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Summary
Analysis summary
Summary:
The raw bam files, one for each RNA-Seq sample, were summarized to a gene read counts table, using the Bioconductor package GenomicRanges. In the final read counts table, each row represented one gene, each column one RNA-Seq sample and each cell, the corresponding read counts associated with each row and column.The gene counts table was normalized for inherent systematic or experimental biases (e.g. sequencing depth, gene length, GC content bias etc.) using the Bioconductor package edgeR after removing genes that had zero counts over all the RNA-Seq samples (3152 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 (163 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 0.22243 average reads per 100 bp), iii) genes with read counts below the median read counts of the total normalized count distribution (8555 genes with cutoff value 559 normalized read counts). The total number of genes excluded due to the application of gene filters was 4209. The total (unified) number of genes excluded due to the application of all filters was 11774. The resulting gene counts table was subjected to differential expression analysis for the contrasts WT versus HET using the Bioconductor package edgeR. The final numbers of differentially expressed genes were (per contrast): for the contrast WT versus HET, 1422 (550) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 2 (2) were up-regulated, 120 (119) were down-regulated and 1300 (429) 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, HET
Samples included: GZS17, GZS35, GZS34, GZS36
Samples excluded:
none
Requested contrasts: WT_vs_HET
Library sizes:
- GZS17: 60068354
- GZS35: 21658853
- GZS34: 15924035
- GZS36: 23391137
Annotation: download
Organism: mouse ( Mus musculus), genome version alias mm9
Annotation source: RefSeq database
Count type: gene
Exon filters:
min.active.exons - min.active.exons
- exons.per.gene: 5
- min.exons: 2
- frac: 0.2
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
- lincRNA: FALSE
- snoRNA: FALSE
- processed_transcript: FALSE
- misc_RNA: FALSE
- rRNA: TRUE
- sense_overlapping: FALSE
- sense_intronic: FALSE
- polymorphic_pseudogene: FALSE
- non_coding: FALSE
- three_prime_overlapping_ncrna: FALSE
- IG_C_gene: FALSE
- IG_J_gene: FALSE
- IG_D_gene: FALSE
- IG_V_gene: FALSE
- ncrna_host: FALSE
Filter application: after normalization
Normalization algorithm: edgeR
Normalization arguments:
method, refColumn, logratioTrim, sumTrim, doWeighting, Acutoff, p - method: TMM
- logratioTrim: 0.3
- sumTrim: 0.05
- doWeighting: TRUE
- Acutoff: -1e+10
- p: 0.75
Statistical algorithm(s): edgeR
Statistical arguments for edgeR: main.method, rowsum.filter, prior.df, trend, span, tag.method, grid.length, grid.range, offset, glm.method, subset, AveLogCPM, trend.method, dispersion, offset, weights, lib.size, prior.count, start, method, test, abundance.trend, robust, winsor.tail.p - main.method: classic
- rowsum.filter: 5
- prior.df: 10
- trend: movingave
- tag.method: grid
- grid.length: 11
- grid.range: -6, 6
- glm.method: CoxReid
- subset: 10000
- trend.method: auto
- prior.count: 0.125
- method: auto
- test: chisq
- abundance.trend: TRUE
- robust: FALSE
- winsor.tail.p: 0.05, 0.1
Meta-analysis method: no meta-analysis, reported p-values from the first supplied statistical algorithm
Multiple testing correction: Benjamini-Hochberg FDR
p-value threshold: 0.05
Logarithmic tranformation offset: 1
Analysis preset: not available
Quality control plots: multidimensional scaling, biotype detection, biotype counts, sample and biotype saturation, correlation heatmap and correlogram, pairwise scatterplots between samples, boxplots, volcano plot, DEG biotype detection, DEG heatmap
Figure format: png, pdf
Output directory: /data/images/proton/Cereghini/e17.5/metaseqr_e17.5
Output data: Annotation, p-value, Adjusted p-value (FDR), Fold change, Statistics, Read counts
Output scale(s): log2 scale
Output values: Normalized values
Output statistics: Mean, Median, Standard deviation, Median Absolute Deviation (MAD), Coefficient of Variation, Robust Coefficient of Variation
Total run time: 05 minutes 39 seconds
Filtered genes
Number of filtered genes: 11774 which is the union of
- Filtered because of zero reads: 3152
-
Filtered because of exon filters: 0
-
Filtered because of gene filters: 8622
which is the union of
- length: 163 genes with filter cutoff value 500
- avg.reads: 4044 genes with filter cutoff value 0.2224328
- expression: 8555 genes further decomposed to (filter name, filtered genes, filter cutoff):
- median: 8555 genes with filter cutoff value 559
- biotype: 1 genes with filter cutoff value rRNA
Differentially expressed genes
Number of differentially expressed genes per contrast:
- WT_vs_HET: 1422 (550) statistically significant genes of which 2 (2) up regulated, 120 (119) down regulated and 1300 (429) 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[ 2017-07-19 14:28:20 ] INFO 2017-07-19 14:28:20: Data processing started... [ 2017-07-19 14:28:20 ] INFO Read counts file: imported sam/bam/bed files [ 2017-07-19 14:28:20 ] INFO Conditions: WT, HET [ 2017-07-19 14:28:20 ] INFO Samples to include: GZS17, GZS35, GZS34, GZS36 [ 2017-07-19 14:28:20 ] INFO Samples to exclude: none [ 2017-07-19 14:28:20 ] INFO Requested contrasts: WT_vs_HET [ 2017-07-19 14:28:20 ] INFO Annotation: download [ 2017-07-19 14:28:20 ] INFO Organism: mm9 [ 2017-07-19 14:28:20 ] INFO Reference source: refseq [ 2017-07-19 14:28:20 ] INFO Count type: gene [ 2017-07-19 14:28:20 ] INFO Exon filters: min.active.exons [ 2017-07-19 14:28:20 ] INFO min.active.exons: [ 2017-07-19 14:28:20 ] INFO exons.per.gene: 5 [ 2017-07-19 14:28:20 ] INFO min.exons: 2 [ 2017-07-19 14:28:20 ] INFO frac: 0.2 [ 2017-07-19 14:28:20 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-07-19 14:28:20 ] INFO length: [ 2017-07-19 14:28:20 ] INFO length: 500 [ 2017-07-19 14:28:20 ] INFO avg.reads: [ 2017-07-19 14:28:20 ] INFO average.per.bp: 100 [ 2017-07-19 14:28:20 ] INFO quantile: 0.25 [ 2017-07-19 14:28:20 ] INFO expression: [ 2017-07-19 14:28:20 ] INFO median: TRUE [ 2017-07-19 14:28:20 ] INFO mean: FALSE [ 2017-07-19 14:28:20 ] INFO quantile: NA [ 2017-07-19 14:28:20 ] INFO known: NA [ 2017-07-19 14:28:20 ] INFO custom: NA [ 2017-07-19 14:28:20 ] INFO biotype: [ 2017-07-19 14:28:20 ] INFO pseudogene: FALSE [ 2017-07-19 14:28:20 ] INFO snRNA: FALSE [ 2017-07-19 14:28:20 ] INFO protein_coding: FALSE [ 2017-07-19 14:28:20 ] INFO antisense: FALSE [ 2017-07-19 14:28:20 ] INFO miRNA: FALSE [ 2017-07-19 14:28:20 ] INFO lincRNA: FALSE [ 2017-07-19 14:28:20 ] INFO snoRNA: FALSE [ 2017-07-19 14:28:20 ] INFO processed_transcript: FALSE [ 2017-07-19 14:28:20 ] INFO misc_RNA: FALSE [ 2017-07-19 14:28:20 ] INFO rRNA: TRUE [ 2017-07-19 14:28:20 ] INFO sense_overlapping: FALSE [ 2017-07-19 14:28:20 ] INFO sense_intronic: FALSE [ 2017-07-19 14:28:20 ] INFO polymorphic_pseudogene: FALSE [ 2017-07-19 14:28:20 ] INFO non_coding: FALSE [ 2017-07-19 14:28:20 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-07-19 14:28:20 ] INFO IG_C_gene: FALSE [ 2017-07-19 14:28:20 ] INFO IG_J_gene: FALSE [ 2017-07-19 14:28:20 ] INFO IG_D_gene: FALSE [ 2017-07-19 14:28:20 ] INFO IG_V_gene: FALSE [ 2017-07-19 14:28:20 ] INFO ncrna_host: FALSE [ 2017-07-19 14:28:20 ] INFO Filter application: postnorm [ 2017-07-19 14:28:20 ] INFO Normalization algorithm: edger [ 2017-07-19 14:28:20 ] INFO Normalization arguments: [ 2017-07-19 14:28:20 ] INFO method: TMM [ 2017-07-19 14:28:20 ] INFO logratioTrim: 0.3 [ 2017-07-19 14:28:20 ] INFO sumTrim: 0.05 [ 2017-07-19 14:28:20 ] INFO doWeighting: TRUE [ 2017-07-19 14:28:20 ] INFO Acutoff: -1e+10 [ 2017-07-19 14:28:20 ] INFO p: 0.75 [ 2017-07-19 14:28:20 ] INFO Statistical algorithm: edger [ 2017-07-19 14:28:20 ] INFO Statistical arguments: [ 2017-07-19 14:28:20 ] INFO edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1) [ 2017-07-19 14:28:20 ] INFO Meta-analysis method: none [ 2017-07-19 14:28:20 ] INFO Multiple testing correction: BH [ 2017-07-19 14:28:20 ] INFO p-value threshold: 0.05 [ 2017-07-19 14:28:20 ] INFO Logarithmic transformation offset: 1 [ 2017-07-19 14:28:20 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, correl, pairwise, boxplot, volcano, biodist, deheatmap [ 2017-07-19 14:28:20 ] INFO Figure format: png, pdf [ 2017-07-19 14:28:20 ] INFO Output directory: /data/images/proton/Cereghini/e17.5/metaseqr_e17.5 [ 2017-07-19 14:28:20 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, stats, counts [ 2017-07-19 14:28:20 ] INFO Output scale(s): log2 [ 2017-07-19 14:28:20 ] INFO Output values: normalized [ 2017-07-19 14:28:20 ] INFO Output statistics: mean, median, sd, mad, cv, rcv [ 2017-07-19 14:28:20 ] INFO Downloading gene annotation for mm9... [ 2017-07-19 14:28:42 ] INFO Converting annotation to GenomicRanges object... [ 2017-07-19 14:28:42 ] INFO Getting DNA sequences... [ 2017-07-19 14:41:49 ] INFO 2017-07-19 14:41:49: Data processing started... [ 2017-07-19 14:41:49 ] INFO Read counts file: imported sam/bam/bed files [ 2017-07-19 14:41:49 ] INFO Conditions: WT, HET [ 2017-07-19 14:41:49 ] INFO Samples to include: GZS17, GZS35, GZS34, GZS36 [ 2017-07-19 14:41:49 ] INFO Samples to exclude: none [ 2017-07-19 14:41:49 ] INFO Requested contrasts: WT_vs_HET [ 2017-07-19 14:41:49 ] INFO Annotation: download [ 2017-07-19 14:41:49 ] INFO Organism: mm9 [ 2017-07-19 14:41:49 ] INFO Reference source: refseq [ 2017-07-19 14:41:49 ] INFO Count type: gene [ 2017-07-19 14:41:49 ] INFO Exon filters: min.active.exons [ 2017-07-19 14:41:49 ] INFO min.active.exons: [ 2017-07-19 14:41:49 ] INFO exons.per.gene: 5 [ 2017-07-19 14:41:49 ] INFO min.exons: 2 [ 2017-07-19 14:41:49 ] INFO frac: 0.2 [ 2017-07-19 14:41:49 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-07-19 14:41:49 ] INFO length: [ 2017-07-19 14:41:49 ] INFO length: 500 [ 2017-07-19 14:41:49 ] INFO avg.reads: [ 2017-07-19 14:41:49 ] INFO average.per.bp: 100 [ 2017-07-19 14:41:49 ] INFO quantile: 0.25 [ 2017-07-19 14:41:49 ] INFO expression: [ 2017-07-19 14:41:49 ] INFO median: TRUE [ 2017-07-19 14:41:49 ] INFO mean: FALSE [ 2017-07-19 14:41:49 ] INFO quantile: NA [ 2017-07-19 14:41:49 ] INFO known: NA [ 2017-07-19 14:41:49 ] INFO custom: NA [ 2017-07-19 14:41:49 ] INFO biotype: [ 2017-07-19 14:41:49 ] INFO pseudogene: FALSE [ 2017-07-19 14:41:49 ] INFO snRNA: FALSE [ 2017-07-19 14:41:49 ] INFO protein_coding: FALSE [ 2017-07-19 14:41:49 ] INFO antisense: FALSE [ 2017-07-19 14:41:49 ] INFO miRNA: FALSE [ 2017-07-19 14:41:49 ] INFO lincRNA: FALSE [ 2017-07-19 14:41:49 ] INFO snoRNA: FALSE [ 2017-07-19 14:41:49 ] INFO processed_transcript: FALSE [ 2017-07-19 14:41:49 ] INFO misc_RNA: FALSE [ 2017-07-19 14:41:49 ] INFO rRNA: TRUE [ 2017-07-19 14:41:49 ] INFO sense_overlapping: FALSE [ 2017-07-19 14:41:49 ] INFO sense_intronic: FALSE [ 2017-07-19 14:41:49 ] INFO polymorphic_pseudogene: FALSE [ 2017-07-19 14:41:49 ] INFO non_coding: FALSE [ 2017-07-19 14:41:49 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-07-19 14:41:49 ] INFO IG_C_gene: FALSE [ 2017-07-19 14:41:49 ] INFO IG_J_gene: FALSE [ 2017-07-19 14:41:49 ] INFO IG_D_gene: FALSE [ 2017-07-19 14:41:49 ] INFO IG_V_gene: FALSE [ 2017-07-19 14:41:49 ] INFO ncrna_host: FALSE [ 2017-07-19 14:41:49 ] INFO Filter application: postnorm [ 2017-07-19 14:41:49 ] INFO Normalization algorithm: edger [ 2017-07-19 14:41:49 ] INFO Normalization arguments: [ 2017-07-19 14:41:49 ] INFO method: TMM [ 2017-07-19 14:41:49 ] INFO logratioTrim: 0.3 [ 2017-07-19 14:41:49 ] INFO sumTrim: 0.05 [ 2017-07-19 14:41:49 ] INFO doWeighting: TRUE [ 2017-07-19 14:41:49 ] INFO Acutoff: -1e+10 [ 2017-07-19 14:41:49 ] INFO p: 0.75 [ 2017-07-19 14:41:49 ] INFO Statistical algorithm: edger [ 2017-07-19 14:41:49 ] INFO Statistical arguments: [ 2017-07-19 14:41:49 ] INFO edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1) [ 2017-07-19 14:41:49 ] INFO Meta-analysis method: none [ 2017-07-19 14:41:49 ] INFO Multiple testing correction: BH [ 2017-07-19 14:41:49 ] INFO p-value threshold: 0.05 [ 2017-07-19 14:41:49 ] INFO Logarithmic transformation offset: 1 [ 2017-07-19 14:41:49 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, correl, pairwise, boxplot, volcano, biodist, deheatmap [ 2017-07-19 14:41:49 ] INFO Figure format: png, pdf [ 2017-07-19 14:41:49 ] INFO Output directory: /data/images/proton/Cereghini/e17.5/metaseqr_e17.5 [ 2017-07-19 14:41:49 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, stats, counts [ 2017-07-19 14:41:49 ] INFO Output scale(s): log2 [ 2017-07-19 14:41:49 ] INFO Output values: normalized [ 2017-07-19 14:41:49 ] INFO Output statistics: mean, median, sd, mad, cv, rcv [ 2017-07-19 14:41:49 ] INFO Downloading gene annotation for mm9... [ 2017-07-19 14:41:49 ] WARN R package RMySQL is not present! Annotation will be retrieved by downloading temporary files from UCSC and the usage of a temporary SQLite database... [ 2017-07-19 14:41:49 ] INFO Retrieving tables for temporary SQLite refseq mm9 gene subset database [ 2017-07-19 14:41:49 ] INFO Retrieving table refFlat [ 2017-07-19 14:41:58 ] INFO Retrieving table knownToRefSeq [ 2017-07-19 14:42:01 ] INFO Retrieving table knownCanonical [ 2017-07-19 14:42:04 ] INFO Retrieving table knownToEnsembl [ 2017-07-19 14:42:08 ] INFO Retrieving table ensemblSource [ 2017-07-19 14:42:13 ] INFO Converting annotation to GenomicRanges object... [ 2017-07-19 14:42:17 ] INFO Getting DNA sequences... [ 2017-07-19 14:42:31 ] INFO Getting GC content... [ 2017-07-19 14:42:33 ] INFO Converting annotation to GenomicRanges object... [ 2017-07-19 14:42:33 ] INFO Reading bam file accepted_hits.bam for sample with name GZS17. This might take some time... [ 2017-07-19 14:42:33 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-07-19 14:42:33 ] INFO Reading bam file accepted_hits.bam for sample with name GZS35. This might take some time... [ 2017-07-19 14:42:33 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-07-19 14:42:33 ] INFO Reading bam file accepted_hits.bam for sample with name GZS34. This might take some time... [ 2017-07-19 14:42:33 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-07-19 14:42:33 ] INFO Reading bam file accepted_hits.bam for sample with name GZS36. This might take some time... [ 2017-07-19 14:42:33 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-07-19 14:43:12 ] INFO Counting reads overlapping with given annotation... [ 2017-07-19 14:43:12 ] INFO ...for single-end reads... [ 2017-07-19 14:43:12 ] INFO ...ignoring strandedness... [ 2017-07-19 14:43:23 ] INFO Counting reads overlapping with given annotation... [ 2017-07-19 14:43:23 ] INFO ...for single-end reads... [ 2017-07-19 14:43:23 ] INFO ...ignoring strandedness... [ 2017-07-19 14:43:26 ] INFO Counting reads overlapping with given annotation... [ 2017-07-19 14:43:26 ] INFO ...for single-end reads... [ 2017-07-19 14:43:26 ] INFO ...ignoring strandedness... [ 2017-07-19 14:44:00 ] INFO Counting reads overlapping with given annotation... [ 2017-07-19 14:44:00 ] INFO ...for single-end reads... [ 2017-07-19 14:44:00 ] INFO ...ignoring strandedness... [ 2017-07-19 14:46:52 ] INFO 2017-07-19 14:46:52: Data processing started... [ 2017-07-19 14:46:52 ] INFO Read counts file: imported sam/bam/bed files [ 2017-07-19 14:46:52 ] INFO Conditions: WT, HET [ 2017-07-19 14:46:52 ] INFO Samples to include: GZS17, GZS35, GZS34, GZS36 [ 2017-07-19 14:46:52 ] INFO Samples to exclude: none [ 2017-07-19 14:46:52 ] INFO Requested contrasts: WT_vs_HET [ 2017-07-19 14:46:52 ] INFO Annotation: download [ 2017-07-19 14:46:52 ] INFO Organism: mm9 [ 2017-07-19 14:46:52 ] INFO Reference source: refseq [ 2017-07-19 14:46:52 ] INFO Count type: gene [ 2017-07-19 14:46:52 ] INFO Exon filters: min.active.exons [ 2017-07-19 14:46:52 ] INFO min.active.exons: [ 2017-07-19 14:46:52 ] INFO exons.per.gene: 5 [ 2017-07-19 14:46:52 ] INFO min.exons: 2 [ 2017-07-19 14:46:52 ] INFO frac: 0.2 [ 2017-07-19 14:46:52 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-07-19 14:46:52 ] INFO length: [ 2017-07-19 14:46:52 ] INFO length: 500 [ 2017-07-19 14:46:52 ] INFO avg.reads: [ 2017-07-19 14:46:52 ] INFO average.per.bp: 100 [ 2017-07-19 14:46:52 ] INFO quantile: 0.25 [ 2017-07-19 14:46:52 ] INFO expression: [ 2017-07-19 14:46:52 ] INFO median: TRUE [ 2017-07-19 14:46:52 ] INFO mean: FALSE [ 2017-07-19 14:46:52 ] INFO quantile: NA [ 2017-07-19 14:46:52 ] INFO known: NA [ 2017-07-19 14:46:52 ] INFO custom: NA [ 2017-07-19 14:46:52 ] INFO biotype: [ 2017-07-19 14:46:52 ] INFO pseudogene: FALSE [ 2017-07-19 14:46:52 ] INFO snRNA: FALSE [ 2017-07-19 14:46:52 ] INFO protein_coding: FALSE [ 2017-07-19 14:46:52 ] INFO antisense: FALSE [ 2017-07-19 14:46:52 ] INFO miRNA: FALSE [ 2017-07-19 14:46:52 ] INFO lincRNA: FALSE [ 2017-07-19 14:46:52 ] INFO snoRNA: FALSE [ 2017-07-19 14:46:52 ] INFO processed_transcript: FALSE [ 2017-07-19 14:46:52 ] INFO misc_RNA: FALSE [ 2017-07-19 14:46:52 ] INFO rRNA: TRUE [ 2017-07-19 14:46:52 ] INFO sense_overlapping: FALSE [ 2017-07-19 14:46:52 ] INFO sense_intronic: FALSE [ 2017-07-19 14:46:52 ] INFO polymorphic_pseudogene: FALSE [ 2017-07-19 14:46:52 ] INFO non_coding: FALSE [ 2017-07-19 14:46:52 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-07-19 14:46:52 ] INFO IG_C_gene: FALSE [ 2017-07-19 14:46:52 ] INFO IG_J_gene: FALSE [ 2017-07-19 14:46:52 ] INFO IG_D_gene: FALSE [ 2017-07-19 14:46:52 ] INFO IG_V_gene: FALSE [ 2017-07-19 14:46:52 ] INFO ncrna_host: FALSE [ 2017-07-19 14:46:52 ] INFO Filter application: postnorm [ 2017-07-19 14:46:52 ] INFO Normalization algorithm: edger [ 2017-07-19 14:46:52 ] INFO Normalization arguments: [ 2017-07-19 14:46:52 ] INFO method: TMM [ 2017-07-19 14:46:52 ] INFO logratioTrim: 0.3 [ 2017-07-19 14:46:52 ] INFO sumTrim: 0.05 [ 2017-07-19 14:46:52 ] INFO doWeighting: TRUE [ 2017-07-19 14:46:52 ] INFO Acutoff: -1e+10 [ 2017-07-19 14:46:52 ] INFO p: 0.75 [ 2017-07-19 14:46:52 ] INFO Statistical algorithm: edger [ 2017-07-19 14:46:52 ] INFO Statistical arguments: [ 2017-07-19 14:46:52 ] INFO edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1) [ 2017-07-19 14:46:52 ] INFO Meta-analysis method: none [ 2017-07-19 14:46:52 ] INFO Multiple testing correction: BH [ 2017-07-19 14:46:52 ] INFO p-value threshold: 0.05 [ 2017-07-19 14:46:52 ] INFO Logarithmic transformation offset: 1 [ 2017-07-19 14:46:52 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, correl, pairwise, boxplot, volcano, biodist, deheatmap [ 2017-07-19 14:46:52 ] INFO Figure format: png, pdf [ 2017-07-19 14:46:52 ] INFO Output directory: /data/images/proton/Cereghini/e17.5/metaseqr_e17.5 [ 2017-07-19 14:46:52 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, stats, counts [ 2017-07-19 14:46:52 ] INFO Output scale(s): log2 [ 2017-07-19 14:46:52 ] INFO Output values: normalized [ 2017-07-19 14:46:52 ] INFO Output statistics: mean, median, sd, mad, cv, rcv [ 2017-07-19 14:46:52 ] INFO Downloading gene annotation for mm9... [ 2017-07-19 14:46:52 ] WARN R package RMySQL is not present! Annotation will be retrieved by downloading temporary files from UCSC and the usage of a temporary SQLite database... [ 2017-07-19 14:46:52 ] INFO Retrieving tables for temporary SQLite refseq mm9 gene subset database [ 2017-07-19 14:46:52 ] INFO Retrieving table refFlat [ 2017-07-19 14:46:59 ] INFO Retrieving table knownToRefSeq [ 2017-07-19 14:47:02 ] INFO Retrieving table knownCanonical [ 2017-07-19 14:47:05 ] INFO Retrieving table knownToEnsembl [ 2017-07-19 14:47:09 ] INFO Retrieving table ensemblSource [ 2017-07-19 14:47:15 ] INFO Converting annotation to GenomicRanges object... [ 2017-07-19 14:47:15 ] INFO Getting DNA sequences... [ 2017-07-19 14:47:21 ] INFO Getting GC content... [ 2017-07-19 14:47:22 ] INFO Converting annotation to GenomicRanges object... [ 2017-07-19 14:47:22 ] INFO Reading bam file accepted_hits.bam for sample with name GZS17. This might take some time... [ 2017-07-19 14:47:22 ] INFO Reading bam file accepted_hits.bam for sample with name GZS35. This might take some time... [ 2017-07-19 14:47:22 ] INFO Reading bam file accepted_hits.bam for sample with name GZS34. This might take some time... [ 2017-07-19 14:47:22 ] INFO Reading bam file accepted_hits.bam for sample with name GZS36. This might take some time... [ 2017-07-19 14:47:34 ] INFO Counting reads overlapping with given annotation... [ 2017-07-19 14:47:34 ] INFO ...for single-end reads... [ 2017-07-19 14:47:34 ] INFO ...assuming forward sequenced reads... [ 2017-07-19 14:47:39 ] INFO Counting reads overlapping with given annotation... [ 2017-07-19 14:47:39 ] INFO ...for single-end reads... [ 2017-07-19 14:47:39 ] INFO ...assuming forward sequenced reads... [ 2017-07-19 14:47:40 ] INFO Counting reads overlapping with given annotation... [ 2017-07-19 14:47:40 ] INFO ...for single-end reads... [ 2017-07-19 14:47:40 ] INFO ...assuming forward sequenced reads... [ 2017-07-19 14:48:07 ] INFO Counting reads overlapping with given annotation... [ 2017-07-19 14:48:07 ] INFO ...for single-end reads... [ 2017-07-19 14:48:07 ] INFO ...assuming forward sequenced reads... [ 2017-07-19 14:50:42 ] INFO Exporting raw read counts table to /data/images/proton/Cereghini/e17.5/metaseqr_e17.5/lists/raw_counts_table.txt.gz [ 2017-07-19 14:50:42 ] INFO Saving gene model to /data/images/proton/Cereghini/e17.5/metaseqr_e17.5/data/gene_model.RData [ 2017-07-19 14:50:42 ] INFO Removing genes with zero counts in all samples... [ 2017-07-19 14:50:42 ] INFO Normalizing with: edger [ 2017-07-19 14:50:42 ] INFO Applying gene filter length... [ 2017-07-19 14:50:42 ] INFO Threshold below which ignored: 500 [ 2017-07-19 14:50:42 ] INFO Applying gene filter avg.reads... [ 2017-07-19 14:50:42 ] INFO Threshold below which ignored: 0.00691467293597013 [ 2017-07-19 14:50:42 ] INFO Applying gene filter expression... [ 2017-07-19 14:50:42 ] INFO Threshold below which ignored: 6 [ 2017-07-19 14:50:42 ] INFO Applying gene filter biotype... [ 2017-07-19 14:50:42 ] INFO Biotypes ignored: rRNA [ 2017-07-19 14:50:42 ] INFO 11332 genes filtered out [ 2017-07-19 14:50:42 ] INFO 9707 genes remain after filtering [ 2017-07-19 14:50:42 ] INFO Running statistical tests with: edger [ 2017-07-19 14:50:43 ] INFO Contrast: WT_vs_HET [ 2017-07-19 14:50:44 ] INFO Contrast WT_vs_HET: found 193 genes [ 2017-07-19 14:50:44 ] INFO Exporting and compressing normalized read counts table to /data/images/proton/Cereghini/e17.5/metaseqr_e17.5/lists/normalized_counts_table.txt [ 2017-07-19 14:50:44 ] INFO Building output files... [ 2017-07-19 14:50:44 ] INFO Contrast: WT_vs_HET [ 2017-07-19 14:50:44 ] INFO Adding non-filtered data... [ 2017-07-19 14:50:44 ] INFO binding annotation... [ 2017-07-19 14:50:45 ] INFO binding p-values... [ 2017-07-19 14:50:45 ] INFO binding FDRs... [ 2017-07-19 14:50:45 ] INFO binding log2 normalized fold changes... [ 2017-07-19 14:50:45 ] INFO binding normalized mean counts... [ 2017-07-19 14:50:45 ] INFO binding normalized median counts... [ 2017-07-19 14:50:46 ] INFO binding normalized count sds... [ 2017-07-19 14:50:47 ] INFO binding normalized count MADs... [ 2017-07-19 14:50:48 ] INFO binding normalized count CVs... [ 2017-07-19 14:50:48 ] INFO binding normalized counts RCVs... [ 