normalized fold changes... [ 2019-09-12 17:59:08 ] INFO binding all normalized counts for Wt_fibro... [ 2019-09-12 17:59:08 ] INFO binding all normalized counts for DAREdd_fibro... [ 2019-09-12 17:59:08 ] INFO binding filtering flags... [ 2019-09-12 17:59:09 ] INFO Writing output... [ 2019-09-12 17:59:11 ] INFO Creating quality control graphs... [ 2019-09-12 17:59:11 ] INFO Plotting in png format... [ 2019-09-12 17:59:11 ] INFO Plotting mds... [ 2019-09-12 17:59:11 ] INFO Plotting biodetection... [ 2019-09-12 17:59:14 ] INFO Plotting countsbio... [ 2019-09-12 17:59:19 ] INFO Plotting saturation... [ 2019-09-12 17:59:43 ] INFO Plotting readnoise... [ 2019-09-12 17:59:56 ] INFO Plotting correl... [ 2019-09-12 17:59:56 ] INFO Plotting boxplot... [ 2019-09-12 17:59:57 ] INFO Plotting gcbias... [ 2019-09-12 18:00:00 ] INFO Plotting lengthbias... [ 2019-09-12 18:00:02 ] INFO Plotting boxplot... [ 2019-09-12 18:00:02 ] INFO Plotting gcbias... [ 2019-09-12 18:00:05 ] INFO Plotting lengthbias... [ 2019-09-12 18:00:07 ] INFO Plotting biodist... [ 2019-09-12 18:00:07 ] INFO Contrast: Wt_endo_vs_DARE_endo [ 2019-09-12 18:00:08 ] INFO Contrast: Wt_fibro_vs_DARE_fibro [ 2019-09-12 18:00:08 ] INFO Contrast: Wt_endo_vs_DARECad_endo [ 2019-09-12 18:00:08 ] INFO Contrast: Wt_fibro_vs_DARECad_fibro [ 2019-09-12 18:00:09 ] INFO Contrast: Wt_endo_vs_DAREdd_endo [ 2019-09-12 18:00:09 ] INFO Contrast: Wt_fibro_vs_DAREdd_fibro [ 2019-09-12 18:00:09 ] INFO Plotting volcano... [ 2019-09-12 18:00:09 ] INFO Contrast: Wt_endo_vs_DARE_endo [ 2019-09-12 18:00:10 ] INFO Contrast: Wt_fibro_vs_DARE_fibro [ 2019-09-12 18:00:11 ] INFO Contrast: Wt_endo_vs_DARECad_endo [ 2019-09-12 18:00:12 ] INFO Contrast: Wt_fibro_vs_DARECad_fibro [ 2019-09-12 18:00:12 ] INFO Contrast: Wt_endo_vs_DAREdd_endo [ 2019-09-12 18:00:13 ] INFO Contrast: Wt_fibro_vs_DAREdd_fibro [ 2019-09-12 18:00:14 ] INFO Plotting deheatmap... [ 2019-09-12 18:00:14 ] INFO Contrast: Wt_endo_vs_DARE_endo [ 2019-09-12 18:01:27 ] INFO Contrast: Wt_fibro_vs_DARE_fibro [ 2019-09-12 18:02:32 ] INFO Contrast: Wt_endo_vs_DARECad_endo [ 2019-09-12 18:03:43 ] INFO Contrast: Wt_fibro_vs_DARECad_fibro [ 2019-09-12 18:04:46 ] INFO Contrast: Wt_endo_vs_DAREdd_endo [ 2019-09-12 18:05:56 ] INFO Contrast: Wt_fibro_vs_DAREdd_fibro [ 2019-09-12 18:07:01 ] INFO Plotting filtered... [ 2019-09-12 18:07:01 ] INFO Plotting in pdf format... [ 2019-09-12 18:07:01 ] INFO Plotting mds... [ 2019-09-12 18:07:01 ] INFO Plotting biodetection... [ 2019-09-12 18:07:03 ] INFO Plotting countsbio... [ 2019-09-12 18:07:05 ] INFO Plotting saturation... [ 2019-09-12 18:07:21 ] INFO Plotting readnoise... [ 2019-09-12 18:07:35 ] INFO Plotting correl... [ 2019-09-12 18:07:35 ] INFO Plotting boxplot... [ 2019-09-12 18:07:35 ] INFO Plotting gcbias... [ 2019-09-12 18:07:39 ] INFO Plotting lengthbias... [ 2019-09-12 18:07:42 ] INFO Plotting boxplot... [ 2019-09-12 18:07:42 ] INFO Plotting gcbias... [ 2019-09-12 18:07:46 ] INFO Plotting lengthbias... [ 2019-09-12 18:07:49 ] INFO Plotting biodist... [ 2019-09-12 18:07:49 ] INFO Contrast: Wt_endo_vs_DARE_endo [ 2019-09-12 18:07:49 ] INFO Contrast: Wt_fibro_vs_DARE_fibro [ 2019-09-12 18:07:49 ] INFO Contrast: Wt_endo_vs_DARECad_endo [ 2019-09-12 18:07:49 ] INFO Contrast: Wt_fibro_vs_DARECad_fibro [ 2019-09-12 18:07:50 ] INFO Contrast: Wt_endo_vs_DAREdd_endo [ 2019-09-12 18:07:50 ] INFO Contrast: Wt_fibro_vs_DAREdd_fibro [ 2019-09-12 18:07:50 ] INFO Plotting volcano... [ 2019-09-12 18:07:50 ] INFO Contrast: Wt_endo_vs_DARE_endo [ 2019-09-12 18:07:51 ] INFO Contrast: Wt_fibro_vs_DARE_fibro [ 2019-09-12 18:07:51 ] INFO Contrast: Wt_endo_vs_DARECad_endo [ 2019-09-12 18:07:51 ] INFO Contrast: Wt_fibro_vs_DARECad_fibro [ 2019-09-12 18:07:52 ] INFO Contrast: Wt_endo_vs_DAREdd_endo [ 2019-09-12 18:07:52 ] INFO Contrast: Wt_fibro_vs_DAREdd_fibro [ 2019-09-12 18:07:52 ] INFO Plotting deheatmap... [ 2019-09-12 18:07:52 ] INFO Contrast: Wt_endo_vs_DARE_endo [ 2019-09-12 18:09:02 ] INFO Contrast: Wt_fibro_vs_DARE_fibro [ 2019-09-12 18:10:07 ] INFO Contrast: Wt_endo_vs_DARECad_endo [ 2019-09-12 18:11:19 ] INFO Contrast: Wt_fibro_vs_DARECad_fibro [ 2019-09-12 18:12:22 ] INFO Contrast: Wt_endo_vs_DAREdd_endo [ 2019-09-12 18:13:33 ] INFO Contrast: Wt_fibro_vs_DAREdd_fibro [ 2019-09-12 18:14:38 ] INFO Plotting filtered... [ 2019-09-12 18:14:38 ] INFO Creating HTML report... [ 2019-09-12 18:14:38 ] INFO Compressing figures...
Multidimensional scaling
Biotype detection
Biotype detection counts
Read and biotype saturation
RNA-Seq reads noise
Correlation plots
Boxplots
GC content bias
Gene/transcript length bias
Chromosome and biotype distribution of filtered genes
Volcano plots
DEG heatmaps
Chromosome and biotype distributions of DEGs
Results
DEG table for the contrast Wt_endo_vs_DARE_endoThe following table presents the top 5% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Wt_endo_vs_DARE_endo. 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 | natural_normalized_fold_change_Wt_endo_vs_DARE_endo | log2_normalized_fold_change_Wt_endo_vs_DARE_endo | natural_normalized_counts_wt1-endo | natural_normalized_counts_wt2-endo | natural_normalized_counts_wt3-endo | log2_normalized_counts_wt1-endo | log2_normalized_counts_wt2-endo | log2_normalized_counts_wt3-endo | rpgm_normalized_counts_wt1-endo | rpgm_normalized_counts_wt2-endo | rpgm_normalized_counts_wt3-endo | natural_normalized_counts_DARE1-endo | natural_normalized_counts_DARE2-endo | natural_normalized_counts_DARE3-endo | log2_normalized_counts_DARE1-endo | log2_normalized_counts_DARE2-endo | log2_normalized_counts_DARE3-endo | rpgm_normalized_counts_DARE1-endo | rpgm_normalized_counts_DARE2-endo | rpgm_normalized_counts_DARE3-endo | LN | AR | MD | MN | QN | KN | CM | BT |
|---|
| chr11 | 83525778 | 83530518 | ENSMUSG00000035042 | 0.4664 | - | Ccl5 | protein_coding | 2.02e-12 | 4.44e-08 | 100.3333 | 6.64866 | 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 | 9.80e+01 | 1.37e+02 | 6.30e+01 | 6.63e+00 | 7.11e+00 | 6.00e+00 | 3.64e-02 | 5.08e-02 | 2.34e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 7445822 | 7455975 | ENSMUSG00000043613 | 0.4079 | + | Mmp3 | protein_coding | 4.73e-10 | 4.61e-06 | 36.7600 | 5.20006 | 1.70e+01 | 5.00e+00 | 0.00e+00 | 4.17e+00 | 2.58e+00 | 0.00e+00 | 1.11e-02 | 3.26e-03 | 0.00e+00 | 4.21e+02 | 3.24e+02 | 1.71e+02 | 8.72e+00 | 8.34e+00 | 7.43e+00 | 2.75e-01 | 2.11e-01 | 1.12e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 46711998 | 46715700 | ENSMUSG00000040026 | 0.4807 | - | Saa3 | protein_coding | 6.31e-10 | 4.61e-06 | 44.7368 | 5.48339 | 0.00e+00 | 9.00e+00 | 7.00e+00 | 0.00e+00 | 3.32e+00 | 3.00e+00 | 0.00e+00 | 1.97e-03 | 1.53e-03 | 2.38e+02 | 4.39e+02 | 1.70e+02 | 7.90e+00 | 8.78e+00 | 7.42e+00 | 5.20e-02 | 9.59e-02 | 3.71e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 109575128 | 109579172 | ENSMUSG00000031722 | 0.5125 | - | Hp | protein_coding | 1.77e-08 | 9.69e-05 | 26.4186 | 4.72348 | 4.00e+00 | 3.00e+01 | 6.00e+00 | 2.32e+00 | 4.95e+00 | 2.81e+00 | 1.41e-03 | 1.06e-02 | 2.12e-03 | 4.28e+02 | 3.26e+02 | 3.79e+02 | 8.74e+00 | 8.35e+00 | 8.57e+00 | 1.51e-01 | 1.15e-01 | 1.34e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 129364570 | 129371139 | ENSMUSG00000027398 | 0.4534 | - | Il1b | protein_coding | 4.27e-08 | 1.87e-04 | 91.6667 | 6.51833 | 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 | 1.58e+02 | 5.80e+01 | 5.60e+01 | 7.31e+00 | 5.88e+00 | 5.83e+00 | 5.18e-02 | 1.90e-02 | 1.84e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 34153072 | 34160230 | ENSMUSG00000079547 | 0.4883 | + | H2-DMb1 | protein_coding | 8.13e-08 | 2.97e-04 | 45.8571 | 5.51907 | 2.00e+00 | 1.00e+00 | 1.00e+00 | 1.58e+00 | 1.00e+00 | 1.00e+00 | 7.18e-04 | 3.59e-04 | 3.59e-04 | 1.18e+02 | 1.09e+02 | 9.10e+01 | 6.89e+00 | 6.78e+00 | 6.52e+00 | 4.23e-02 | 3.91e-02 | 3.27e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 95526786 | 95556403 | ENSMUSG00000038642 | 0.4437 | + | Ctss | protein_coding | 4.37e-07 | 1.37e-03 | 23.3200 | 4.54350 | 7.00e+00 | 1.10e+01 | 4.00e+00 | 3.00e+00 | 3.58e+00 | 2.32e+00 | 4.77e-03 | 7.50e-03 | 2.73e-03 | 2.06e+02 | 1.76e+02 | 1.98e+02 | 7.69e+00 | 7.47e+00 | 7.64e+00 | 1.41e-01 | 1.20e-01 | 1.35e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 164354070 | 164389095 | ENSMUSG00000017002 | 0.4508 | - | Slpi | protein_coding | 1.76e-06 | 4.82e-03 | 23.0000 | 4.52356 | 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 | 2.20e+01 | 2.60e+01 | 1.80e+01 | 4.52e+00 | 4.75e+00 | 4.25e+00 | 5.88e-03 | 6.95e-03 | 4.81e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 24336853 | 24351494 | ENSMUSG00000026981 | 0.4277 | + | Il1rn | protein_coding | 9.91e-06 | 2.22e-02 | 40.0000 | 5.32193 | 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 | 4.20e+01 | 5.90e+01 | 1.60e+01 | 5.43e+00 | 5.91e+00 | 4.09e+00 | 7.22e-03 | 1.01e-02 | 2.75e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 103510586 | 103750211 | ENSMUSG00000030077 | 0.3788 | + | Chl1 | protein_coding | 1.01e-05 | 2.22e-02 | 20.0000 | 4.32193 | 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 | 2.50e+01 | 2.70e+01 | 5.00e+00 | 4.70e+00 | 4.81e+00 | 2.58e+00 | 2.71e-03 | 2.93e-03 | 5.42e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 34305867 | 34316674 | ENSMUSG00000060586 | 0.4833 | + | H2-Eb1 | protein_coding | 1.42e-05 | 2.83e-02 | 10.3967 | 3.37805 | 3.40e+01 | 5.20e+01 | 3.20e+01 | 5.13e+00 | 5.73e+00 | 5.04e+00 | 4.39e-03 | 6.72e-03 | 4.13e-03 | 4.25e+02 | 4.75e+02 | 3.55e+02 | 8.73e+00 | 8.89e+00 | 8.48e+00 | 5.49e-02 | 6.14e-02 | 4.59e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 42772860 | 42773993 | ENSMUSG00000094686 | 0.5670 | - | Ccl21a | protein_coding | 1.63e-05 | 2.95e-02 | 9.0322 | 3.17508 | 1.75e+02 | 2.08e+02 | 1.42e+02 | 7.46e+00 | 7.71e+00 | 7.16e+00 | 1.07e-01 | 1.27e-01 | 8.65e-02 | 2.59e+03 | 6.64e+02 | 1.51e+03 | 1.13e+01 | 9.38e+00 | 1.06e+01 | 1.58e+00 | 4.05e-01 | 9.20e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 68276567 | 68347699 | ENSMUSG00000053886 | 0.4190 | + | Sh2d4a | protein_coding | 1.76e-05 | 2.95e-02 | 18.6667 | 4.22239 | 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 | 2.00e+01 | 3.30e+01 | 0.00e+00 | 4.39e+00 | 5.09e+00 | 0.00e+00 | 9.09e-03 | 1.50e-02 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 57203970 | 57228136 | ENSMUSG00000024164 | 0.5201 | - | C3 | protein_coding | 1.88e-05 | 2.95e-02 | 11.2043 | 3.48598 | 5.10e+01 | 1.90e+01 | 2.00e+01 | 5.70e+00 | 4.32e+00 | 4.39e+00 | 1.35e-02 | 5.02e-03 | 5.28e-03 | 4.58e+02 | 3.87e+02 | 1.94e+02 | 8.84e+00 | 8.60e+00 | 7.61e+00 | 1.21e-01 | 1.02e-01 | 5.12e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 42612121 | 42613253 | ENSMUSG00000096596 | 0.5640 | + | Gm10591 | protein_coding | 2.63e-05 | 3.84e-02 | 11.0353 | 3.46405 | 4.30e+01 | 1.70e+01 | 2.20e+01 | 5.46e+00 | 4.17e+00 | 4.52e+00 | 2.62e-02 | 1.04e-02 | 1.34e-02 | 5.18e+02 | 1.24e+02 | 2.93e+02 | 9.02e+00 | 6.97e+00 | 8.20e+00 | 3.16e-01 | 7.56e-02 | 1.79e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 117277331 | 117282321 | ENSMUSG00000069516 | 0.4708 | - | Lyz2 | protein_coding | 4.61e-05 | 6.32e-02 | 9.0090 | 3.17136 | 5.50e+01 | 8.00e+01 | 8.50e+01 | 5.81e+00 | 6.34e+00 | 6.43e+00 | 2.70e-02 | 3.93e-02 | 4.17e-02 | 5.70e+02 | 8.12e+02 | 6.24e+02 | 9.16e+00 | 9.67e+00 | 9.29e+00 | 2.80e-01 | 3.98e-01 | 3.06e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 90903871 | 90905938 | ENSMUSG00000058427 | 0.4507 | + | Cxcl2 | protein_coding | 6.28e-05 | 8.10e-02 | 10.7333 | 3.42403 | 1.10e+01 | 1.00e+00 | 0.00e+00 | 3.58e+00 | 1.00e+00 | 0.00e+00 | 3.89e-03 | 3.54e-04 | 0.00e+00 | 5.70e+01 | 8.00e+01 | 2.10e+01 | 5.86e+00 | 6.34e+00 | 4.46e+00 | 2.02e-02 | 2.83e-02 | 7.43e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 42114817 | 42115917 | ENSMUSG00000073878 | 0.5649 | + | Gm13304 | protein_coding | 6.81e-05 | 8.29e-02 | 11.3621 | 3.50615 | 2.20e+01 | 1.70e+01 | 1.60e+01 | 4.52e+00 | 4.17e+00 | 4.09e+00 | 1.34e-02 | 1.04e-02 | 9.75e-03 | 3.75e+02 | 8.30e+01 | 1.98e+02 | 8.55e+00 | 6.39e+00 | 7.64e+00 | 2.29e-01 | 5.06e-02 | 1.21e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 124829547 | 124833701 | ENSMUSG00000023505 | 0.5016 | + | Cdca3 | protein_coding | 7.90e-05 | 8.85e-02 | 20.1429 | 4.33220 | 4.00e+00 | 0.00e+00 | 0.00e+00 | 2.32e+00 | 0.00e+00 | 0.00e+00 | 8.83e-04 | 0.00e+00 | 0.00e+00 | 8.50e+01 | 4.30e+01 | 1.00e+01 | 6.43e+00 | 5.46e+00 | 3.46e+00 | 1.88e-02 | 9.49e-03 | 2.21e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 75636706 | 75644008 | ENSMUSG00000006342 | 0.5626 | - | Susd2 | protein_coding | 8.08e-05 | 8.85e-02 | 17.1000 | 4.09592 | 1.00e+00 | 6.00e+00 | 0.00e+00 | 1.00e+00 | 2.81e+00 | 0.00e+00 | 5.30e-04 | 3.18e-03 | 0.00e+00 | 7.00e+01 | 5.90e+01 | 3.90e+01 | 6.15e+00 | 5.91e+00 | 5.32e+00 | 3.71e-02 | 3.12e-02 | 2.07e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 65890237 | 65903266 | ENSMUSG00000040204 | 0.4104 | + | Pclaf | protein_coding | 8.77e-05 | 9.16e-02 | 30.0000 | 4.90689 | 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 | 4.10e+01 | 1.90e+01 | 2.70e+01 | 5.39e+00 | 4.32e+00 | 4.81e+00 | 7.58e-03 | 3.51e-03 | 4.99e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 35170991 | 35176068 | ENSMUSG00000024397 | 0.5228 | - | Aif1 | protein_coding | 1.12e-04 | 1.12e-01 | 22.4000 | 4.48543 | 0.00e+00 | 2.00e+00 | 0.00e+00 | 0.00e+00 | 1.58e+00 | 0.00e+00 | 0.00e+00 | 5.18e-04 | 0.00e+00 | 3.80e+01 | 3.50e+01 | 3.60e+01 | 5.29e+00 | 5.17e+00 | 5.21e+00 | 9.84e-03 | 9.06e-03 | 9.32e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 110360917 | 110363183 | ENSMUSG00000074971 | 0.4583 | - | Fibin | protein_coding | 1.21e-04 | 1.14e-01 | 15.2500 | 3.93074 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 4.50e-04 | 0.00e+00 | 0.00e+00 | 1.60e+01 | 1.90e+01 | 2.30e+01 | 4.09e+00 | 4.32e+00 | 4.58e+00 | 7.19e-03 | 8.54e-03 | 1.03e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for Wt_endo_vs_DARE_endo.Download the whole result list for Wt_endo_vs_DARE_endo.DEG table for the contrast Wt_fibro_vs_DARE_fibroThe following table presents the top 5% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Wt_fibro_vs_DARE_fibro. 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 | natural_normalized_fold_change_Wt_fibro_vs_DARE_fibro | log2_normalized_fold_change_Wt_fibro_vs_DARE_fibro | natural_normalized_counts_wt1-fibro | natural_normalized_counts_wt2-fibro | natural_normalized_counts_wt3-fibro | log2_normalized_counts_wt1-fibro | log2_normalized_counts_wt2-fibro | log2_normalized_counts_wt3-fibro | rpgm_normalized_counts_wt1-fibro | rpgm_normalized_counts_wt2-fibro | rpgm_normalized_counts_wt3-fibro | natural_normalized_counts_DARE1-fibro | natural_normalized_counts_DARE2-fibro | natural_normalized_counts_DARE3-fibro | log2_normalized_counts_DARE1-fibro | log2_normalized_counts_DARE2-fibro | log2_normalized_counts_DARE3-fibro | rpgm_normalized_counts_DARE1-fibro | rpgm_normalized_counts_DARE2-fibro | rpgm_normalized_counts_DARE3-fibro | LN | AR | MD | MN | QN | KN | CM | BT |
|---|
| chr11 | 83525778 | 83530518 | ENSMUSG00000035042 | 0.4664 | - | Ccl5 | protein_coding | 3.02e-15 | 6.61e-11 | 192.1250 | 7.58590 | 3.00e+00 | 2.00e+00 | 8.00e+00 | 2.00e+00 | 1.58e+00 | 3.17e+00 | 1.11e-03 | 7.42e-04 | 2.97e-03 | 7.58e+02 | 1.18e+03 | 1.14e+03 | 9.57e+00 | 1.02e+01 | 1.02e+01 | 2.81e-01 | 4.36e-01 | 4.22e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 46711998 | 46715700 | ENSMUSG00000040026 | 0.4807 | - | Saa3 | protein_coding | 9.85e-15 | 1.08e-10 | 180.9322 | 7.49931 | 1.30e+01 | 3.10e+01 | 1.20e+01 | 3.81e+00 | 5.00e+00 | 3.70e+00 | 2.84e-03 | 6.77e-03 | 2.62e-03 | 1.25e+03 | 5.16e+03 | 4.26e+03 | 1.03e+01 | 1.23e+01 | 1.21e+01 | 2.74e-01 | 1.13e+00 | 9.30e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 33875659 | 33890661 | ENSMUSG00000079553 | 0.4940 | - | Kifc1 | protein_coding | 4.40e-14 | 3.21e-10 | 307.8571 | 8.26612 | 1.00e+00 | 1.00e+00 | 2.00e+00 | 1.00e+00 | 1.00e+00 | 1.58e+00 | 1.56e-04 | 1.56e-04 | 3.12e-04 | 2.00e+00 | 2.15e+03 | 4.00e+00 | 1.58e+00 | 1.11e+01 | 2.32e+00 | 3.12e-04 | 3.34e-01 | 6.23e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 78920787 | 78960254 | ENSMUSG00000020826 | 0.5008 | + | Nos2 | protein_coding | 1.68e-11 | 9.21e-08 | 148.2500 | 7.21189 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 3.34e-04 | 0.00e+00 | 3.79e+02 | 7.30e+01 | 1.38e+02 | 8.57e+00 | 6.21e+00 | 7.12e+00 | 1.26e-01 | 2.43e-02 | 4.60e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 101264378 | 101268255 | ENSMUSG00000031304 | 0.4814 | - | Il2rg | protein_coding | 6.15e-10 | 2.70e-06 | 80.5000 | 6.33092 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.84e-04 | 0.00e+00 | 1.22e+02 | 8.60e+01 | 1.11e+02 | 6.94e+00 | 6.44e+00 | 6.81e+00 | 2.24e-02 | 1.58e-02 | 2.04e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 109575128 | 109579172 | ENSMUSG00000031722 | 0.5125 | - | Hp | protein_coding | 1.41e-09 | 5.15e-06 | 35.5514 | 5.15183 | 1.38e+02 | 6.90e+01 | 8.20e+01 | 7.12e+00 | 6.13e+00 | 6.38e+00 | 4.87e-02 | 2.44e-02 | 2.90e-02 | 3.23e+03 | 4.12e+03 | 3.03e+03 | 1.17e+01 | 1.20e+01 | 1.16e+01 | 1.14e+00 | 1.45e+00 | 1.07e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 129875979 | 129876947 | ENSMUSG00000106840 | 0.4303 | - | Gm42790 | TEC | 4.65e-09 | 1.46e-05 | 26.9796 | 4.75380 | 1.70e+01 | 2.50e+01 | 5.30e+01 | 4.17e+00 | 4.70e+00 | 5.75e+00 | 1.36e-02 | 2.00e-02 | 4.25e-02 | 1.54e+03 | 8.40e+02 | 2.57e+02 | 1.06e+01 | 9.72e+00 | 8.01e+00 | 1.24e+00 | 6.73e-01 | 2.06e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 90759360 | 90761624 | ENSMUSG00000029371 | 0.4190 | + | Cxcl5 | protein_coding | 4.56e-08 | 1.25e-04 | 44.9000 | 5.48864 | 0.00e+00 | 7.00e+00 | 0.00e+00 | 0.00e+00 | 3.00e+00 | 0.00e+00 | 0.00e+00 | 2.97e-03 | 0.00e+00 | 2.41e+02 | 9.80e+01 | 1.07e+02 | 7.92e+00 | 6.63e+00 | 6.75e+00 | 1.02e-01 | 4.15e-02 | 4.54e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 117287797 | 117292868 | ENSMUSG00000069515 | 0.4608 | - | Lyz1 | protein_coding | 8.46e-08 | 2.06e-04 | 62.6667 | 5.96963 | 0.00e+00 | 1.00e+00 | 2.00e+00 | 0.00e+00 | 1.00e+00 | 1.58e+00 | 0.00e+00 | 4.92e-04 | 9.83e-04 | 5.80e+01 | 9.80e+01 | 2.17e+02 | 5.88e+00 | 6.63e+00 | 7.77e+00 | 2.85e-02 | 4.82e-02 | 1.07e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 134082448 | 134095082 | ENSMUSG00000000682 | 0.4953 | - | Cd52 | protein_coding | 3.10e-07 | 6.80e-04 | 36.2667 | 5.18057 | 6.00e+00 | 6.00e+00 | 0.00e+00 | 2.81e+00 | 2.81e+00 | 0.00e+00 | 1.52e-03 | 1.52e-03 | 0.00e+00 | 1.15e+02 | 2.01e+02 | 2.25e+02 | 6.86e+00 | 7.66e+00 | 7.82e+00 | 2.92e-02 | 5.11e-02 | 5.72e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 7445822 | 7455975 | ENSMUSG00000043613 | 0.4079 | + | Mmp3 | protein_coding | 7.22e-07 | 1.44e-03 | 15.0275 | 3.90954 | 2.17e+02 | 1.14e+02 | 1.38e+02 | 7.77e+00 | 6.85e+00 | 7.12e+00 | 1.42e-01 | 7.44e-02 | 9.00e-02 | 3.17e+03 | 1.93e+03 | 1.99e+03 | 1.16e+01 | 1.09e+01 | 1.10e+01 | 2.07e+00 | 1.26e+00 | 1.30e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 34305867 | 34316674 | ENSMUSG00000060586 | 0.4833 | + | H2-Eb1 | protein_coding | 1.03e-06 | 1.89e-03 | 17.3103 | 4.11356 | 6.00e+00 | 3.50e+01 | 4.30e+01 | 2.81e+00 | 5.17e+00 | 5.46e+00 | 7.75e-04 | 4.52e-03 | 5.55e-03 | 2.11e+02 | 7.06e+02 | 5.86e+02 | 7.73e+00 | 9.47e+00 | 9.20e+00 | 2.73e-02 | 9.12e-02 | 7.57e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 34282744 | 34287823 | ENSMUSG00000036594 | 0.4636 | - | H2-Aa | protein_coding | 1.18e-06 | 1.99e-03 | 21.1818 | 4.40475 | 2.00e+00 | 3.80e+01 | 1.20e+01 | 1.58e+00 | 5.29e+00 | 3.70e+00 | 6.74e-04 | 1.28e-02 | 4.04e-03 | 1.01e+02 | 4.50e+02 | 6.11e+02 | 6.67e+00 | 8.82e+00 | 9.26e+00 | 3.40e-02 | 1.52e-01 | 2.06e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 35439155 | 35443773 | ENSMUSG00000060550 | 0.5373 | + | H2-Q7 | protein_coding | 1.92e-06 | 3.00e-03 | 55.3333 | 5.79008 | 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 | 4.10e+01 | 4.70e+01 | 7.50e+01 | 5.39e+00 | 5.58e+00 | 6.25e+00 | 1.10e-02 | 1.26e-02 | 2.01e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 94772009 | 94782427 | ENSMUSG00000031778 | 0.5268 | + | Cx3cl1 | protein_coding | 2.44e-06 | 3.57e-03 | 14.9643 | 3.90345 | 3.30e+01 | 7.00e+00 | 1.30e+01 | 5.09e+00 | 3.00e+00 | 3.81e+00 | 3.40e-03 | 7.20e-04 | 1.34e-03 | 4.62e+02 | 1.37e+02 | 2.36e+02 | 8.85e+00 | 7.11e+00 | 7.89e+00 | 4.76e-02 | 1.41e-02 | 2.43e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr16 | 95359169 | 95586593 | ENSMUSG00000040732 | 0.4595 | - | Erg | protein_coding | 3.81e-06 | 5.22e-03 | 22.0000 | 4.45943 | 0.00e+00 | 2.00e+00 | 1.00e+00 | 0.00e+00 | 1.58e+00 | 1.00e+00 | 0.00e+00 | 6.93e-04 | 3.47e-04 | 1.26e+02 | 0.00e+00 | 3.00e+00 | 6.99e+00 | 0.00e+00 | 2.00e+00 | 4.37e-02 | 0.00e+00 | 1.04e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 24594087 | 24595423 | ENSMUSG00000099997 | 0.5393 | - | Tubb4b-ps2 | processed_pseudogene | 6.56e-06 | 8.46e-03 | 11.1333 | 3.47681 | 1.00e+01 | 2.00e+01 | 1.20e+01 | 3.46e+00 | 4.39e+00 | 3.70e+00 | 8.01e-03 | 1.60e-02 | 9.62e-03 | 2.77e+02 | 7.20e+01 | 1.49e+02 | 8.12e+00 | 6.19e+00 | 7.23e+00 | 2.22e-01 | 5.77e-02 | 1.19e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 95526786 | 95556403 | ENSMUSG00000038642 | 0.4437 | + | Ctss | protein_coding | 8.79e-06 | 1.07e-02 | 17.2286 | 4.10673 | 2.00e+00 | 2.10e+01 | 9.00e+00 | 1.58e+00 | 4.46e+00 | 3.32e+00 | 1.36e-03 | 1.43e-02 | 6.14e-03 | 9.50e+01 | 2.83e+02 | 2.22e+02 | 6.58e+00 | 8.15e+00 | 7.80e+00 | 6.48e-02 | 1.93e-01 | 1.51e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 117277331 | 117282321 | ENSMUSG00000069516 | 0.4708 | - | Lyz2 | protein_coding | 1.19e-05 | 1.37e-02 | 11.9257 | 3.57600 | 3.30e+01 | 9.30e+01 | 4.60e+01 | 5.09e+00 | 6.55e+00 | 5.55e+00 | 1.62e-02 | 4.56e-02 | 2.26e-02 | 5.33e+02 | 6.54e+02 | 8.97e+02 | 9.06e+00 | 9.36e+00 | 9.81e+00 | 2.62e-01 | 3.21e-01 | 4.40e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 34257689 | 34269419 | ENSMUSG00000073421 | 0.4964 | + | H2-Ab1 | protein_coding | 1.72e-05 | 1.82e-02 | 15.8235 | 3.98400 | 1.00e+00 | 1.40e+01 | 1.60e+01 | 1.00e+00 | 3.91e+00 | 4.09e+00 | 1.84e-04 | 2.58e-03 | 2.95e-03 | 6.30e+01 | 2.37e+02 | 2.35e+02 | 6.00e+00 | 7.89e+00 | 7.88e+00 | 1.16e-02 | 4.37e-02 | 4.33e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 57203970 | 57228136 | ENSMUSG00000024164 | 0.5201 | - | C3 | protein_coding | 1.74e-05 | 1.82e-02 | 10.3063 | 3.36545 | 1.13e+03 | 3.43e+02 | 2.88e+02 | 1.01e+01 | 8.43e+00 | 8.17e+00 | 2.98e-01 | 9.06e-02 | 7.60e-02 | 1.45e+04 | 1.55e+03 | 2.12e+03 | 1.38e+01 | 1.06e+01 | 1.10e+01 | 3.83e+00 | 4.08e-01 | 5.59e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for Wt_fibro_vs_DARE_fibro.Download the whole result list for Wt_fibro_vs_DARE_fibro.DEG table for the contrast Wt_endo_vs_DARECad_endoThe following table presents the top 5% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Wt_endo_vs_DARECad_endo. 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 | natural_normalized_fold_change_Wt_endo_vs_DARECad_endo | log2_normalized_fold_change_Wt_endo_vs_DARECad_endo | natural_normalized_counts_wt1-endo | natural_normalized_counts_wt2-endo | natural_normalized_counts_wt3-endo | log2_normalized_counts_wt1-endo | log2_normalized_counts_wt2-endo | log2_normalized_counts_wt3-endo | rpgm_normalized_counts_wt1-endo | rpgm_normalized_counts_wt2-endo | rpgm_normalized_counts_wt3-endo | natural_normalized_counts_DARECad1-endo | natural_normalized_counts_DARECad2-endo | natural_normalized_counts_DARECad3-endo | log2_normalized_counts_DARECad1-endo | log2_normalized_counts_DARECad2-endo | log2_normalized_counts_DARECad3-endo | rpgm_normalized_counts_DARECad1-endo | rpgm_normalized_counts_DARECad2-endo | rpgm_normalized_counts_DARECad3-endo | LN | AR | MD | MN | QN | KN | CM | BT |
|---|
| chr11 | 83525778 | 83530518 | ENSMUSG00000035042 | 0.4664 | - | Ccl5 | protein_coding | 3.92e-12 | 8.59e-08 | 85.6667 | 6.420662 | 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 | 9.60e+01 | 2.80e+01 | 1.30e+02 | 6.60e+00 | 4.86e+00 | 7.03e+00 | 3.56e-02 | 1.04e-02 | 4.82e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 92215799 | 92221911 | ENSMUSG00000078664 | 0.4044 | + | Sprr2a1 | protein_coding | 9.96e-12 | 1.09e-07 | 74.3333 | 6.215937 | 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 | 2.20e+02 | 0.00e+00 | 0.00e+00 | 7.79e+00 | 0.00e+00 | 0.00e+00 | 5.77e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 92215920 | 92256724 | ENSMUSG00000068893 | 0.3908 | + | Sprr2a2 | protein_coding | 1.71e-11 | 1.25e-07 | 81.6667 | 6.351675 | 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 | 2.42e+02 | 0.00e+00 | 0.00e+00 | 7.92e+00 | 0.00e+00 | 0.00e+00 | 6.34e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 46711998 | 46715700 | ENSMUSG00000040026 | 0.4807 | - | Saa3 | protein_coding | 2.63e-11 | 1.44e-07 | 60.6316 | 5.921997 | 0.00e+00 | 9.00e+00 | 7.00e+00 | 0.00e+00 | 3.32e+00 | 3.00e+00 | 0.00e+00 | 1.97e-03 | 1.53e-03 | 3.20e+02 | 2.96e+02 | 5.33e+02 | 8.33e+00 | 8.21e+00 | 9.06e+00 | 6.99e-02 | 6.46e-02 | 1.16e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 10179852 | 10197262 | ENSMUSG00000103124 | 0.4214 | - | Gm37389 | protein_coding | 1.86e-10 | 8.14e-07 | 59.2571 | 5.888917 | 1.50e+01 | 1.30e+01 | 4.00e+00 | 4.00e+00 | 3.81e+00 | 2.32e+00 | 3.36e-03 | 2.92e-03 | 8.97e-04 | 5.00e+00 | 8.00e+00 | 2.06e+03 | 2.58e+00 | 3.17e+00 | 1.10e+01 | 1.12e-03 | 1.79e-03 | 4.62e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 7445822 | 7455975 | ENSMUSG00000043613 | 0.4079 | + | Mmp3 | protein_coding | 5.33e-10 | 1.95e-06 | 33.6400 | 5.072106 | 1.70e+01 | 5.00e+00 | 0.00e+00 | 4.17e+00 | 2.58e+00 | 0.00e+00 | 1.11e-02 | 3.26e-03 | 0.00e+00 | 2.01e+02 | 1.90e+02 | 4.47e+02 | 7.66e+00 | 7.58e+00 | 8.81e+00 | 1.31e-01 | 1.24e-01 | 2.92e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 92285417 | 92291405 | ENSMUSG00000074445 | 0.4002 | + | Sprr2a3 | protein_coding | 8.69e-09 | 2.72e-05 | 46.3333 | 5.533979 | 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 | 1.36e+02 | 0.00e+00 | 0.00e+00 | 7.10e+00 | 0.00e+00 | 0.00e+00 | 3.57e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr19 | 32757497 | 32826160 | ENSMUSG00000013663 | 0.3811 | + | Pten | protein_coding | 2.64e-08 | 7.25e-05 | 32.0137 | 5.000618 | 2.04e+02 | 2.49e+02 | 2.00e+02 | 7.68e+00 | 7.97e+00 | 7.65e+00 | 2.07e-02 | 2.52e-02 | 2.03e-02 | 4.45e+03 | 1.64e+04 | 1.54e+02 | 1.21e+01 | 1.40e+01 | 7.28e+00 | 4.51e-01 | 1.66e+00 | 1.56e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 109575128 | 109579172 | ENSMUSG00000031722 | 0.5125 | - | Hp | protein_coding | 4.09e-08 | 9.97e-05 | 17.6977 | 4.145488 | 4.00e+00 | 3.00e+01 | 6.00e+00 | 2.32e+00 | 4.95e+00 | 2.81e+00 | 1.41e-03 | 1.06e-02 | 2.12e-03 | 3.70e+01 | 1.54e+02 | 5.67e+02 | 5.25e+00 | 7.28e+00 | 9.15e+00 | 1.31e-02 | 5.44e-02 | 2.00e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr13 | 54458837 | 54468849 | ENSMUSG00000025872 | 0.4620 | - | Thoc3 | protein_coding | 4.80e-08 | 1.05e-04 | 15.3825 | 3.943217 | 6.30e+01 | 8.90e+01 | 6.20e+01 | 6.00e+00 | 6.49e+00 | 5.98e+00 | 1.26e-02 | 1.79e-02 | 1.24e-02 | 6.40e+01 | 1.87e+02 | 3.08e+03 | 6.02e+00 | 7.55e+00 | 1.16e+01 | 1.28e-02 | 3.75e-02 | 6.19e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 57203970 | 57228136 | ENSMUSG00000024164 | 0.5201 | - | C3 | protein_coding | 8.38e-08 | 1.67e-04 | 25.8172 | 4.690261 | 5.10e+01 | 1.90e+01 | 2.00e+01 | 5.70e+00 | 4.32e+00 | 4.39e+00 | 1.35e-02 | 5.02e-03 | 5.28e-03 | 1.67e+02 | 1.49e+03 | 7.43e+02 | 7.39e+00 | 1.05e+01 | 9.54e+00 | 4.41e-02 | 3.93e-01 | 1.96e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 34153072 | 34160230 | ENSMUSG00000079547 | 0.4883 | + | H2-DMb1 | protein_coding | 3.56e-07 | 6.44e-04 | 24.4286 | 4.610498 | 2.00e+00 | 1.00e+00 | 1.00e+00 | 1.58e+00 | 1.00e+00 | 1.00e+00 | 7.18e-04 | 3.59e-04 | 3.59e-04 | 9.00e+00 | 7.00e+00 | 1.52e+02 | 3.32e+00 | 3.00e+00 | 7.26e+00 | 3.23e-03 | 2.51e-03 | 5.45e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 43596049 | 43601540 | ENSMUSG00000020405 | 0.4468 | - | Fabp6 | protein_coding | 3.82e-07 | 6.44e-04 | 27.6667 | 4.790077 | 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 | 8.00e+01 | 0.00e+00 | 0.00e+00 | 6.34e+00 | 0.00e+00 | 0.00e+00 | 6.10e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 95526786 | 95556403 | ENSMUSG00000038642 | 0.4437 | + | Ctss | protein_coding | 4.62e-07 | 7.18e-04 | 23.4800 | 4.553361 | 7.00e+00 | 1.10e+01 | 4.00e+00 | 3.00e+00 | 3.58e+00 | 2.32e+00 | 4.77e-03 | 7.50e-03 | 2.73e-03 | 1.90e+02 | 1.73e+02 | 2.21e+02 | 7.58e+00 | 7.44e+00 | 7.79e+00 | 1.30e-01 | 1.18e-01 | 1.51e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 103510586 | 103750211 | ENSMUSG00000030077 | 0.3788 | + | Chl1 | protein_coding | 4.91e-07 | 7.18e-04 | 28.3333 | 4.824428 | 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 | 2.00e+00 | 2.60e+01 | 5.40e+01 | 1.58e+00 | 4.75e+00 | 5.78e+00 | 2.17e-04 | 2.82e-03 | 5.85e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 25024929 | 25038962 | ENSMUSG00000037406 | 0.4708 | - | Htra4 | protein_coding | 5.44e-07 | 7.45e-04 | 0.0299 | -5.066089 | 5.80e+01 | 1.29e+02 | 7.80e+01 | 5.88e+00 | 7.02e+00 | 6.30e+00 | 1.85e-02 | 4.11e-02 | 2.49e-02 | 0.00e+00 | 0.00e+00 | 5.00e+00 | 0.00e+00 | 0.00e+00 | 2.58e+00 | 0.00e+00 | 0.00e+00 | 1.59e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 164354070 | 164389095 | ENSMUSG00000017002 | 0.4508 | - | Slpi | protein_coding | 1.07e-06 | 1.38e-03 | 24.0000 | 4.584963 | 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 | 2.10e+01 | 1.60e+01 | 3.20e+01 | 4.46e+00 | 4.09e+00 | 5.04e+00 | 5.61e-03 | 4.28e-03 | 8.56e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 78370657 | 78373466 | ENSMUSG00000071356 | 0.4171 | + | Reg3b | protein_coding | 1.51e-06 | 1.84e-03 | 30.0000 | 4.906891 | 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 | 8.70e+01 | 0.00e+00 | 0.00e+00 | 6.46e+00 | 0.00e+00 | 0.00e+00 | 3.22e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 42772860 | 42773993 | ENSMUSG00000094686 | 0.5670 | - | Ccl21a | protein_coding | 1.89e-06 | 2.18e-03 | 12.5682 | 3.651704 | 1.75e+02 | 2.08e+02 | 1.42e+02 | 7.46e+00 | 7.71e+00 | 7.16e+00 | 1.07e-01 | 1.27e-01 | 8.65e-02 | 1.55e+03 | 2.36e+03 | 2.73e+03 | 1.06e+01 | 1.12e+01 | 1.14e+01 | 9.44e-01 | 1.44e+00 | 1.66e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 129364570 | 129371139 | ENSMUSG00000027398 | 0.4534 | - | Il1b | protein_coding | 2.28e-06 | 2.50e-03 | 36.6667 | 5.196397 | 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 | 1.60e+01 | 3.60e+01 | 5.50e+01 | 4.09e+00 | 5.21e+00 | 5.81e+00 | 5.25e-03 | 1.18e-02 | 1.80e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr14 | 31012433 | 31019152 | ENSMUSG00000042354 | 0.4329 | - | Gnl3 | protein_coding | 2.68e-06 | 2.80e-03 | 0.0164 | -5.930737 | 5.60e+01 | 5.30e+01 | 7.10e+01 | 5.83e+00 | 5.75e+00 | 6.17e+00 | 4.42e-03 | 4.18e-03 | 5.61e-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 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 117849251 | 117855743 | ENSMUSG00000017716 | 0.4694 | + | Birc5 | protein_coding | 5.91e-06 | 5.41e-03 | 21.2857 | 4.411814 | 4.00e+00 | 0.00e+00 | 0.00e+00 | 2.32e+00 | 0.00e+00 | 0.00e+00 | 9.56e-04 | 0.00e+00 | 0.00e+00 | 7.00e+00 | 5.20e+01 | 8.70e+01 | 3.00e+00 | 5.73e+00 | 6.46e+00 | 1.67e-03 | 1.24e-02 | 2.08e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 35170991 | 35176068 | ENSMUSG00000024397 | 0.5228 | - | Aif1 | protein_coding | 5.91e-06 | 5.41e-03 | 39.0000 | 5.285402 | 0.00e+00 | 2.00e+00 | 0.00e+00 | 0.00e+00 | 1.58e+00 | 0.00e+00 | 0.00e+00 | 5.18e-04 | 0.00e+00 | 0.00e+00 | 8.20e+01 | 1.10e+02 | 0.00e+00 | 6.38e+00 | 6.79e+00 | 0.00e+00 | 2.12e-02 | 2.85e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 90903871 | 90905938 | ENSMUSG00000058427 | 0.4507 | + | Cxcl2 | protein_coding | 6.03e-06 | 5.41e-03 | 14.8000 | 3.887525 | 1.10e+01 | 1.00e+00 | 0.00e+00 | 3.58e+00 | 1.00e+00 | 0.00e+00 | 3.89e-03 | 3.54e-04 | 0.00e+00 | 5.50e+01 | 6.40e+01 | 1.00e+02 | 5.81e+00 | 6.02e+00 | 6.66e+00 | 1.95e-02 | 2.27e-02 | 3.54e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 4133531 | 4138819 | ENSMUSG00000045573 | 0.4386 | - | Penk | protein_coding | 6.30e-06 | 5.41e-03 | 0.0606 | -4.044394 | 6.49e+02 | 3.15e+02 | 2.87e+02 | 9.34e+00 | 8.30e+00 | 8.17e+00 | 2.31e-01 | 1.12e-01 | 1.02e-01 | 0.00e+00 | 4.90e+01 | 2.40e+01 | 0.00e+00 | 5.64e+00 | 4.64e+00 | 0.00e+00 | 1.75e-02 | 8.56e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 34305867 | 34316674 | ENSMUSG00000060586 | 0.4833 | + | H2-Eb1 | protein_coding | 6.42e-06 | 5.41e-03 | 9.8678 | 3.302724 | 3.40e+01 | 5.20e+01 | 3.20e+01 | 5.13e+00 | 5.73e+00 | 5.04e+00 | 4.39e-03 | 6.72e-03 | 4.13e-03 | 2.35e+02 | 2.82e+02 | 6.74e+02 | 7.88e+00 | 8.14e+00 | 9.40e+00 | 3.04e-02 | 3.64e-02 | 8.71e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 44302687 | 44306902 | ENSMUSG00000004473 | 0.5384 | - | Clec11a | protein_coding | 1.22e-05 | 9.90e-03 | 30.5000 | 4.930737 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 3.22e-04 | 0.00e+00 | 0.00e+00 | 8.00e+01 | 2.80e+01 | 1.10e+01 | 6.34e+00 | 4.86e+00 | 3.58e+00 | 2.58e-02 | 9.03e-03 | 3.55e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 42612121 | 42613253 | ENSMUSG00000096596 | 0.5640 | + | Gm10591 | protein_coding | 2.59e-05 | 2.03e-02 | 11.8588 | 3.567889 | 4.30e+01 | 1.70e+01 | 2.20e+01 | 5.46e+00 | 4.17e+00 | 4.52e+00 | 2.62e-02 | 1.04e-02 | 1.34e-02 | 2.58e+02 | 3.57e+02 | 3.90e+02 | 8.02e+00 | 8.48e+00 | 8.61e+00 | 1.57e-01 | 2.18e-01 | 2.38e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 74713574 | 74737892 | ENSMUSG00000026170 | 0.4563 | + | Cyp27a1 | protein_coding | 3.26e-05 | 2.46e-02 | 94.0000 | 6.554589 | 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 | 2.79e+02 | 0.00e+00 | 0.00e+00 | 8.13e+00 | 0.00e+00 | 0.00e+00 | 1.02e-01 | 0.00e+00 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 108014791 | 108096445 | ENSMUSG00000028600 | 0.4651 | - | Podn | protein_coding | 3.57e-05 | 2.61e-02 | 0.0361 | -4.790077 | 3.40e+01 | 3.30e+01 | 1.30e+01 | 5.13e+00 | 5.09e+00 | 3.81e+00 | 7.04e-03 | 6.83e-03 | 2.69e-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 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 79618051 | 79637918 | ENSMUSG00000020312 | 0.5341 | - | Shc2 | protein_coding | 4.68e-05 | 3.31e-02 | 26.6667 | 4.736966 | 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 | 7.70e+01 | 0.00e+00 | 0.00e+00 | 6.29e+00 | 0.00e+00 | 0.00e+00 | 1.56e-02 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 97606879 | 97613692 | ENSMUSG00000019932 | 0.3926 | + | Kera | protein_coding | 4.99e-05 | 3.42e-02 | 16.6667 | 4.058894 | 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 | 7.00e+00 | 2.50e+01 | 1.50e+01 | 3.00e+00 | 4.70e+00 | 4.00e+00 | 3.56e-03 | 1.27e-02 | 