2017-07-19 14:50:50 ] INFO binding normalized mean counts... [ 2017-07-19 14:50:50 ] INFO binding normalized median counts... [ 2017-07-19 14:50:51 ] INFO binding normalized count sds... [ 2017-07-19 14:50:51 ] INFO binding normalized count MADs... [ 2017-07-19 14:50:52 ] INFO binding normalized count CVs... [ 2017-07-19 14:50:53 ] INFO binding normalized counts RCVs... [ 2017-07-19 14:50:55 ] INFO binding all normalized counts for WT... [ 2017-07-19 14:50:55 ] INFO binding all normalized counts for HET... [ 2017-07-19 14:50:55 ] INFO Writing output... [ 2017-07-19 14:50:55 ] INFO Adding filtered data... [ 2017-07-19 14:50:55 ] INFO binding annotation... [ 2017-07-19 14:50:55 ] INFO binding p-values... [ 2017-07-19 14:50:55 ] INFO binding FDRs... [ 2017-07-19 14:50:55 ] INFO binding log2 normalized fold changes... [ 2017-07-19 14:50:55 ] INFO binding normalized mean counts... [ 2017-07-19 14:50:55 ] INFO binding normalized median counts... [ 2017-07-19 14:50:56 ] INFO binding normalized count sds... [ 2017-07-19 14:50:56 ] INFO binding normalized count MADs... [ 2017-07-19 14:50:58 ] INFO binding normalized count CVs... [ 2017-07-19 14:50:58 ] INFO binding normalized counts RCVs... [ 2017-07-19 14:51:00 ] INFO binding normalized mean counts... [ 2017-07-19 14:51:00 ] INFO binding normalized median counts... [ 2017-07-19 14:51:01 ] INFO binding normalized count sds... [ 2017-07-19 14:51:02 ] INFO binding normalized count MADs... [ 2017-07-19 14:51:03 ] INFO binding normalized count CVs... [ 2017-07-19 14:51:04 ] INFO binding normalized counts RCVs... [ 2017-07-19 14:51:06 ] INFO binding all normalized counts for WT... [ 2017-07-19 14:51:06 ] INFO binding all normalized counts for HET... [ 2017-07-19 14:51:06 ] INFO Writing output... [ 2017-07-19 14:51:07 ] INFO Creating quality control graphs... [ 2017-07-19 14:51:07 ] INFO Plotting in png format... [ 2017-07-19 14:51:07 ] INFO Plotting mds... [ 2017-07-19 14:51:07 ] INFO Plotting biodetection... [ 2017-07-19 14:51:08 ] INFO Plotting countsbio... [ 2017-07-19 14:51:09 ] INFO Plotting saturation... [ 2017-07-19 14:51:11 ] INFO Plotting readnoise... [ 2017-07-19 14:51:11 ] INFO Plotting correl... [ 2017-07-19 14:51:12 ] INFO Plotting pairwise... [ 2017-07-19 14:51:15 ] INFO Plotting boxplot... [ 2017-07-19 14:51:15 ] INFO Plotting boxplot... [ 2017-07-19 14:51:15 ] INFO Plotting volcano... [ 2017-07-19 14:51:15 ] INFO Contrast: WT_vs_HET [ 2017-07-19 14:51:15 ] INFO Plotting biodist... [ 2017-07-19 14:51:15 ] INFO Contrast: WT_vs_HET [ 2017-07-19 14:51:16 ] INFO Plotting deheatmap... [ 2017-07-19 14:51:16 ] INFO Contrast: WT_vs_HET [ 2017-07-19 14:51:32 ] INFO Plotting in pdf format... [ 2017-07-19 14:51:32 ] INFO Plotting mds... [ 2017-07-19 14:51:33 ] INFO Plotting biodetection... [ 2017-07-19 14:51:34 ] INFO Plotting countsbio... [ 2017-07-19 14:51:34 ] INFO Plotting saturation... [ 2017-07-19 14:51:36 ] INFO Plotting readnoise... [ 2017-07-19 14:51:36 ] INFO Plotting correl... [ 2017-07-19 14:51:36 ] INFO Plotting pairwise... [ 2017-07-19 14:51:38 ] INFO Plotting boxplot... [ 2017-07-19 14:51:38 ] INFO Plotting boxplot... [ 2017-07-19 14:51:38 ] INFO Plotting volcano... [ 2017-07-19 14:51:38 ] INFO Contrast: WT_vs_HET [ 2017-07-19 14:51:38 ] INFO Plotting biodist... [ 2017-07-19 14:51:38 ] INFO Contrast: WT_vs_HET [ 2017-07-19 14:51:38 ] INFO Plotting deheatmap... [ 2017-07-19 14:51:38 ] INFO Contrast: WT_vs_HET [ 2017-07-19 14:51:55 ] INFO Creating HTML report... [ 2017-07-19 14:51:55 ] INFO Compressing figures... [ 2017-07-19 14:51:57 ] INFO 2017-07-19 14:51:57: Data processing finished! [ 2017-07-19 14:51:57 ] INFO Total processing time: 05 minutes 05 seconds [ 2017-07-19 15:00:45 ] INFO 2017-07-19 15:00:45: Data processing started... [ 2017-07-19 15:00:45 ] INFO Read counts file: imported sam/bam/bed files [ 2017-07-19 15:00:45 ] INFO Conditions: WT, HET [ 2017-07-19 15:00:45 ] INFO Samples to include: GZS17, GZS35, GZS34, GZS36 [ 2017-07-19 15:00:45 ] INFO Samples to exclude: none [ 2017-07-19 15:00:45 ] INFO Requested contrasts: WT_vs_HET [ 2017-07-19 15:00:45 ] INFO Annotation: download [ 2017-07-19 15:00:45 ] INFO Organism: mm9 [ 2017-07-19 15:00:45 ] INFO Reference source: refseq [ 2017-07-19 15:00:45 ] INFO Count type: gene [ 2017-07-19 15:00:45 ] INFO Exon filters: min.active.exons [ 2017-07-19 15:00:45 ] INFO min.active.exons: [ 2017-07-19 15:00:45 ] INFO exons.per.gene: 5 [ 2017-07-19 15:00:45 ] INFO min.exons: 2 [ 2017-07-19 15:00:45 ] INFO frac: 0.2 [ 2017-07-19 15:00:45 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-07-19 15:00:45 ] INFO length: [ 2017-07-19 15:00:45 ] INFO length: 500 [ 2017-07-19 15:00:45 ] INFO avg.reads: [ 2017-07-19 15:00:45 ] INFO average.per.bp: 100 [ 2017-07-19 15:00:45 ] INFO quantile: 0.25 [ 2017-07-19 15:00:45 ] INFO expression: [ 2017-07-19 15:00:45 ] INFO median: TRUE [ 2017-07-19 15:00:45 ] INFO mean: FALSE [ 2017-07-19 15:00:45 ] INFO quantile: NA [ 2017-07-19 15:00:45 ] INFO known: NA [ 2017-07-19 15:00:45 ] INFO custom: NA [ 2017-07-19 15:00:45 ] INFO biotype: [ 2017-07-19 15:00:45 ] INFO pseudogene: FALSE [ 2017-07-19 15:00:45 ] INFO snRNA: FALSE [ 2017-07-19 15:00:45 ] INFO protein_coding: FALSE [ 2017-07-19 15:00:45 ] INFO antisense: FALSE [ 2017-07-19 15:00:45 ] INFO miRNA: FALSE [ 2017-07-19 15:00:45 ] INFO lincRNA: FALSE [ 2017-07-19 15:00:45 ] INFO snoRNA: FALSE [ 2017-07-19 15:00:45 ] INFO processed_transcript: FALSE [ 2017-07-19 15:00:45 ] INFO misc_RNA: FALSE [ 2017-07-19 15:00:45 ] INFO rRNA: TRUE [ 2017-07-19 15:00:45 ] INFO sense_overlapping: FALSE [ 2017-07-19 15:00:45 ] INFO sense_intronic: FALSE [ 2017-07-19 15:00:45 ] INFO polymorphic_pseudogene: FALSE [ 2017-07-19 15:00:45 ] INFO non_coding: FALSE [ 2017-07-19 15:00:45 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-07-19 15:00:45 ] INFO IG_C_gene: FALSE [ 2017-07-19 15:00:45 ] INFO IG_J_gene: FALSE [ 2017-07-19 15:00:45 ] INFO IG_D_gene: FALSE [ 2017-07-19 15:00:45 ] INFO IG_V_gene: FALSE [ 2017-07-19 15:00:45 ] INFO ncrna_host: FALSE [ 2017-07-19 15:00:45 ] INFO Filter application: postnorm [ 2017-07-19 15:00:45 ] INFO Normalization algorithm: edger [ 2017-07-19 15:00:45 ] INFO Normalization arguments: [ 2017-07-19 15:00:45 ] INFO method: TMM [ 2017-07-19 15:00:45 ] INFO logratioTrim: 0.3 [ 2017-07-19 15:00:45 ] INFO sumTrim: 0.05 [ 2017-07-19 15:00:45 ] INFO doWeighting: TRUE [ 2017-07-19 15:00:45 ] INFO Acutoff: -1e+10 [ 2017-07-19 15:00:45 ] INFO p: 0.75 [ 2017-07-19 15:00:45 ] INFO Statistical algorithm: edger [ 2017-07-19 15:00:45 ] INFO Statistical arguments: [ 2017-07-19 15:00:45 ] INFO edger: classic, 5, 10, movingave, NULL, grid, 11, c(-6, 6), NULL, CoxReid, 10000, NULL, auto, NULL, NULL, NULL, NULL, 0.125, NULL, auto, chisq, TRUE, FALSE, c(0.05, 0.1) [ 2017-07-19 15:00:45 ] INFO Meta-analysis method: none [ 2017-07-19 15:00:45 ] INFO Multiple testing correction: BH [ 2017-07-19 15:00:45 ] INFO p-value threshold: 0.05 [ 2017-07-19 15:00:45 ] INFO Logarithmic transformation offset: 1 [ 2017-07-19 15:00:45 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, correl, pairwise, boxplot, volcano, biodist, deheatmap [ 2017-07-19 15:00:45 ] INFO Figure format: png, pdf [ 2017-07-19 15:00:45 ] INFO Output directory: /data/images/proton/Cereghini/e17.5/metaseqr_e17.5 [ 2017-07-19 15:00:45 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, stats, counts [ 2017-07-19 15:00:45 ] INFO Output scale(s): log2 [ 2017-07-19 15:00:45 ] INFO Output values: normalized [ 2017-07-19 15:00:45 ] INFO Output statistics: mean, median, sd, mad, cv, rcv [ 2017-07-19 15:00:45 ] INFO Downloading gene annotation for mm9... [ 2017-07-19 15:00:45 ] WARN R package RMySQL is not present! Annotation will be retrieved by downloading temporary files from