7.63e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr13 | 16011851 | 16031621 | ENSMUSG00000041324 | 0.4311 | + | Inhba | protein_coding | 5.22e-05 | 3.47e-02 | 18.1429 | 4.181330 | 4.00e+00 | 0.00e+00 | 0.00e+00 | 2.32e+00 | 0.00e+00 | 0.00e+00 | 6.97e-04 | 0.00e+00 | 0.00e+00 | 6.90e+01 | 3.60e+01 | 1.90e+01 | 6.13e+00 | 5.21e+00 | 4.32e+00 | 1.20e-02 | 6.27e-03 | 3.31e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 113254830 | 113260236 | ENSMUSG00000095079 | 0.5130 | - | Igha | IG_C_gene | 5.52e-05 | 3.47e-02 | 10.0000 | 3.321928 | 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 | 2.70e+01 | 0.00e+00 | 0.00e+00 | 4.81e+00 | 0.00e+00 | 0.00e+00 | 6.86e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 42114817 | 42115917 | ENSMUSG00000073878 | 0.5649 | + | Gm13304 | protein_coding | 5.59e-05 | 3.47e-02 | 12.1897 | 3.607585 | 2.20e+01 | 1.70e+01 | 1.60e+01 | 4.52e+00 | 4.17e+00 | 4.09e+00 | 1.34e-02 | 1.04e-02 | 9.75e-03 | 1.58e+02 | 2.42e+02 | 3.04e+02 | 7.31e+00 | 7.92e+00 | 8.25e+00 | 9.63e-02 | 1.47e-01 | 1.85e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr16 | 23146536 | 23158028 | ENSMUSG00000022878 | 0.4547 | + | Adipoq | protein_coding | 5.70e-05 | 3.47e-02 | 28.7174 | 4.843853 | 0.00e+00 | 8.00e+00 | 3.50e+01 | 0.00e+00 | 3.17e+00 | 5.17e+00 | 0.00e+00 | 2.73e-03 | 1.19e-02 | 1.24e+03 | 7.50e+01 | 0.00e+00 | 1.03e+01 | 6.25e+00 | 0.00e+00 | 4.24e-01 | 2.56e-02 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 24336853 | 24351494 | ENSMUSG00000026981 | 0.4277 | + | Il1rn | protein_coding | 5.98e-05 | 3.55e-02 | 20.0000 | 4.321928 | 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 | 2.00e+00 | 1.80e+01 | 3.70e+01 | 1.58e+00 | 4.25e+00 | 5.25e+00 | 3.44e-04 | 3.09e-03 | 6.36e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 117277331 | 117282321 | ENSMUSG00000069516 | 0.4708 | - | Lyz2 | protein_coding | 6.65e-05 | 3.84e-02 | 8.0045 | 3.000808 | 5.50e+01 | 8.00e+01 | 8.50e+01 | 5.81e+00 | 6.34e+00 | 6.43e+00 | 2.70e-02 | 3.93e-02 | 4.17e-02 | 4.80e+02 | 5.55e+02 | 7.47e+02 | 8.91e+00 | 9.12e+00 | 9.55e+00 | 2.36e-01 | 2.72e-01 | 3.67e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for Wt_endo_vs_DARECad_endo.Download the whole result list for Wt_endo_vs_DARECad_endo.DEG table for the contrast Wt_fibro_vs_DARECad_fibroThe following table presents the top 5% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Wt_fibro_vs_DARECad_fibro. 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 | natural_normalized_fold_change_Wt_fibro_vs_DARECad_fibro | log2_normalized_fold_change_Wt_fibro_vs_DARECad_fibro | natural_normalized_counts_wt1-fibro | natural_normalized_counts_wt2-fibro | natural_normalized_counts_wt3-fibro | log2_normalized_counts_wt1-fibro | log2_normalized_counts_wt2-fibro | log2_normalized_counts_wt3-fibro | rpgm_normalized_counts_wt1-fibro | rpgm_normalized_counts_wt2-fibro | rpgm_normalized_counts_wt3-fibro | natural_normalized_counts_DARECad1-fibro | natural_normalized_counts_DARECad2-fibro | natural_normalized_counts_DARECad3-fibro | log2_normalized_counts_DARECad1-fibro | log2_normalized_counts_DARECad2-fibro | log2_normalized_counts_DARECad3-fibro | rpgm_normalized_counts_DARECad1-fibro | rpgm_normalized_counts_DARECad2-fibro | rpgm_normalized_counts_DARECad3-fibro | LN | AR | MD | MN | QN | KN | CM | BT |
|---|
| chr3 | 92215799 | 92221911 | ENSMUSG00000078664 | 0.4044 | + | Sprr2a1 | protein_coding | 1.35e-18 | 2.96e-14 | 894.6667 | 9.80521 | 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 | 2.57e+03 | 1.13e+02 | 0.00e+00 | 1.13e+01 | 6.83e+00 | 0.00e+00 | 6.73e-01 | 2.96e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 92215920 | 92256724 | ENSMUSG00000068893 | 0.3908 | + | Sprr2a2 | protein_coding | 7.78e-17 | 8.53e-13 | 679.0000 | 9.40727 | 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 | 1.97e+03 | 6.20e+01 | 0.00e+00 | 1.09e+01 | 5.98e+00 | 0.00e+00 | 5.17e-01 | 1.62e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 83525778 | 83530518 | ENSMUSG00000035042 | 0.4664 | - | Ccl5 | protein_coding | 3.05e-15 | 1.70e-11 | 177.1250 | 7.46862 | 3.00e+00 | 2.00e+00 | 8.00e+00 | 2.00e+00 | 1.58e+00 | 3.17e+00 | 1.11e-03 | 7.42e-04 | 2.97e-03 | 7.89e+02 | 9.67e+02 | 1.08e+03 | 9.63e+00 | 9.92e+00 | 1.01e+01 | 2.93e-01 | 3.59e-01 | 3.99e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 24594087 | 24595423 | ENSMUSG00000099997 | 0.5393 | - | Tubb4b-ps2 | processed_pseudogene | 3.10e-15 | 1.70e-11 | 161.1778 | 7.33251 | 1.00e+01 | 2.00e+01 | 1.20e+01 | 3.46e+00 | 4.39e+00 | 3.70e+00 | 8.01e-03 | 1.60e-02 | 9.62e-03 | 9.00e+00 | 6.20e+01 | 7.18e+03 | 3.32e+00 | 5.98e+00 | 1.28e+01 | 7.21e-03 | 4.97e-02 | 5.75e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 46711998 | 46715700 | ENSMUSG00000040026 | 0.4807 | - | Saa3 | protein_coding | 4.41e-14 | 1.93e-10 | 133.7119 | 7.06298 | 1.30e+01 | 3.10e+01 | 1.20e+01 | 3.81e+00 | 5.00e+00 | 3.70e+00 | 2.84e-03 | 6.77e-03 | 2.62e-03 | 1.42e+03 | 2.03e+03 | 4.44e+03 | 1.05e+01 | 1.10e+01 | 1.21e+01 | 3.09e-01 | 4.42e-01 | 9.70e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 69964779 | 69967885 | ENSMUSG00000018569 | 0.5848 | + | Cldn7 | protein_coding | 5.86e-14 | 2.14e-10 | 412.7500 | 8.68912 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 3.66e-04 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 1.62e+03 | 3.10e+01 | 0.00e+00 | 1.07e+01 | 5.00e+00 | 0.00e+00 | 5.93e-01 | 1.14e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 92285417 | 92291405 | ENSMUSG00000074445 | 0.4002 | + | Sprr2a3 | protein_coding | 1.94e-13 | 6.07e-10 | 408.0000 | 8.67243 | 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 | 1.22e+03 | 1.00e+00 | 0.00e+00 | 1.03e+01 | 1.00e+00 | 0.00e+00 | 3.20e-01 | 2.62e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 43596049 | 43601540 | ENSMUSG00000020405 | 0.4468 | - | Fabp6 | protein_coding | 2.10e-12 | 5.75e-09 | 364.6667 | 8.51043 | 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 | 1.08e+03 | 1.50e+01 | 0.00e+00 | 1.01e+01 | 4.00e+00 | 0.00e+00 | 8.21e-01 | 1.14e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 113254830 | 113260236 | ENSMUSG00000095079 | 0.5130 | - | Igha | IG_C_gene | 1.18e-11 | 2.87e-08 | 228.0000 | 7.83289 | 0.00e+00 | 3.00e+00 | 0.00e+00 | 0.00e+00 | 2.00e+00 | 0.00e+00 | 0.00e+00 | 7.63e-04 | 0.00e+00 | 0.00e+00 | 1.34e+03 | 3.00e+01 | 0.00e+00 | 1.04e+01 | 4.95e+00 | 0.00e+00 | 3.39e-01 | 7.63e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 129875979 | 129876947 | ENSMUSG00000106840 | 0.4303 | - | Gm42790 | TEC | 3.17e-11 | 6.95e-08 | 51.9490 | 5.69902 | 1.70e+01 | 2.50e+01 | 5.30e+01 | 4.17e+00 | 4.70e+00 | 5.75e+00 | 1.36e-02 | 2.00e-02 | 4.25e-02 | 2.00e+01 | 1.82e+03 | 3.24e+03 | 4.39e+00 | 1.08e+01 | 1.17e+01 | 1.60e-02 | 1.46e+00 | 2.60e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 81194609 | 81210877 | ENSMUSG00000085779 | 0.5215 | + | Atcayos | lncRNA | 6.69e-11 | 1.33e-07 | 45.2576 | 5.50009 | 1.30e+01 | 3.60e+01 | 1.40e+01 | 3.81e+00 | 5.21e+00 | 3.91e+00 | 3.47e-03 | 9.62e-03 | 3.74e-03 | 1.70e+01 | 2.95e+03 | 1.60e+01 | 4.17e+00 | 1.15e+01 | 4.09e+00 | 4.54e-03 | 7.88e-01 | 4.27e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 101264378 | 101268255 | ENSMUSG00000031304 | 0.4814 | - | Il2rg | protein_coding | 3.66e-10 | 6.68e-07 | 88.0000 | 6.45943 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.84e-04 | 0.00e+00 | 1.76e+02 | 6.20e+01 | 1.11e+02 | 7.47e+00 | 5.98e+00 | 6.81e+00 | 3.24e-02 | 1.14e-02 | 2.04e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 78466269 | 78468872 | ENSMUSG00000030017 | 0.4213 | - | Reg3g | protein_coding | 3.97e-10 | 6.69e-07 | 275.6667 | 8.10678 | 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 | 8.20e+02 | 4.00e+00 | 0.00e+00 | 9.68e+00 | 2.32e+00 | 0.00e+00 | 5.60e-01 | 2.73e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 78370657 | 78373466 | ENSMUSG00000071356 | 0.4171 | + | Reg3b | protein_coding | 5.32e-10 | 8.14e-07 | 248.0000 | 7.95420 | 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 | 7.41e+02 | 0.00e+00 | 0.00e+00 | 9.54e+00 | 0.00e+00 | 0.00e+00 | 2.74e-01 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 78920787 | 78960254 | ENSMUSG00000020826 | 0.5008 | + | Nos2 | protein_coding | 5.57e-10 | 8.14e-07 | 97.2500 | 6.60363 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 3.34e-04 | 0.00e+00 | 2.77e+02 | 3.90e+01 | 7.00e+01 | 8.12e+00 | 5.32e+00 | 6.15e+00 | 9.24e-02 | 1.30e-02 | 2.33e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 58379043 | 58390728 | ENSMUSG00000013643 | 0.4701 | + | Lypd8 | protein_coding | 1.04e-09 | 1.39e-06 | 246.0000 | 7.94251 | 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 | 7.35e+02 | 0.00e+00 | 0.00e+00 | 9.52e+00 | 0.00e+00 | 