UCSC and the usage of a temporary SQLite database... [ 2017-07-19 15:00:45 ] INFO Retrieving tables for temporary SQLite refseq mm9 gene subset database [ 2017-07-19 15:00:45 ] INFO Retrieving table refFlat [ 2017-07-19 15:00:52 ] INFO Retrieving table knownToRefSeq [ 2017-07-19 15:00:55 ] INFO Retrieving table knownCanonical [ 2017-07-19 15:00:58 ] INFO Retrieving table knownToEnsembl [ 2017-07-19 15:01:02 ] INFO Retrieving table ensemblSource [ 2017-07-19 15:01:07 ] INFO Converting annotation to GenomicRanges object... [ 2017-07-19 15:01:07 ] INFO Getting DNA sequences... [ 2017-07-19 15:01:14 ] INFO Getting GC content... [ 2017-07-19 15:01:16 ] INFO Converting annotation to GenomicRanges object... [ 2017-07-19 15:01:16 ] INFO Reading bam file accepted_hits.bam for sample with name GZS17. This might take some time... [ 2017-07-19 15:01:16 ] INFO Reading bam file accepted_hits.bam for sample with name GZS35. This might take some time... [ 2017-07-19 15:01:16 ] INFO Reading bam file accepted_hits.bam for sample with name GZS34. This might take some time... [ 2017-07-19 15:01:16 ] INFO Reading bam file accepted_hits.bam for sample with name GZS36. This might take some time... [ 2017-07-19 15:01:28 ] INFO Counting reads overlapping with given annotation... [ 2017-07-19 15:01:28 ] INFO ...for single-end reads... [ 2017-07-19 15:01:28 ] INFO ...assuming reverse sequenced reads... [ 2017-07-19 15:01:32 ] INFO Counting reads overlapping with given annotation... [ 2017-07-19 15:01:32 ] INFO ...for single-end reads... [ 2017-07-19 15:01:32 ] INFO ...assuming reverse sequenced reads... [ 2017-07-19 15:01:34 ] INFO Counting reads overlapping with given annotation... [ 2017-07-19 15:01:34 ] INFO ...for single-end reads... [ 2017-07-19 15:01:34 ] INFO ...assuming reverse sequenced reads... [ 2017-07-19 15:02:00 ] INFO Counting reads overlapping with given annotation... [ 2017-07-19 15:02:00 ] INFO ...for single-end reads... [ 2017-07-19 15:02:00 ] INFO ...assuming reverse sequenced reads... [ 2017-07-19 15:05:12 ] INFO Exporting raw read counts table to /data/images/proton/Cereghini/e17.5/metaseqr_e17.5/lists/raw_counts_table.txt.gz [ 2017-07-19 15:05:13 ] INFO Saving gene model to /data/images/proton/Cereghini/e17.5/metaseqr_e17.5/data/gene_model.RData [ 2017-07-19 15:05:13 ] INFO Removing genes with zero counts in all samples... [ 2017-07-19 15:05:13 ] INFO Normalizing with: edger [ 2017-07-19 15:05:13 ] INFO Applying gene filter length... [ 2017-07-19 15:05:13 ] INFO Threshold below which ignored: 500 [ 2017-07-19 15:05:13 ] INFO Applying gene filter avg.reads... [ 2017-07-19 15:05:13 ] INFO Threshold below which ignored: 0.222432845246075 [ 2017-07-19 15:05:13 ] INFO Applying gene filter expression... [ 2017-07-19 15:05:13 ] INFO Threshold below which ignored: 559 [ 2017-07-19 15:05:13 ] INFO Applying gene filter biotype... [ 2017-07-19 15:05:13 ] INFO Biotypes ignored: rRNA [ 2017-07-19 15:05:13 ] INFO 11774 genes filtered out [ 2017-07-19 15:05:13 ] INFO 9265 genes remain after filtering [ 2017-07-19 15:05:13 ] INFO Running statistical tests with: edger [ 2017-07-19 15:05:14 ] INFO Contrast: WT_vs_HET [ 2017-07-19 15:05:15 ] INFO Contrast WT_vs_HET: found 1422 genes [ 2017-07-19 15:05:15 ] INFO Exporting and compressing normalized read counts table to /data/images/proton/Cereghini/e17.5/metaseqr_e17.5/lists/normalized_counts_table.txt [ 2017-07-19 15:05:15 ] INFO Building output files... [ 2017-07-19 15:05:15 ] INFO Contrast: WT_vs_HET [ 2017-07-19 15:05:15 ] INFO Adding non-filtered data... [ 2017-07-19 15:05:15 ] INFO binding annotation... [ 2017-07-19 15:05:15 ] INFO binding p-values... [ 2017-07-19 15:05:15 ] INFO binding FDRs... [ 2017-07-19 15:05:16 ] INFO binding log2 normalized fold changes... [ 2017-07-19 15:05:16 ] INFO binding normalized mean counts... [ 2017-07-19 15:05:16 ] INFO binding normalized median counts... [ 2017-07-19 15:05:16 ] INFO binding normalized count sds... [ 2017-07-19 15:05:17 ] INFO binding normalized count MADs... [ 2017-07-19 15:05:18 ] INFO binding normalized count CVs... [ 2017-07-19 15:05:19 ] INFO binding normalized counts RCVs... [ 2017-07-19 15:05:20 ] INFO binding normalized mean counts... [ 2017-07-19 15:05:20 ] INFO binding normalized median counts... [ 2017-07-19 15:05:21 ] INFO binding normalized count sds... [ 2017-07-19 15:05:21 ] INFO binding normalized count MADs... [ 2017-07-19 15:05:23 ] INFO binding normalized count CVs... [ 2017-07-19 15:05:23 ] INFO binding normalized counts RCVs... [ 2017-07-19 15:05:25 ] INFO binding all normalized counts for WT... [ 2017-07-19 15:05:25 ] INFO binding all normalized counts for HET... [ 2017-07-19 15:05:25 ] INFO Writing output... [ 2017-07-19 15:05:25 ] INFO Adding filtered data... [ 2017-07-19 15:05:25 ] INFO binding annotation... [ 2017-07-19 15:05:25 ] INFO binding p-values... [ 2017-07-19 15:05:25 ] INFO binding FDRs... [ 2017-07-19 15:05:25 ] INFO binding log2 normalized fold changes... [ 2017-07-19 15:05:25 ] INFO binding normalized mean counts... [ 2017-07-19 15:05:26 ] INFO binding normalized median counts... [ 2017-07-19 15:05:26 ] INFO binding normalized count sds... [ 2017-07-19 15:05:27 ] INFO binding normalized count MADs... [ 2017-07-19 15:05:28 ] INFO binding normalized count CVs... [ 2017-07-19 15:05:29 ] INFO binding normalized counts RCVs... [ 2017-07-19 15:05:31 ] INFO binding normalized mean counts... [ 2017-07-19 15:05:31 ] INFO binding normalized median counts... [ 2017-07-19 15:05:32 ] INFO binding normalized count sds... [ 2017-07-19 15:05:33 ] INFO binding normalized count MADs... [ 2017-07-19 15:05:34 ] INFO binding normalized count CVs... [ 2017-07-19 15:05:35 ] INFO binding normalized counts RCVs... [ 2017-07-19 15:05:37 ] INFO binding all normalized counts for WT... [ 2017-07-19 15:05:37 ] INFO binding all normalized counts for HET... [ 2017-07-19 15:05:37 ] INFO Writing output... [ 2017-07-19 15:05:38 ] INFO Creating quality control graphs... [ 2017-07-19 15:05:38 ] INFO Plotting in png format... [ 2017-07-19 15:05:38 ] INFO Plotting mds... [ 2017-07-19 15:05:38 ] INFO Plotting biodetection... [ 2017-07-19 15:05:39 ] INFO Plotting countsbio... [ 2017-07-19 15:05:40 ] INFO Plotting saturation... [ 2017-07-19 15:05:42 ] INFO Plotting readnoise... [ 2017-07-19 15:05:42 ] INFO Plotting correl... [ 2017-07-19 15:05:42 ] INFO Plotting pairwise... [ 2017-07-19 15:05:45 ] INFO Plotting boxplot... [ 2017-07-19 15:05:45 ] INFO Plotting boxplot... [ 2017-07-19 15:05:45 ] INFO Plotting volcano... [ 2017-07-19 15:05:45 ] INFO Contrast: WT_vs_HET [ 2017-07-19 15:05:46 ] INFO Plotting biodist... [ 2017-07-19 15:05:46 ] INFO Contrast: WT_vs_HET [ 2017-07-19 15:05:46 ] INFO Plotting deheatmap... [ 2017-07-19 15:05:46 ] INFO Contrast: WT_vs_HET [ 2017-07-19 15:06:02 ] INFO Plotting in pdf format... [ 2017-07-19 15:06:02 ] INFO Plotting mds... [ 2017-07-19 15:06:02 ] INFO Plotting biodetection... [ 2017-07-19 15:06:03 ] INFO Plotting countsbio... [ 2017-07-19 15:06:03 ] INFO Plotting saturation... [ 2017-07-19 15:06:05 ] INFO Plotting readnoise... [ 2017-07-19 15:06:06 ] INFO Plotting correl... [ 2017-07-19 15:06:06 ] INFO Plotting pairwise... [ 2017-07-19 15:06:08 ] INFO Plotting boxplot... [ 2017-07-19 15:06:08 ] INFO Plotting boxplot... [ 2017-07-19 15:06:08 ] INFO Plotting volcano... [ 2017-07-19 15:06:08 ] INFO Contrast: WT_vs_HET [ 2017-07-19 15:06:08 ] INFO Plotting biodist... [ 2017-07-19 15:06:08 ] INFO Contrast: WT_vs_HET [ 2017-07-19 15:06:08 ] INFO Plotting deheatmap... [ 2017-07-19 15:06:08 ] INFO Contrast: WT_vs_HET [ 2017-07-19 15:06:24 ] INFO Creating HTML report... [ 2017-07-19 15:06:24 ] INFO Compressing figures...
Multidimensional scaling
Biotype detection
Biotype detection counts
Read and biotype saturation
RNA-Seq reads noise
Correlation plots
Pairwise scatterplots
Boxplots
Volcano plots
DEG heatmaps
Chromosome and biotype distributions of DEGs
Results
DEG table for the contrast WT_vs_HETThe following table presents the top 10% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast WT_vs_HET. The fields of the table correspond to the requested features to be exported. The table can be searched using the search field on the top right. | chromosome | start | end | gene_id | gc_content | strand | gene_name | biotype | p-value_edger | FDR_edger | log2_normalized_fold_change_WT_vs_HET | log2_normalized_mean_counts_WT | log2_normalized_median_counts_WT | log2_normalized_sd_counts_WT | log2_normalized_mad_counts_WT | log2_normalized_cv_counts_WT | log2_normalized_rcv_counts_WT | log2_normalized_mean_counts_HET | log2_normalized_median_counts_HET | log2_normalized_sd_counts_HET | log2_normalized_mad_counts_HET | log2_normalized_cv_counts_HET | log2_normalized_rcv_counts_HET | log2_normalized_counts_GZS17 | log2_normalized_counts_GZS35 | log2_normalized_counts_GZS34 | log2_normalized_counts_GZS36 |
|---|
| chr19 | 8410112 | 8479595 | NM_177002 | 0.3896 | - | Slc22a30 | protein_coding | 1.08e-142 | 9.97e-139 | -3.646940 | 10.57 | 10.57 | 0.087130 | 0.091343 | 8.24e-03 | 8.64e-03 | 6.94 | 6.94 | 0.041644 | 0.043658 | 6.00e-03 | 6.29e-03 | 10.63 | 10.51 | 6.91 | 6.97 | | chr19 | 8136698 | 8206472 | NM_001013820 | 0.3964 | - | Slc22a28 | protein_coding | 5.88e-131 | 2.72e-127 | -3.639199 | 10.36 | 10.36 | 0.041106 | 0.043094 | 3.97e-03 | 4.16e-03 | 6.73 | 6.73 | 0.067076 | 0.070319 | 9.96e-03 | 1.04e-02 | 10.39 | 10.33 | 6.69 | 6.78 | | chr4 | 19745873 | 19769360 | NM_028746 | 0.3922 | + | Slc7a13 | protein_coding | 8.64e-92 | 2.67e-88 | -3.213071 | 9.73 | 9.73 | 0.085311 | 0.089437 | 8.77e-03 | 9.19e-03 | 6.53 | 6.53 | 0.099335 | 0.104139 | 1.52e-02 | 1.59e-02 | 9.79 | 9.67 | 6.60 | 6.46 | | chr19 | 6535855 | 6543070 | NM_009203 | 0.5572 | - | Slc22a12 | protein_coding | 4.58e-58 | 1.06e-54 | -2.204192 | 10.14 | 10.14 | 0.028891 | 0.030288 | 2.85e-03 | 2.99e-03 | 7.93 | 7.93 | 0.258482 | 0.270982 | 3.26e-02 | 3.42e-02 | 10.16 | 10.12 | 8.11 | 7.75 | | chr18 | 21230844 | 21258700 | NM_008586 | 0.4271 | + | Mep1b | protein_coding | 8.73e-57 | 1.62e-53 | -2.697805 | 10.67 | 10.67 | 0.278094 | 0.291542 | 2.61e-02 | 2.73e-02 | 7.97 | 7.97 | 0.324000 | 0.339668 | 4.06e-02 | 4.26e-02 | 10.86 | 10.47 | 8.20 | 7.74 | | chr10 | 102830441 | 102882013 | NM_175328 | 0.3690 | + | Slc6a15 | protein_coding | 4.46e-56 | 6.88e-53 | -2.497425 | 9.15 | 9.15 | 0.066418 | 0.069629 | 7.26e-03 | 7.61e-03 | 6.66 | 6.66 | 0.070382 | 0.073786 | 1.06e-02 | 1.11e-02 | 9.10 | 9.20 | 6.71 | 6.61 | | chr13 | 23962141 | 23987599 | NM_001170638 | 0.4083 | + | Slc17a1 | protein_coding | 1.88e-54 | 2.48e-51 | -2.794609 | 10.67 | 10.67 | 0.104914 | 0.109987 | 9.83e-03 | 1.03e-02 | 7.83 | 7.83 | 0.552292 | 0.578998 | 7.05e-02 | 7.39e-02 | 10.75 | 10.60 | 8.22 | 7.44 | | chr10 | 86984539 | 87046882 | NM_008777 | 0.4290 | + | Pah | protein_coding | 1.57e-53 | 1.82e-50 | -3.227476 | 9.64 | 9.64 | 0.340864 | 0.357347 | 3.54e-02 | 3.71e-02 | 6.40 | 6.40 | 0.477564 | 0.500658 | 7.46e-02 | 7.82e-02 | 9.88 | 9.39 | 6.74 | 6.07 | | chr10 | 127286983 | 127298232 | NM_147222 | 0.4302 | + | Rdh19 | protein_coding | 1.34e-50 | 1.38e-47 | -2.699942 | 9.49 | 9.49 | 0.261556 | 0.274203 | 2.76e-02 | 2.89e-02 | 6.80 | 6.80 | 0.301415 | 0.315990 | 4.43e-02 | 4.65e-02 | 9.68 | 9.31 | 7.01 | 6.58 | | chr12 | 104884840 | 104895428 | NM_007618 | 0.4495 | - | Serpina6 | protein_coding | 2.15e-48 | 1.99e-45 | -3.156039 | 9.57 | 9.57 | 0.436125 | 0.457214 | 4.56e-02 | 4.78e-02 | 6.45 | 6.45 | 0.185993 | 0.194987 | 2.88e-02 | 3.02e-02 | 9.88 | 9.26 | 6.32 | 6.58 | | chr4 | 25536479 | 25727150 | NM_010243 | 0.3729 | - | Fut9 | protein_coding | 2.39e-47 | 2.01e-44 | -1.791163 | 11.87 | 11.87 | 0.215031 | 0.225430 | 1.81e-02 | 1.90e-02 | 10.09 | 10.09 | 0.056220 | 0.058939 | 5.57e-03 | 5.84e-03 | 12.02 | 11.72 | 10.13 | 10.05 | | chr19 | 43856797 | 43912708 | NM_013806 | 0.4467 | + | Abcc2 | protein_coding | 7.82e-46 | 6.04e-43 | -1.985786 | 10.24 | 10.24 | 0.153351 | 0.160767 | 1.50e-02 | 1.57e-02 | 8.26 | 8.26 | 0.173207 | 0.181583 | 2.10e-02 | 2.20e-02 | 10.35 | 10.13 | 8.38 | 8.13 | | chr2 | 110437455 | 110489502 | NM_001177624 | 0.3718 | + | Slc5a12 | protein_coding | 4.19e-45 | 2.99e-42 | -1.767886 | 9.94 | 9.94 | 0.025933 | 0.027187 | 2.61e-03 | 2.73e-03 | 8.18 | 8.18 | 0.038766 | 0.040641 | 4.74e-03 | 4.97e-03 | 9.96 | 9.92 | 8.20 | 8.15 | | chr1 | 90303584 | 90323013 | NM_029269 | 0.4581 | + | Spp2 | protein_coding | 4.55e-45 | 3.01e-42 | -2.260496 | 11.47 | 11.47 | 0.085541 | 0.089677 | 7.46e-03 | 7.82e-03 | 9.19 | 9.19 | 0.380789 | 0.399203 | 4.14e-02 | 4.34e-02 | 11.53 | 11.41 | 9.46 | 8.92 | | chr7 | 126705221 | 126744208 | NM_146197 | 0.4246 | + | Acsm2 | protein_coding | 1.03e-44 | 6.35e-42 | -1.993053 | 12.18 | 12.18 | 0.252237 | 0.264434 | 2.07e-02 | 2.17e-02 | 10.19 | 10.19 | 0.197329 | 0.206871 | 1.94e-02 | 2.03e-02 | 12.35 | 12.00 | 10.33 | 10.05 | | chr19 | 8692485 | 8702789 | NM_008766 | 0.4858 | + | Slc22a6 | protein_coding | 3.51e-44 | 2.03e-41 | -1.716917 | 11.64 | 11.64 | 0.153004 | 0.160402 | 1.31e-02 | 1.38e-02 | 9.92 | 9.92 | 0.170418 | 0.178659 | 1.72e-02 | 1.80e-02 | 11.74 | 11.53 | 10.04 | 9.80 | | chr13 | 23931302 | 23952583 | NM_134069 | 0.4132 | + | Slc17a3 | protein_coding | 8.88e-43 | 4.84e-40 | -2.613230 | 9.37 | 9.37 | 0.334394 | 0.350564 | 3.57e-02 | 3.74e-02 | 6.78 | 6.78 | 0.250516 | 0.262630 | 3.70e-02 | 3.88e-02 | 9.61 | 9.13 | 6.95 | 6.60 | | chr2 | 13197964 | 13413503 | NM_001081084 | 0.3986 | - | Cubn | protein_coding | 2.33e-42 | 1.20e-39 | -1.923827 | 11.97 | 11.97 | 0.299136 | 0.313601 | 2.50e-02 | 2.62e-02 | 10.06 | 10.06 | 0.074538 | 0.078142 | 7.41e-03 | 7.77e-03 | 12.18 | 11.76 | 10.11 | 10.01 | | chr9 | 123502937 | 123541683 | NM_011731 | 0.4345 | - | Slc6a20b | protein_coding | 8.78e-42 | 4.28e-39 | -2.665016 | 9.43 | 9.43 | 0.392572 | 0.411555 | 4.16e-02 | 4.36e-02 | 6.81 | 6.81 | 0.036437 | 0.038199 | 5.35e-03 | 5.61e-03 | 9.71 | 9.16 | 6.83 | 6.78 | | chr3 | 14480698 | 14505818 | NM_080852 | 0.3601 | + | Slc7a12 | protein_coding | 8.12e-40 | 3.76e-37 | -2.601451 | 9.76 | 9.76 | 0.393887 | 0.412934 | 4.04e-02 | 4.23e-02 | 7.18 | 7.18 | 0.238649 | 0.250189 | 3.32e-02 | 3.48e-02 | 10.03 | 9.48 | 7.01 | 7.35 | | chr4 | 115236253 | 115251620 | NM_201640 | 0.4239 | + | Cyp4a31 | protein_coding | 1.15e-39 | 5.06e-37 | -1.598138 | 11.27 | 11.27 | 0.117140 | 0.122804 | 1.04e-02 | 1.09e-02 | 9.68 | 9.68 | 0.018696 | 0.019600 | 1.93e-03 | 2.03e-03 | 11.35 | 11.19 | 9.66 | 9.69 | | chr4 | 96294122 | 96330810 | NM_010007 | 0.3786 | - | Cyp2j5 | protein_coding | 4.62e-39 | 1.94e-36 | -2.476241 | 11.10 | 11.10 | 0.292807 | 0.306966 | 2.64e-02 | 2.76e-02 | 8.62 | 8.62 | 0.394562 | 0.413642 | 4.58e-02 | 4.80e-02 | 11.31 | 10.90 | 8.90 | 8.34 | | chr19 | 56362401 | 56395310 | NM_146101 | 0.4820 | + | Habp2 | protein_coding | 8.54e-39 | 3.44e-36 | -1.644132 | 10.35 | 10.35 | 0.135176 | 0.141712 | 1.31e-02 | 1.37e-02 | 8.71 | 8.71 | 0.107225 | 0.112410 | 1.23e-02 | 1.29e-02 | 10.45 | 10.25 | 8.78 | 8.63 | | chr16 | 95479164 | 95521865 | NM_001039057 | 0.4546 | + | Kcnj15 | protein_coding | 6.54e-38 | 2.53e-35 | -1.768695 | 10.37 | 10.37 | 0.218471 | 0.229036 | 2.11e-02 | 2.21e-02 | 8.61 | 8.61 | 0.068035 | 0.071324 | 7.90e-03 | 8.29e-03 | 10.52 | 10.21 | 8.65 | 8.56 | | chr1 | 164805177 | 164828843 | NM_018881 | 0.4155 | - | Fmo2 | protein_coding | 1.06e-37 | 3.91e-35 | -1.745485 | 9.52 | 9.52 | 0.069235 | 0.072583 | 7.27e-03 | 7.62e-03 | 7.78 | 7.78 | 0.004626 | 0.004850 | 5.94e-04 | 6.23e-04 | 9.57 | 9.48 | 7.78 | 7.79 | | chr16 | 37580238 | 