0.00e+00 | 4.61e-01 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 127050156 | 127087328 | ENSMUSG00000049350 | 0.4615 | - | Zg16 | protein_coding | 1.08e-09 | 1.39e-06 | 263.6667 | 8.04257 | 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 | 7.71e+02 | 1.70e+01 | 0.00e+00 | 9.59e+00 | 4.17e+00 | 0.00e+00 | 2.74e-01 | 6.04e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 87635979 | 87651129 | ENSMUSG00000045394 | 0.4631 | + | Epcam | protein_coding | 6.93e-09 | 8.44e-06 | 104.7000 | 6.71012 | 0.00e+00 | 0.00e+00 | 7.00e+00 | 0.00e+00 | 0.00e+00 | 3.00e+00 | 0.00e+00 | 0.00e+00 | 1.24e-03 | 1.00e+00 | 1.03e+03 | 1.40e+01 | 1.00e+00 | 1.00e+01 | 3.91e+00 | 1.77e-04 | 1.82e-01 | 2.48e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 90759360 | 90761624 | ENSMUSG00000029371 | 0.4190 | + | Cxcl5 | protein_coding | 7.73e-09 | 8.92e-06 | 63.3000 | 5.98413 | 0.00e+00 | 7.00e+00 | 0.00e+00 | 0.00e+00 | 3.00e+00 | 0.00e+00 | 0.00e+00 | 2.97e-03 | 0.00e+00 | 2.30e+02 | 1.47e+02 | 2.53e+02 | 7.85e+00 | 7.21e+00 | 7.99e+00 | 9.75e-02 | 6.23e-02 | 1.07e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 109575128 | 109579172 | ENSMUSG00000031722 | 0.5125 | - | Hp | protein_coding | 1.03e-08 | 1.13e-05 | 26.4144 | 4.72325 | 1.38e+02 | 6.90e+01 | 8.20e+01 | 7.12e+00 | 6.13e+00 | 6.38e+00 | 4.87e-02 | 2.44e-02 | 2.90e-02 | 1.55e+03 | 2.80e+03 | 3.36e+03 | 1.06e+01 | 1.15e+01 | 1.17e+01 | 5.47e-01 | 9.90e-01 | 1.19e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 141078218 | 141090510 | ENSMUSG00000054065 | 0.5310 | + | Pkp3 | protein_coding | 2.34e-08 | 2.44e-05 | 139.4000 | 7.12309 | 0.00e+00 | 0.00e+00 | 2.00e+00 | 0.00e+00 | 0.00e+00 | 1.58e+00 | 0.00e+00 | 0.00e+00 | 2.24e-04 | 0.00e+00 | 6.85e+02 | 9.00e+00 | 0.00e+00 | 9.42e+00 | 3.32e+00 | 0.00e+00 | 7.67e-02 | 1.01e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 106603351 | 106670246 | ENSMUSG00000000303 | 0.4703 | + | Cdh1 | protein_coding | 3.39e-08 | 3.38e-05 | 90.7778 | 6.50427 | 1.00e+00 | 0.00e+00 | 5.00e+00 | 1.00e+00 | 0.00e+00 | 2.58e+00 | 2.42e-04 | 0.00e+00 | 1.21e-03 | 2.00e+00 | 7.85e+02 | 2.70e+01 | 1.58e+00 | 9.62e+00 | 4.81e+00 | 4.85e-04 | 1.90e-01 | 6.54e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr15 | 100674421 | 100687921 | ENSMUSG00000023031 | 0.4975 | - | Cela1 | protein_coding | 3.81e-08 | 3.63e-05 | 196.0000 | 7.61471 | 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 | 4.00e+00 | 5.81e+02 | 0.00e+00 | 2.32e+00 | 9.18e+00 | 0.00e+00 | 7.40e-04 | 1.07e-01 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 119325784 | 119335962 | ENSMUSG00000027314 | 0.5287 | + | Dll4 | protein_coding | 6.25e-08 | 5.70e-05 | 30.8000 | 4.94486 | 1.00e+00 | 1.00e+00 | 0.00e+00 | 1.00e+00 | 1.00e+00 | 0.00e+00 | 2.61e-04 | 2.61e-04 | 0.00e+00 | 2.00e+00 | 1.45e+02 | 4.00e+00 | 1.58e+00 | 7.19e+00 | 2.32e+00 | 5.23e-04 | 3.79e-02 | 1.05e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 115967145 | 116017926 | ENSMUSG00000034171 | 0.4981 | - | Faah | protein_coding | 1.22e-07 | 1.07e-04 | 20.9216 | 4.38692 | 6.00e+00 | 2.80e+01 | 1.40e+01 | 2.81e+00 | 4.86e+00 | 3.91e+00 | 8.53e-04 | 3.98e-03 | 1.99e-03 | 1.60e+01 | 8.73e+02 | 1.75e+02 | 4.09e+00 | 9.77e+00 | 7.46e+00 | 2.27e-03 | 1.24e-01 | 2.49e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 134945119 | 134946934 | ENSMUSG00000047501 | 0.5683 | - | Cldn4 | protein_coding | 1.33e-07 | 1.12e-04 | 180.3333 | 7.49452 | 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 | 5.38e+02 | 0.00e+00 | 0.00e+00 | 9.07e+00 | 0.00e+00 | 0.00e+00 | 2.70e-01 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 70726435 | 70726966 | ENSMUSG00000076609 | 0.4925 | + | Igkc | IG_C_gene | 2.14e-07 | 1.74e-04 | 50.5294 | 5.65905 | 2.00e+00 | 1.10e+01 | 1.00e+00 | 1.58e+00 | 3.58e+00 | 1.00e+00 | 1.66e-03 | 9.11e-03 | 8.28e-04 | 4.00e+00 | 7.01e+02 | 1.51e+02 | 2.32e+00 | 9.46e+00 | 7.25e+00 | 3.31e-03 | 5.80e-01 | 1.25e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 43993620 | 44102032 | ENSMUSG00000029086 | 0.4440 | - | Prom1 | protein_coding | 2.24e-07 | 1.75e-04 | 37.2000 | 5.21723 | 8.00e+00 | 8.00e+00 | 1.00e+00 | 3.17e+00 | 3.17e+00 | 1.00e+00 | 5.44e-04 | 5.44e-04 | 6.81e-05 | 3.00e+00 | 7.35e+02 | 3.00e+00 | 2.00e+00 | 9.52e+00 | 2.00e+00 | 2.04e-04 | 5.00e-02 | 2.04e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 117287797 | 117292868 | ENSMUSG00000069515 | 0.4608 | - | Lyz1 | protein_coding | 2.51e-07 | 1.89e-04 | 42.3333 | 5.40372 | 0.00e+00 | 1.00e+00 | 2.00e+00 | 0.00e+00 | 1.00e+00 | 1.58e+00 | 0.00e+00 | 4.92e-04 | 9.83e-04 | 7.00e+01 | 1.25e+02 | 5.60e+01 | 6.15e+00 | 6.98e+00 | 5.83e+00 | 3.44e-02 | 6.15e-02 | 2.75e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for Wt_fibro_vs_DARECad_fibro.Download the whole result list for Wt_fibro_vs_DARECad_fibro.DEG table for the contrast Wt_endo_vs_DAREdd_endoThe following table presents the top 5% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Wt_endo_vs_DAREdd_endo. 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 | natural_normalized_fold_change_Wt_endo_vs_DAREdd_endo | log2_normalized_fold_change_Wt_endo_vs_DAREdd_endo | natural_normalized_counts_wt1-endo | natural_normalized_counts_wt2-endo | natural_normalized_counts_wt3-endo | log2_normalized_counts_wt1-endo | log2_normalized_counts_wt2-endo | log2_normalized_counts_wt3-endo | rpgm_normalized_counts_wt1-endo | rpgm_normalized_counts_wt2-endo | rpgm_normalized_counts_wt3-endo | natural_normalized_counts_DAREdd1-endo | natural_normalized_counts_DAREdd2-endo | natural_normalized_counts_DAREdd3-endo | log2_normalized_counts_DAREdd1-endo | log2_normalized_counts_DAREdd2-endo | log2_normalized_counts_DAREdd3-endo | rpgm_normalized_counts_DAREdd1-endo | rpgm_normalized_counts_DAREdd2-endo | rpgm_normalized_counts_DAREdd3-endo | LN | AR | MD | MN | QN | KN | CM | BT |
|---|
| chr3 | 92215799 | 92221911 | ENSMUSG00000078664 | 0.4044 | + | Sprr2a1 | protein_coding | 6.00e-12 | 1.32e-07 | 116.6667 | 6.86625 | 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 | 4.00e+00 | 0.00e+00 | 3.43e+02 | 2.32e+00 | 0.00e+00 | 8.43e+00 | 1.05e-03 | 0.00e+00 | 8.99e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 83525778 | 83530518 | ENSMUSG00000035042 | 0.4664 | - | Ccl5 | protein_coding | 5.12e-11 | 5.62e-07 | 67.6667 | 6.08037 | 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 | 1.10e+01 | 9.40e+01 | 9.50e+01 | 3.58e+00 | 6.57e+00 | 6.58e+00 | 4.08e-03 | 3.49e-02 | 3.53e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 92215920 | 92256724 | ENSMUSG00000068893 | 0.3908 | + | Sprr2a2 | protein_coding | 1.06e-10 | 7.77e-07 | 91.0000 | 6.50779 | 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 | 1.00e+00 | 0.00e+00 | 2.69e+02 | 1.00e+00 | 0.00e+00 | 8.08e+00 | 2.62e-04 | 0.00e+00 | 7.05e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 46711998 | 46715700 | ENSMUSG00000040026 | 0.4807 | - | Saa3 | protein_coding | 5.79e-10 | 3.17e-06 | 47.6316 | 5.57385 | 0.00e+00 | 9.00e+00 | 7.00e+00 | 0.00e+00 | 3.32e+00 | 3.00e+00 | 0.00e+00 | 1.97e-03 | 1.53e-03 | 2.87e+02 | 3.12e+02 | 3.03e+02 | 8.17e+00 | 8.29e+00 | 8.25e+00 | 6.27e-02 | 6.81e-02 | 6.62e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 33875659 | 33890661 | ENSMUSG00000079553 | 0.4940 | - | Kifc1 | protein_coding | 3.12e-09 | 1.37e-05 | 64.8571 | 6.01919 | 2.00e+00 | 2.00e+00 | 0.00e+00 | 1.58e+00 | 1.58e+00 | 0.00e+00 | 3.12e-04 | 3.12e-04 | 0.00e+00 | 1.10e+01 | 4.38e+02 | 2.00e+00 | 3.58e+00 | 8.78e+00 | 1.58e+00 | 1.71e-03 | 6.83e-02 | 3.12e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 7445822 | 7455975 | ENSMUSG00000043613 | 0.4079 | + | Mmp3 | protein_coding | 9.45e-09 | 3.45e-05 | 29.7200 | 4.89336 | 1.70e+01 | 5.00e+00 | 0.00e+00 | 4.17e+00 | 2.58e+00 | 0.00e+00 | 1.11e-02 | 3.26e-03 | 0.00e+00 | 2.92e+02 | 2.43e+02 | 2.05e+02 | 8.19e+00 | 7.93e+00 | 7.69e+00 | 1.90e-01 | 1.59e-01 | 1.34e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 92285417 | 92291405 | ENSMUSG00000074445 | 0.4002 | + | Sprr2a3 | protein_coding | 1.76e-08 | 5.50e-05 | 59.6667 | 5.89885 | 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 | 1.00e+00 | 0.00e+00 | 1.75e+02 | 1.00e+00 | 0.00e+00 | 7.46e+00 | 2.62e-04 | 0.00e+00 | 4.59e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 69964779 | 69967885 | ENSMUSG00000018569 | 0.5848 | + | Cldn7 | protein_coding | 4.45e-08 | 1.22e-04 | 45.0000 | 5.49185 | 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 | 1.32e+02 | 0.00e+00 | 0.00e+00 | 7.06e+00 | 0.00e+00 | 0.00e+00 | 4.84e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 90030348 | 90036508 | ENSMUSG00000069763 | 0.4507 | + | Tmem100 | protein_coding | 1.43e-07 | 3.47e-04 | 0.0316 | -4.98489 | 3.00e+01 | 2.60e+01 | 3.60e+01 | 4.95e+00 | 4.75e+00 | 5.21e+00 | 1.50e-02 | 1.30e-02 | 1.80e-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 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr14 | 31208312 | 31211729 | ENSMUSG00000091898 | 0.5278 | + | Tnnc1 | protein_coding | 6.74e-07 | 1.48e-03 | 0.0122 | -6.35168 | 1.00e+01 | 2.09e+02 | 2.30e+01 | 3.46e+00 | 7.71e+00 | 4.58e+00 | 2.61e-03 | 5.46e-02 | 6.01e-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 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 34153072 | 34160230 | ENSMUSG00000079547 | 0.4883 | + | H2-DMb1 | protein_coding | 1.26e-06 | 2.52e-03 | 32.7143 | 5.03185 | 2.00e+00 | 1.00e+00 | 1.00e+00 | 1.58e+00 | 1.00e+00 | 1.00e+00 | 7.18e-04 | 3.59e-04 | 3.59e-04 | 8.90e+01 | 9.00e+01 | 4.70e+01 | 6.49e+00 | 6.51e+00 | 5.58e+00 | 3.19e-02 | 3.23e-02 | 1.69e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 34305867 | 34316674 | ENSMUSG00000060586 | 0.4833 | + | H2-Eb1 | protein_coding | 2.06e-06 | 3.77e-03 | 16.2727 | 4.02438 | 3.40e+01 | 5.20e+01 | 3.20e+01 | 5.13e+00 | 5.73e+00 | 5.04e+00 | 4.39e-03 | 6.72e-03 | 4.13e-03 | 8.31e+02 | 1.04e+03 | 9.90e+01 | 9.70e+00 | 1.00e+01 | 6.64e+00 | 1.07e-01 | 1.34e-01 | 1.28e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 109575128 | 109579172 | ENSMUSG00000031722 | 0.5125 | - | Hp | protein_coding | 2.83e-06 | 4.77e-03 | 15.0698 | 3.91359 | 4.00e+00 | 3.00e+01 | 6.00e+00 | 2.32e+00 | 4.95e+00 | 2.81e+00 | 1.41e-03 | 1.06e-02 | 2.12e-03 | 2.10e+02 | 2.49e+02 | 1.86e+02 | 7.72e+00 | 7.97e+00 | 7.55e+00 | 7.42e-02 | 8.80e-02 | 6.57e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 127538161 | 127621148 | ENSMUSG00000040249 | 0.5340 | - | Lrp1 | protein_coding | 9.91e-06 | 1.55e-02 | 0.0632 | -3.98489 | 1.10e+02 | 4.80e+01 | 2.90e+01 | 6.79e+00 | 5.61e+00 | 4.91e+00 | 6.10e-03 | 2.66e-03 | 1.61e-03 | 1.00e+00 | 5.00e+00 | 3.00e+00 | 1.00e+00 | 2.58e+00 | 2.00e+00 | 5.55e-05 | 2.77e-04 | 1.66e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 129364570 | 129371139 | ENSMUSG00000027398 | 0.4534 | - | Il1b | protein_coding | 1.10e-05 | 1.60e-02 | 33.0000 | 5.04439 | 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 | 4.10e+01 | 3.60e+01 | 1.90e+01 | 5.39e+00 | 5.21e+00 | 4.32e+00 | 1.35e-02 | 1.18e-02 | 6.23e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 30787896 | 30791097 | ENSMUSG00000074199 | 0.5081 | + | Krtdap | protein_coding | 1.17e-05 | 1.61e-02 | 0.0714 | -3.80735 | 9.00e+00 | 3.00e+01 | 0.00e+00 | 3.32e+00 | 4.95e+00 | 0.00e+00 | 3.42e-03 | 1.14e-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 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 57203970 | 57228136 | ENSMUSG00000024164 | 0.5201 | - | C3 | protein_coding | 1.34e-05 | 1.73e-02 | 14.9892 | 3.90586 | 5.10e+01 | 1.90e+01 | 2.00e+01 | 5.70e+00 | 4.32e+00 | 4.39e+00 | 1.35e-02 | 5.02e-03 | 5.28e-03 | 7.30e+02 | 5.32e+02 | 1.29e+02 | 9.51e+00 | 9.06e+00 | 7.02e+00 | 1.93e-01 | 1.40e-01 | 3.41e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 43662346 | 43740972 | ENSMUSG00000039765 | 0.4323 | + | Cc2d2a | protein_coding | 1.70e-05 | 2.07e-02 | 0.0423 | -4.56478 | 6.00e+01 | 8.00e+00 | 0.00e+00 | 5.93e+00 | 3.17e+00 | 0.00e+00 | 1.17e-02 | 1.57e-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 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 42772860 | 42773993 | ENSMUSG00000094686 | 0.5670 | - | Ccl21a | protein_coding | 1.91e-05 | 2.20e-02 | 11.8106 | 3.56201 | 1.75e+02 | 2.08e+02 | 1.42e+02 | 7.46e+00 | 7.71e+00 | 7.16e+00 | 1.07e-01 | 1.27e-01 | 8.65e-02 | 3.15e+03 | 2.77e+03 | 3.16e+02 | 1.16e+01 | 1.14e+01 | 8.31e+00 | 1.92e+00 | 1.69e+00 | 1.93e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr16 | 17797282 | 17808293 | ENSMUSG00000012017 | 0.5805 | + | Scarf2 | protein_coding | 2.18e-05 | 2.39e-02 | 0.0755 | -3.72792 | 2.90e+01 | 8.00e+00 | 1.30e+01 | 4.91e+00 | 3.17e+00 | 3.81e+00 | 9.64e-03 | 2.66e-03 | 4.32e-03 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 3.32e-04 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 173331886 | 173333750 | ENSMUSG00000037872 | 0.5003 | - | Ackr1 | protein_coding | 2.30e-05 | 2.40e-02 | 10.5585 | 3.40033 | 1.54e+02 | 1.65e+02 | 9.70e+01 | 7.28e+00 | 7.38e+00 | 6.61e+00 | 9.70e-02 | 1.04e-01 | 6.11e-02 | 1.72e+03 | 1.60e+03 | 1.11e+03 | 1.07e+01 | 1.06e+01 | 1.01e+01 | 1.08e+00 | 1.00e+00 | 6.97e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 95526786 | 95556403 | ENSMUSG00000038642 | 0.4437 | + | Ctss | protein_coding | 2.45e-05 | 2.44e-02 | 15.4400 | 3.94860 | 7.00e+00 | 1.10e+01 | 4.00e+00 | 3.00e+00 | 3.58e+00 | 2.32e+00 | 4.77e-03 | 7.50e-03 | 2.73e-03 | 1.68e+02 | 2.08e+02 | 7.00e+00 | 7.40e+00 | 7.71e+00 | 3.00e+00 | 1.15e-01 | 1.42e-01 | 4.77e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 116109949 | 116129688 | ENSMUSG00000027962 | 0.3991 | - | Vcam1 | protein_coding | 2.77e-05 | 2.64e-02 | 11.4545 | 3.51785 | 3.00e+01 | 2.30e+01 | 3.20e+01 | 4.95e+00 | 4.58e+00 | 5.04e+00 | 4.10e-03 | 3.14e-03 | 4.37e-03 | 4.82e+02 | 3.33e+02 | 1.90e+02 | 8.92e+00 | 8.38e+00 | 7.58e+00 | 6.58e-02 | 4.55e-02 | 2.59e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 58379043 | 58390728 | ENSMUSG00000013643 | 0.4701 | + | Lypd8 | protein_coding | 2.89e-05 | 2.64e-02 | 23.3333 | 4.54432 | 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 | 6.70e+01 | 0.00e+00 | 0.00e+00 | 6.09e+00 | 0.00e+00 | 0.00e+00 | 4.20e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 75636706 | 75644008 | ENSMUSG00000006342 | 0.5626 | - | Susd2 | protein_coding | 3.08e-05 | 2.70e-02 | 25.5000 | 4.67243 | 1.00e+00 | 6.00e+00 | 0.00e+00 | 1.00e+00 | 2.81e+00 | 0.00e+00 | 5.30e-04 | 3.18e-03 | 0.00e+00 | 1.31e+02 | 7.60e+01 | 4.50e+01 | 7.04e+00 | 6.27e+00 | 5.52e+00 | 6.94e-02 | 4.03e-02 | 2.38e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 20870166 | 20874735 | ENSMUSG00000001131 | 0.4696 | + | Timp1 | protein_coding | 3.55e-05 | 2.99e-02 | 11.8929 | 3.57202 | 1.00e+01 | 5.00e+00 | 1.00e+01 | 3.46e+00 | 2.58e+00 | 3.46e+00 | 7.40e-03 | 3.70e-03 | 7.40e-03 | 1.84e+02 | 1.08e+02 | 3.80e+01 | 7.53e+00 | 6.77e+00 | 5.29e+00 | 1.36e-01 | 7.99e-02 | 2.81e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 4133531 | 4138819 | ENSMUSG00000045573 | 0.4386 | - | Penk | protein_coding | 3.89e-05 | 3.16e-02 | 0.0989 | -3.33813 | 6.49e+02 | 3.15e+02 | 2.87e+02 | 9.34e+00 | 8.30e+00 | 8.17e+00 | 2.31e-01 | 1.12e-01 | 1.02e-01 | 7.80e+01 | 9.00e+00 | 3.40e+01 | 6.30e+00 | 3.32e+00 | 5.13e+00 | 2.78e-02 | 3.21e-03 | 1.21e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 19535454 | 19538583 | ENSMUSG00000083218 | 0.5367 | + | Gm16425 | processed_pseudogene | 4.25e-05 | 3.33e-02 | 103.3333 | 6.69116 | 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 | 1.00e+00 | 0.00e+00 | 3.06e+02 | 1.00e+00 | 0.00e+00 | 8.26e+00 | 8.01e-04 | 0.00e+00 | 2.45e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr16 | 38396117 | 38433145 | ENSMUSG00000002847 | 0.4528 | - | Pla1a | protein_coding | 4.80e-05 | 3.63e-02 | 0.0491 | -4.34873 | 1.80e+01 | 6.80e+01 | 7.40e+01 | 4.25e+00 | 6.11e+00 | 6.23e+00 | 6.36e-03 | 2.40e-02 | 2.61e-02 | 0.00e+00 | 0.00e+00 | 5.00e+00 | 0.00e+00 | 0.00e+00 | 2.58e+00 | 0.00e+00 | 0.00e+00 | 1.77e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 34354119 | 34368463 | ENSMUSG00000029762 | 0.4523 | + | Akr1b8 | protein_coding | 5.17e-05 | 3.68e-02 | 28.0000 | 4.80735 | 3.00e+00 | 0.00e+00 | 0.00e+00 | 2.00e+00 | 0.00e+00 | 0.00e+00 | 1.07e-03 | 0.00e+00 | 0.00e+00 | 5.70e+01 | 3.50e+01 | 7.30e+01 | 5.86e+00 | 5.17e+00 | 6.21e+00 | 2.04e-02 | 1.25e-02 | 2.62e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 87635979 | 87651129 | ENSMUSG00000045394 | 0.4631 | + | Epcam | protein_coding | 5.21e-05 | 3.68e-02 | 16.3333 | 4.02975 | 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 | 1.30e+01 | 3.30e+01 | 0.00e+00 | 3.81e+00 | 5.09e+00 | 0.00e+00 | 2.30e-03 | 5.84e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 63241537 | 63386030 | ENSMUSG00000027820 | 0.3846 | + | Mme | protein_coding | 6.28e-05 | 4.18e-02 | 18.5000 | 4.20945 | 4.00e+00 | 1.00e+00 | 0.00e+00 | 2.32e+00 | 1.00e+00 | 0.00e+00 | 4.08e-04 | 1.02e-04 | 0.00e+00 | 8.50e+01 | 2.30e+01 | 3.70e+01 | 6.43e+00 | 4.58e+00 | 5.25e+00 | 8.66e-03 | 2.34e-03 | 3.77e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 103510586 | 103750211 | ENSMUSG00000030077 | 0.3788 | + | Chl1 | protein_coding | 6.62e-05 | 4.18e-02 | 21.0000 | 4.39232 | 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 | 5.80e+01 | 2.00e+00 | 0.00e+00 | 5.88e+00 | 1.58e+00 | 0.00e+00 | 6.28e-03 | 2.17e-04 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 20888175 | 20892178 | ENSMUSG00000004100 | 0.5597 | + | Ppan | protein_coding | 6.83e-05 | 4.18e-02 | 0.0429 | -4.54432 | 1.00e+01 | 2.80e+01 | 2.90e+01 | 3.46e+00 | 4.86e+00 | 4.91e+00 | 1.36e-03 | 3.81e-03 | 3.94e-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 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 88835231 | 88910103 | ENSMUSG00000054199 | 0.4384 | + | Gon4l | protein_coding | 6.86e-05 | 4.18e-02 | 0.0280 | -5.15650 | 5.50e+01 | 1.60e+01 | 3.30e+01 | 5.81e+00 | 4.09e+00 | 5.09e+00 | 1.23e-02 | 3.59e-03 | 7.40e-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 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 117849251 | 117855743 | ENSMUSG00000017716 | 0.4694 | + | Birc5 | protein_coding | 6.87e-05 | 4.18e-02 | 18.2857 | 4.19265 | 4.00e+00 | 0.00e+00 | 0.00e+00 | 2.32e+00 | 0.00e+00 | 0.00e+00 | 9.56e-04 | 0.00e+00 | 0.00e+00 | 6.10e+01 | 3.30e+01 | 3.10e+01 | 5.95e+00 | 5.09e+00 | 5.00e+00 | 1.46e-02 | 7.89e-03 | 7.41e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for Wt_endo_vs_DAREdd_endo.Download the whole result list for Wt_endo_vs_DAREdd_endo.DEG table for the contrast Wt_fibro_vs_DAREdd_fibroThe following table presents the top 5% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Wt_fibro_vs_DAREdd_fibro. 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 | natural_normalized_fold_change_Wt_fibro_vs_DAREdd_fibro | log2_normalized_fold_change_Wt_fibro_vs_DAREdd_fibro | natural_normalized_counts_wt1-fibro | natural_normalized_counts_wt2-fibro | natural_normalized_counts_wt3-fibro | log2_normalized_counts_wt1-fibro | log2_normalized_counts_wt2-fibro | log2_normalized_counts_wt3-fibro | rpgm_normalized_counts_wt1-fibro | rpgm_normalized_counts_wt2-fibro | rpgm_normalized_counts_wt3-fibro | natural_normalized_counts_DAREdd1-fibro | natural_normalized_counts_DAREdd2-fibro | natural_normalized_counts_DAREdd3_fibro | log2_normalized_counts_DAREdd1-fibro | log2_normalized_counts_DAREdd2-fibro | log2_normalized_counts_DAREdd3_fibro | rpgm_normalized_counts_DAREdd1-fibro | rpgm_normalized_counts_DAREdd2-fibro | rpgm_normalized_counts_DAREdd3_fibro | LN | AR | MD | MN | QN | KN | CM | BT |
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| chr11 | 83525778 | 83530518 | ENSMUSG00000035042 | 0.4664 | - | Ccl5 | protein_coding | 7.24e-15 | 1.21e-10 | 160.3125 | 7.32474 | 3.00e+00 | 2.00e+00 | 8.00e+00 | 2.00e+00 | 1.58e+00 | 3.17e+00 | 1.11e-03 | 7.42e-04 | 2.97e-03 | 7.81e+02 | 7.08e+02 | 1.07e+03 | 9.61e+00 | 9.47e+00 | 1.01e+01 | 2.90e-01 | 2.63e-01 | 3.98e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 46711998 | 46715700 | ENSMUSG00000040026 | 0.4807 | - | Saa3 | protein_coding | 1.11e-14 | 1.21e-10 | 170.5593 | 7.41413 | 1.30e+01 | 3.10e+01 | 1.20e+01 | 3.81e+00 | 5.00e+00 | 3.70e+00 | 2.84e-03 | 6.77e-03 | 2.62e-03 | 1.73e+03 | 4.20e+03 | 4.14e+03 | 1.08e+01 | 1.20e+01 | 1.20e+01 | 3.77e-01 | 9.16e-01 | 9.03e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 129875979 | 129876947 | ENSMUSG00000106840 | 0.4303 | - | Gm42790 | TEC | 4.02e-12 | 2.93e-08 | 60.8265 | 5.92663 | 1.70e+01 | 2.50e+01 | 5.30e+01 | 4.17e+00 | 4.70e+00 | 5.75e+00 | 1.36e-02 | 2.00e-02 | 4.25e-02 | 1.02e+03 | 3.20e+01 | 4.91e+03 | 9.99e+00 | 5.04e+00 | 1.23e+01 | 8.15e-01 | 2.56e-02 | 3.93e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 101264378 | 101268255 | ENSMUSG00000031304 | 0.4814 | - | Il2rg | protein_coding | 4.77e-11 | 2.62e-07 | 112.0000 | 6.80735 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.84e-04 | 0.00e+00 | 2.33e+02 | 1.20e+02 | 9.20e+01 | 7.87e+00 | 6.92e+00 | 6.54e+00 | 4.28e-02 | 2.21e-02 | 1.69e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 78920787 | 78960254 | ENSMUSG00000020826 | 0.5008 | + | Nos2 | protein_coding | 1.46e-10 | 6.39e-07 | 111.0000 | 6.79442 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 3.34e-04 | 0.00e+00 | 2.36e+02 | 1.32e+02 | 7.30e+01 | 7.89e+00 | 7.06e+00 | 6.21e+00 | 7.87e-02 | 4.40e-02 | 2.43e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 90759360 | 90761624 | ENSMUSG00000029371 | 0.4190 | + | Cxcl5 | protein_coding | 1.64e-09 | 5.99e-06 | 78.2000 | 6.28910 | 0.00e+00 | 7.00e+00 | 0.00e+00 | 0.00e+00 | 3.00e+00 | 0.00e+00 | 0.00e+00 | 2.97e-03 | 0.00e+00 | 4.43e+02 | 2.25e+02 | 1.11e+02 | 8.79e+00 | 7.82e+00 | 6.81e+00 | 1.88e-01 | 9.54e-02 | 4.71e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 128933818 | 128958282 | ENSMUSG00000025348 | 0.4999 | + | Itga7 | protein_coding | 1.10e-08 | 3.46e-05 | 27.4414 | 4.77828 | 4.70e+01 | 3.00e+01 | 3.10e+01 | 5.58e+00 | 4.95e+00 | 5.00e+00 | 1.08e-02 | 6.90e-03 | 7.13e-03 | 1.40e+01 | 2.72e+02 | 2.76e+03 | 3.91e+00 | 8.09e+00 | 1.14e+01 | 3.22e-03 | 6.26e-02 | 6.35e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 109575128 | 109579172 | ENSMUSG00000031722 | 0.5125 | - | Hp | protein_coding | 2.37e-08 | 6.50e-05 | 25.1027 | 4.64977 | 1.38e+02 | 6.90e+01 | 8.20e+01 | 7.12e+00 | 6.13e+00 | 6.38e+00 | 4.87e-02 | 2.44e-02 | 2.90e-02 | 2.19e+03 | 2.68e+03 | 2.46e+03 | 1.11e+01 | 1.14e+01 | 1.13e+01 | 7.74e-01 | 9.45e-01 | 8.69e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 7445822 | 7455975 | ENSMUSG00000043613 | 0.4079 | + | Mmp3 | protein_coding | 3.75e-07 | 9.14e-04 | 17.4131 | 4.12210 | 2.17e+02 | 1.14e+02 | 1.38e+02 | 7.77e+00 | 6.85e+00 | 7.12e+00 | 1.42e-01 | 7.44e-02 | 9.00e-02 | 2.05e+03 | 3.17e+03 | 2.99e+03 | 1.10e+01 | 1.16e+01 | 1.15e+01 | 1.34e+00 | 2.07e+00 | 1.95e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 25024929 | 25038962 | ENSMUSG00000037406 | 0.4708 | - | Htra4 | protein_coding | 5.81e-07 | 1.27e-03 | 0.0700 | -3.83656 | 1.01e+03 | 2.82e+03 | 3.55e+03 | 9.99e+00 | 1.15e+01 | 1.18e+01 | 3.23e-01 | 8.98e-01 | 1.13e+00 | 8.10e+01 | 3.17e+02 | 1.16e+02 | 6.36e+00 | 8.31e+00 | 6.87e+00 | 2.58e-02 | 1.01e-01 | 3.70e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 24594087 | 24595423 | ENSMUSG00000099997 | 0.5393 | - | Tubb4b-ps2 | processed_pseudogene | 8.68e-07 | 1.73e-03 | 15.2222 | 3.92811 | 1.00e+01 | 2.00e+01 | 1.20e+01 | 3.46e+00 | 4.39e+00 | 3.70e+00 | 8.01e-03 | 1.60e-02 | 9.62e-03 | 2.67e+02 | 2.22e+02 | 1.93e+02 | 8.07e+00 | 7.80e+00 | 7.60e+00 | 2.14e-01 | 1.78e-01 | 1.55e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 92215799 | 92221911 | ENSMUSG00000078664 | 0.4044 | + | Sprr2a1 | protein_coding | 1.84e-06 | 3.13e-03 | 18.3333 | 4.19640 | 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 | 5.20e+01 | 0.00e+00 | 0.00e+00 | 5.73e+00 | 0.00e+00 | 0.00e+00 | 1.36e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 43596049 | 43601540 | ENSMUSG00000020405 | 0.4468 | - | Fabp6 | protein_coding | 1.86e-06 | 3.13e-03 | 28.3333 | 4.82443 | 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 | 8.20e+01 | 0.00e+00 | 0.00e+00 | 6.38e+00 | 0.00e+00 | 0.00e+00 | 6.25e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 35439155 | 35443773 | ENSMUSG00000060550 | 0.5373 | + | H2-Q7 | protein_coding | 2.00e-06 | 3.13e-03 | 47.6667 | 5.57491 | 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 | 5.40e+01 | 2.50e+01 | 6.10e+01 | 5.78e+00 | 4.70e+00 | 5.95e+00 | 1.45e-02 | 6.71e-03 | 1.64e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 124918465 | 124939311 | ENSMUSG00000028873 | 0.4711 | - | Cdca8 | protein_coding | 3.19e-06 | 4.54e-03 | 68.6667 | 6.10154 | 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 | 3.60e+01 | 8.20e+01 | 8.50e+01 | 5.21e+00 | 6.38e+00 | 6.43e+00 | 6.09e-03 | 1.39e-02 | 1.44e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 94772009 | 94782427 | ENSMUSG00000031778 | 0.5268 | + | Cx3cl1 | protein_coding | 3.31e-06 | 4.54e-03 | 15.3036 | 3.93580 | 3.30e+01 | 7.00e+00 | 1.30e+01 | 5.09e+00 | 3.00e+00 | 3.81e+00 | 3.40e-03 | 7.20e-04 | 1.34e-03 | 3.71e+02 | 3.16e+02 | 1.67e+02 | 8.54e+00 | 8.31e+00 | 7.39e+00 | 3.82e-02 | 3.25e-02 | 1.72e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 34305867 | 34316674 | ENSMUSG00000060586 | 0.4833 | + | H2-Eb1 | protein_coding | 8.18e-06 | 1.05e-02 | 15.5862 | 3.96220 | 6.00e+00 | 3.50e+01 | 4.30e+01 | 2.81e+00 | 5.17e+00 | 5.46e+00 | 7.75e-04 | 4.52e-03 | 5.55e-03 | 2.46e+02 | 9.98e+02 | 1.09e+02 | 7.95e+00 | 9.96e+00 | 6.78e+00 | 3.18e-02 | 1.29e-01 | 1.41e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 172581758 | 172590568 | ENSMUSG00000053318 | 0.4926 | - | Slamf8 | protein_coding | 9.55e-06 | 1.16e-02 | 55.2500 | 5.78790 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 3.14e-04 | 0.00e+00 | 6.00e+01 | 5.50e+01 | 1.03e+02 | 5.93e+00 | 5.81e+00 | 6.70e+00 | 1.89e-02 | 1.73e-02 | 3.24e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for Wt_fibro_vs_DAREdd_fibro.Download the whole result list for Wt_fibro_vs_DAREdd_fibro.Download the raw read counts table for the experiment.Download the normalized read counts table for the experiment.
References
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