37632112 | NM_013547 | 0.4406 | + | Hgd | protein_coding | 2.05e-37 | 7.32e-35 | -1.930187 | 9.35 | 9.35 | 0.166638 | 0.174696 | 1.78e-02 | 1.87e-02 | 7.43 | 7.43 | 0.106238 | 0.111375 | 1.43e-02 | 1.50e-02 | 9.47 | 9.24 | 7.51 | 7.36 | | chr10 | 88348736 | 88392260 | NM_145423 | 0.3962 | + | Slc5a8 | protein_coding | 5.11e-37 | 1.75e-34 | -2.152980 | 10.98 | 10.98 | 0.335334 | 0.351549 | 3.05e-02 | 3.20e-02 | 8.85 | 8.85 | 0.037501 | 0.039315 | 4.24e-03 | 4.44e-03 | 11.22 | 10.75 | 8.88 | 8.83 | | chr17 | 85427686 | 85463581 | NM_009205 | 0.4584 | + | Slc3a1 | protein_coding | 1.74e-36 | 5.76e-34 | -1.825111 | 11.16 | 11.16 | 0.186728 | 0.195758 | 1.67e-02 | 1.75e-02 | 9.33 | 9.33 | 0.215229 | 0.225637 | 2.31e-02 | 2.42e-02 | 11.29 | 11.02 | 9.48 | 9.18 | | chr15 | 82620536 | 82624675 | NM_029562 | 0.5196 | - | Cyp2d26 | protein_coding | 1.33e-35 | 4.25e-33 | -1.808181 | 10.77 | 10.77 | 0.122084 | 0.127987 | 1.13e-02 | 1.19e-02 | 8.96 | 8.96 | 0.196472 | 0.205973 | 2.19e-02 | 2.30e-02 | 10.68 | 10.86 | 9.10 | 8.82 | | chr13 | 73799197 | 73815471 | NM_001040692 | 0.4721 | - | Slc6a18 | protein_coding | 1.45e-35 | 4.48e-33 | -1.482777 | 11.89 | 11.89 | 0.093267 | 0.097778 | 7.84e-03 | 8.22e-03 | 10.41 | 10.41 | 0.192854 | 0.202180 | 1.85e-02 | 1.94e-02 | 11.96 | 11.83 | 10.54 | 10.27 | | chr2 | 122420208 | 122437013 | NM_025961 | 0.4162 | - | Gatm | protein_coding | 1.64e-34 | 4.91e-32 | -1.676520 | 12.34 | 12.34 | 0.079221 | 0.083051 | 6.42e-03 | 6.73e-03 | 10.66 | 10.66 | 0.287451 | 0.301351 | 2.70e-02 | 2.83e-02 | 12.40 | 12.29 | 10.86 | 10.45 | | chr3 | 28596824 | 28627282 | NM_031197 | 0.4306 | + | Slc2a2 | protein_coding | 4.61e-34 | 1.34e-31 | -1.626802 | 10.13 | 10.13 | 0.110270 | 0.115602 | 1.09e-02 | 1.14e-02 | 8.50 | 8.50 | 0.182907 | 0.191751 | 2.15e-02 | 2.26e-02 | 10.21 | 10.05 | 8.63 | 8.37 | | chr4 | 42786391 | 42787525 | NM_001193667 | 0.5674 | - | Gm1987 | protein_coding | 1.48e-33 | 4.16e-31 | 1.612218 | 7.66 | 7.66 | 0.030303 | 0.031769 | 3.96e-03 | 4.15e-03 | 9.27 | 9.27 | 0.034809 | 0.036492 | 3.76e-03 | 3.94e-03 | 7.68 | 7.64 | 9.24 | 9.29 | | chr2 | 126378759 | 126413979 | NM_011978 | 0.4448 | + | Slc27a2 | protein_coding | 2.51e-31 | 6.85e-29 | -1.479099 | 11.47 | 11.47 | 0.154869 | 0.162358 | 1.35e-02 | 1.42e-02 | 9.99 | 9.99 | 0.172263 | 0.180593 | 1.72e-02 | 1.81e-02 | 11.58 | 11.36 | 10.11 | 9.87 | | chr13 | 62966112 | 62989642 | NM_019395 | 0.4759 | - | Fbp1 | protein_coding | 5.22e-31 | 1.38e-28 | -1.779897 | 11.82 | 11.82 | 0.033961 | 0.035603 | 2.87e-03 | 3.01e-03 | 10.01 | 10.01 | 0.408374 | 0.428121 | 4.08e-02 | 4.28e-02 | 11.79 | 11.84 | 10.30 | 9.72 | | chr5 | 89316284 | 89668681 | NM_001136260 | 0.4151 | + | Slc4a4 | protein_coding | 1.07e-30 | 2.76e-28 | -1.361933 | 11.58 | 11.58 | 0.182768 | 0.191606 | 1.58e-02 | 1.65e-02 | 10.22 | 10.22 | 0.071678 | 0.075144 | 7.01e-03 | 7.35e-03 | 11.71 | 11.45 | 10.27 | 10.17 | | chr5 | 33446867 | 33505348 | NM_019810 | 0.4365 | + | Slc5a1 | protein_coding | 1.32e-30 | 3.30e-28 | -1.652345 | 9.58 | 9.58 | 0.159722 | 0.167446 | 1.67e-02 | 1.75e-02 | 7.93 | 7.93 | 0.125071 | 0.131119 | 1.58e-02 | 1.65e-02 | 9.69 | 9.47 | 8.02 | 7.85 | | chr19 | 8667671 | 8686325 | NM_001164635 | 0.4688 | + | Slc22a8 | protein_coding | 2.50e-30 | 6.10e-28 | -1.339746 | 10.35 | 10.35 | 0.108803 | 0.114065 | 1.05e-02 | 1.10e-02 | 9.01 | 9.01 | 0.055370 | 0.058047 | 6.14e-03 | 6.44e-03 | 10.42 | 10.27 | 9.05 | 8.97 | | chr3 | 129539656 | 129578250 | NM_007686 | 0.4326 | + | Cfi | protein_coding | 7.71e-30 | 1.83e-27 | -1.662538 | 9.14 | 9.14 | 0.092228 | 0.096688 | 1.01e-02 | 1.06e-02 | 7.48 | 7.48 | 0.171375 | 0.179662 | 2.29e-02 | 2.40e-02 | 9.20 | 9.07 | 7.60 | 7.36 | | chr3 | 98356473 | 98367961 | NM_008294 | 0.4190 | - | Hsd3b4 | protein_coding | 2.51e-29 | 5.81e-27 | -1.710485 | 13.01 | 13.01 | 0.176697 | 0.185242 | 1.36e-02 | 1.42e-02 | 11.31 | 11.31 | 0.133207 | 0.139648 | 1.18e-02 | 1.24e-02 | 13.14 | 12.89 | 11.40 | 11.21 | | chr7 | 59134336 | 59249831 | NM_008087 | 0.4022 | + | Gas2 | protein_coding | 2.78e-29 | 6.29e-27 | -1.144192 | 11.90 | 11.90 | 0.002665 | 0.002794 | 2.24e-04 | 2.35e-04 | 10.76 | 10.76 | 0.019432 | 0.020371 | 1.81e-03 | 1.89e-03 | 11.90 | 11.90 | 10.77 | 10.74 | | chr5 | 104864129 | 104870072 | NM_009263 | 0.3794 | + | Spp1 | protein_coding | 5.94e-29 | 1.31e-26 | -1.619636 | 12.54 | 12.54 | 0.026877 | 0.028176 | 2.14e-03 | 2.25e-03 | 10.92 | 10.92 | 0.170771 | 0.179029 | 1.56e-02 | 1.64e-02 | 12.52 | 12.56 | 11.04 | 10.80 | | chr13 | 94426051 | 94444257 | NM_022884 | 0.4585 | - | Bhmt2 | protein_coding | 4.00e-28 | 8.63e-26 | -1.877457 | 9.13 | 9.13 | 0.232107 | 0.243331 | 2.54e-02 | 2.66e-02 | 7.25 | 7.25 | 0.312761 | 0.327885 | 4.31e-02 | 4.52e-02 | 9.30 | 8.97 | 7.48 | 7.03 | | chrX | 160528118 | 160556791 | NM_020626 | 0.4054 | + | Tmem27 | protein_coding | 8.51e-28 | 1.79e-25 | -1.367335 | 11.63 | 11.63 | 0.052244 | 0.054770 | 4.49e-03 | 4.71e-03 | 10.25 | 10.25 | 0.257432 | 0.269880 | 2.51e-02 | 2.63e-02 | 11.66 | 11.59 | 10.43 | 10.07 | | chr19 | 4510471 | 4621752 | NM_001162946 | 0.4622 | + | Pcx | protein_coding | 1.32e-27 | 2.72e-25 | -1.414571 | 11.59 | 11.59 | 0.198989 | 0.208611 | 1.72e-02 | 1.80e-02 | 10.18 | 10.18 | 0.186637 | 0.195662 | 1.83e-02 | 1.92e-02 | 11.73 | 11.45 | 10.31 | 10.04 | | chr5 | 90919739 | 90937933 | NM_007423 | 0.4054 | + | Afp | protein_coding | 3.77e-27 | 7.60e-25 | -1.310904 | 11.84 | 11.84 | 0.211763 | 0.222003 | 1.79e-02 | 1.88e-02 | 10.54 | 10.54 | 0.032279 | 0.033840 | 3.06e-03 | 3.21e-03 | 11.69 | 11.99 | 10.51 | 10.56 | | chr17 | 12841740 | 12868704 | NM_009202 | 0.4865 | - | Slc22a1 | protein_coding | 1.94e-26 | 3.82e-24 | -1.694981 | 9.29 | 9.29 | 0.213748 | 0.224084 | 2.30e-02 | 2.41e-02 | 7.59 | 7.59 | 0.226458 | 0.237408 | 2.98e-02 | 3.13e-02 | 9.44 | 9.13 | 7.75 | 7.43 | | chr6 | 85860147 | 85865671 | NM_023160 | 0.4418 | - | Nat8f1 | protein_coding | 3.52e-26 | 6.79e-24 | -1.317608 | 10.55 | 10.55 | 0.008832 | 0.009260 | 8.37e-04 | 8.78e-04 | 9.23 | 9.23 | 0.084637 | 0.088730 | 9.17e-03 | 9.61e-03 | 10.56 | 10.55 | 9.29 | 9.17 | | chr9 | 44607482 | 44611034 | NM_138951 | 0.5283 | - | Ttc36 | protein_coding | 4.61e-26 | 8.71e-24 | -1.588637 | 10.42 | 10.42 | 0.221639 | 0.232356 | 2.13e-02 | 2.23e-02 | 8.83 | 8.83 | 0.275328 | 0.288642 | 3.12e-02 | 3.27e-02 | 10.58 | 10.26 | 9.02 | 8.63 | | chrX | 136335346 | 136345927 | NM_016675 | 0.4605 | + | Cldn2 | protein_coding | 4.96e-26 | 9.19e-24 | -1.444868 | 11.50 | 11.50 | 0.202339 | 0.212123 | 1.76e-02 | 1.84e-02 | 10.05 | 10.05 | 0.202977 | 0.212792 | 2.02e-02 | 2.12e-02 | 11.64 | 11.36 | 10.20 | 9.91 | | chr13 | 55501008 | 55516056 | NM_011392 | 0.5065 | + | Slc34a1 | protein_coding | 1.56e-25 | 2.83e-23 | -1.718395 | 13.71 | 13.71 | 0.218126 | 0.228674 | 1.59e-02 | 1.67e-02 | 12.00 | 12.00 | 0.151131 | 0.158439 | 1.26e-02 | 1.32e-02 | 13.86 | 13.56 | 12.10 | 11.89 | | chr19 | 7747565 | 7785800 | NM_144785 | 0.3942 | - | Slc22a19 | protein_coding | 1.61e-25 | 2.87e-23 | -1.888715 | 10.95 | 10.95 | 0.306415 | 0.321232 | 2.80e-02 | 2.93e-02 | 9.06 | 9.06 | 0.313285 | 0.328434 | 3.46e-02 | 3.62e-02 | 11.17 | 10.73 | 9.29 | 8.84 | | chr17 | 12777054 | 12821354 | NM_013667 | 0.4423 | + | Slc22a2 | protein_coding | 2.11e-25 | 3.70e-23 | -1.864161 | 9.81 | 9.81 | 0.272522 | 0.285701 | 2.78e-02 | 2.91e-02 | 7.94 | 7.94 | 0.388190 | 0.406961 | 4.89e-02 | 5.13e-02 | 10.01 | 9.62 | 8.21 | 7.67 | | chr9 | 54765096 | 54797731 | NM_177351 | 0.4124 | + | Hykk | protein_coding | 8.32e-25 | 1.43e-22 | -1.322956 | 10.45 | 10.45 | 0.212125 | 0.222383 | 2.03e-02 | 2.13e-02 | 9.13 | 9.13 | 0.010891 | 0.011418 | 1.19e-03 | 1.25e-03 | 10.60 | 10.30 | 9.14 | 9.13 | | chr7 | 31278676 | 31298421 | NM_019546 | 0.4983 | + | Prodh2 | protein_coding | 8.67e-25 | 1.46e-22 | -1.605163 | 9.81 | 9.81 | 0.209293 | 0.219414 | 2.13e-02 | 2.24e-02 | 8.20 | 8.20 | 0.266431 | 0.279314 | 3.25e-02 | 3.41e-02 | 9.66 | 9.95 | 8.39 | 8.01 | | chr6 | 24901140 | 24906125 | NM_177013 | 0.4505 | - | Tmem229a | protein_coding | 2.45e-24 | 4.05e-22 | -1.455292 | 10.89 | 10.89 | 0.228956 | 0.240028 | 2.10e-02 | 2.20e-02 | 9.45 | 9.45 | 0.017514 | 0.018360 | 1.85e-03 | 1.94e-03 | 11.06 | 10.73 | 9.46 | 9.44 | | chr13 | 99404932 | 99407365 | NM_026685 | 0.5004 | - | Tmem174 | protein_coding | 6.07e-24 | 9.87e-22 | -1.529253 | 10.57 | 10.57 | 0.221619 | 0.232336 | 2.10e-02 | 2.20e-02 | 9.04 | 9.04 | 0.236320 | 0.247747 | 2.61e-02 | 2.74e-02 | 10.72 | 10.41 | 9.20 | 8.87 | | chr3 | 154239483 | 154260062 | NM_172474 | 0.4707 | - | Tyw3 | protein_coding | 1.36e-23 | 2.18e-21 | -1.136140 | 11.12 | 11.12 | 0.026630 | 0.027918 | 2.40e-03 | 2.51e-03 | 9.98 | 9.98 | 0.031267 | 0.032779 | 3.13e-03 | 3.28e-03 | 11.10 | 11.14 | 9.96 | 10.00 | | chr3 | 98678441 | 98697153 | NM_019545 | 0.4128 | - | Hao2 | protein_coding | 3.89e-23 | 6.11e-21 | -1.323984 | 10.92 | 10.92 | 0.083981 | 0.088042 | 7.69e-03 | 8.07e-03 | 9.59 | 9.59 | 0.216057 | 0.226504 | 2.25e-02 | 2.36e-02 | 10.97 | 10.86 | 9.74 | 9.43 | | chr7 | 86966688 | 86987238 | NM_008486 | 0.5105 | - | Anpep | protein_coding | 4.98e-23 | 7.70e-21 | -1.397004 | 13.39 | 13.39 | 0.037975 | 0.039811 | 2.84e-03 | 2.97e-03 | 12.00 | 12.00 | 0.059607 | 0.062490 | 4.97e-03 | 5.21e-03 | 13.42 | 13.37 | 12.04 | 11.96 | | chr10 | 126485301 | 126490062 | NM_010009 | 0.5325 | + | Cyp27b1 | nonsense_mediated_decay | 7.80e-23 | 1.19e-20 | -1.677657 | 10.42 | 10.42 | 0.319407 | 0.334852 | 3.06e-02 | 3.21e-02 | 8.75 | 8.75 | 0.290061 | 0.304087 | 3.31e-02 | 3.47e-02 | 10.20 | 10.65 | 8.96 | 8.55 | | chr11 | 61156901 | 61191577 | NM_026183 | 0.4683 | - | Slc47a1 | protein_coding | 1.50e-22 | 2.25e-20 | -1.246954 | 11.39 | 11.39 | 0.087771 | 0.092016 | 7.71e-03 | 8.08e-03 | 10.14 | 10.14 | 0.230678 | 0.241833 | 2.28e-02 | 2.39e-02 | 11.45 | 11.33 | 10.30 | 9.97 | | chr1 | 13615979 | 13650590 | NM_145381 | 0.4308 | - | Lactb2 | protein_coding | 2.36e-22 | 3.48e-20 | -1.202946 | 11.30 | 11.30 | 0.140486 | 0.147279 | 1.24e-02 | 1.30e-02 | 10.10 | 10.10 | 0.059370 | 0.062241 | 5.88e-03 | 6.16e-03 | 11.40 | 11.20 | 10.14 | 10.06 | | chr4 | 137297645 | 137352299 | NM_007431 | 0.5122 | - | Alpl | protein_coding | 5.54e-22 | 8.01e-20 | -1.401188 | 9.28 | 9.28 | 0.183892 | 0.192785 | 1.98e-02 | 2.08e-02 | 7.88 | 7.88 | 0.073361 | 0.076908 | 9.30e-03 | 9.75e-03 | 9.41 | 9.15 | 7.94 | 7.83 | | chr3 | 107094209 | 107115033 | NM_146136 | 0.3886 | + | Slc16a4 | protein_coding | 1.58e-21 | 2.25e-19 | -1.412724 | 9.28 | 9.28 | 0.203391 | 0.213226 | 2.19e-02 | 2.30e-02 | 7.88 | 7.88 | 0.086873 | 0.091074 | 1.10e-02 | 1.16e-02 | 9.42 | 9.13 | 7.94 | 7.81 | | chr7 | 126761341 | 126806029 | NM_054094 | 0.4148 | + | Acsm1 | protein_coding | 3.35e-21 | 4.70e-19 | -1.720314 | 9.21 | 9.21 | 0.386257 | 0.404935 | 4.19e-02 | 4.40e-02 | 7.52 | 7.52 | 0.022178 | 0.023250 | 2.95e-03 | 3.09e-03 | 9.49 | 8.94 | 7.54 | 7.51 | | chr9 | 76799504 | 76893588 | NM_012033 | 0.3738 | - | Tinag | protein_coding | 5.90e-21 | 8.16e-19 | -1.253512 | 9.82 | 9.82 | 0.150990 | 0.158292 | 1.54e-02 | 1.61e-02 | 8.57 | 8.57 | 0.139448 | 0.146192 | 1.63e-02 | 1.71e-02 | 9.93 | 9.71 | 8.67 | 8.47 | | chr18 | 84779900 | 84819487 | NM_177450 | 0.4458 | - | Cndp1 | protein_coding | 1.01e-20 | 1.38e-18 | -1.280291 | 9.14 | 9.14 | 0.059653 | 0.062538 | 6.53e-03 | 6.84e-03 | 7.86 | 7.86 | 0.043790 | 0.045907 | 5.57e-03 | 5.84e-03 | 9.10 | 9.18 | 7.83 | 7.89 | | chr11 | 73118489 | 73138139 | NM_023113 | 0.4068 | - | Aspa | protein_coding | 1.04e-20 | 1.40e-18 | -1.341308 | 10.93 | 10.93 | 0.057053 | 0.059812 | 5.22e-03 | 5.47e-03 | 9.57 | 9.57 | 0.296181 | 0.310504 | 3.09e-02 | 3.24e-02 | 10.97 | 10.89 | 9.78 | 9.36 | | chr19 | 12707797 | 12726227 | NM_145935 | 0.3965 | + | Glyat | protein_coding | 1.72e-20 | 2.25e-18 | -1.189854 | 9.60 | 9.60 | 0.053946 | 0.056555 | 5.62e-03 | 5.89e-03 | 8.41 | 8.41 | 0.116972 | 0.122629 | 1.39e-02 | 1.46e-02 | 9.64 | 9.56 | 8.49 | 8.33 | | chr7 | 51827814 | 51842216 | NM_008437 | 0.4781 | + | Napsa | protein_coding | 1.72e-20 | 2.25e-18 | -1.339220 | 10.91 | 10.91 | 0.210422 | 0.220597 | 1.93e-02 | 2.02e-02 | 9.57 | 9.57 | 0.190156 | 0.199351 | 1.99e-02 | 2.08e-02 | 11.06 | 10.76 | 9.71 | 9.44 | | chr8 | 62984920 | 63024474 | NM_011834 | 0.3988 | + | Aadat | protein_coding | 2.18e-20 | 2.81e-18 | -1.271106 | 11.97 | 11.97 | 0.288925 | 0.302896 | 2.41e-02 | 2.53e-02 | 10.71 | 10.71 | 0.099085 | 0.103877 | 9.25e-03 | 9.70e-03 | 12.17 | 11.77 | 10.64 | 10.78 | | chr5 | 151755181 | 151796392 | NM_013823 | 0.4437 | + | Kl | protein_coding | 3.00e-20 | 3.81e-18 | -1.119610 | 11.87 | 11.87 | 0.166456 | 0.174506 | 1.40e-02 | 1.47e-02 | 10.75 | 10.75 | 0.151782 | 0.159122 | 1.41e-02 | 1.48e-02 | 11.99 | 11.75 | 10.86 | 10.65 | | chr1 | 164759691 | 164796741 | NM_010231 | 0.4302 | - | Fmo1 | protein_coding | 3.40e-20 | 4.25e-18 | -1.311111 | 10.78 | 10.78 | 0.152595 | 0.159974 | 1.42e-02 | 1.48e-02 | 9.47 | 9.47 | 0.185730 | 0.194711 | 1.96e-02 | 2.06e-02 | 10.89 | 10.67 | 9.60 | 9.34 | | chr18 | 35774257 | 35786881 | NM_011397 | 0.4755 | - | Slc23a1 | protein_coding | 5.49e-20 | 6.78e-18 | -1.168221 | 10.53 | 10.53 | 0.033044 | 0.034642 | 3.14e-03 | 3.29e-03 | 9.36 | 9.36 | 0.139326 | 0.146063 | 1.49e-02 | 1.56e-02 | 10.56 | 10.51 | 9.46 | 9.26 | | chr6 | 55286292 | 55298549 | NM_007472 | 0.5305 | + | Aqp1 | protein_coding | 6.15e-20 | 7.50e-18 | -1.054427 | 11.39 | 11.39 | 0.021629 | 0.022675 | 1.90e-03 | 1.99e-03 | 10.33 | 10.33 | 0.159450 | 0.167160 | 1.54e-02 | 1.62e-02 | 11.41 | 11.38 | 10.45 | 10.22 | | chr17 | 73843090 | 74059791 | NM_027864 | 0.4549 | - | Galnt14 | sense_intronic | 8.81e-20 | 1.06e-17 | -1.070572 | 10.21 | 10.21 | 0.114666 | 0.120210 | 1.12e-02 | 1.18e-02 | 9.14 | 9.14 | 0.052419 | 0.054954 | 5.73e-03 | 6.01e-03 | 10.29 | 10.13 | 9.10 | 9.18 | | chr5 | 52755042 | 52760977 | NM_011435 | 0.5086 | + | Sod3 | protein_coding | 3.62e-19 | 4.29e-17 | -1.493593 | 10.03 | 10.03 | 0.350485 | 0.367433 | 3.49e-02 | 3.66e-02 | 8.56 | 8.56 | 0.132251 | 0.138646 | 1.54e-02 | 1.62e-02 | 10.28 | 9.79 | 8.65 | 8.47 | | chr7 | 142703138 | 142720337 | NM_178669 | 0.4591 | - | Clrn3 | protein_coding | 6.39e-19 | 7.49e-17 | -1.079520 | 10.31 | 10.31 | 0.107822 | 0.113036 | 1.05e-02 | 1.10e-02 | 9.23 | 9.23 | 0.156467 | 0.164033 | 1.70e-02 | 1.78e-02 | 10.38 | 10.23 | 9.34 | 9.12 | | chr17 | 43611277 | 43639722 | NM_008585 | 0.4155 | - | Mep1a | protein_coding | 8.04e-19 | 9.31e-17 | -1.337249 | 12.72 | 12.72 | 0.160017 | 0.167755 | 1.26e-02 | 1.32e-02 | 11.38 | 11.38 | 0.119704 | 0.125493 | 1.05e-02 | 1.10e-02 | 12.83 | 12.60 | 11.47 | 11.30 | | chr2 | 31325789 | 31376190 | NM_007494 | 0.5279 | + | Ass1 | protein_coding | 1.19e-18 | 1.36e-16 | -1.465058 | 11.81 | 11.81 | 0.260516 | 0.273114 | 2.21e-02 | 2.31e-02 | 10.34 | 10.34 | 0.372434 | 0.390443 | 3.60e-02 | 3.78e-02 | 12.00 | 11.63 | 10.60 | 10.07 | | chr5 | 87983674 | 87998031 | NM_016771 | 0.3344 | - | Sult1d1 | protein_coding | 1.37e-18 | 1.55e-16 | -1.038415 | 11.95 | 11.95 | 0.151275 | 0.158590 | 1.27e-02 | 1.33e-02 | 10.91 | 10.91 | 0.138843 | 0.145557 | 1.27e-02 | 1.33e-02 | 12.05 | 11.84 | 11.01 | 10.81 | | chr3 | 135488620 | 135551536 | NM_001135149 | 0.4153 | + | Slc39a8 | protein_coding | 3.53e-18 | 3.93e-16 | -1.076611 | 10.37 | 10.37 | 0.025399 | 0.026627 | 2.45e-03 | 2.57e-03 | 9.29 | 9.29 | 0.224719 | 0.235585 | 2.42e-02 | 2.54e-02 | 10.39 | 10.35 | 9.45 | 9.13 | | chr12 | 85714825 | 85749979 | NM_007647 | 0.4543 | - | Entpd5 | protein_coding | 4.46e-18 | 4.92e-16 | -0.939827 | 11.95 | 11.95 | 0.114239 | 0.119763 | 9.56e-03 | 1.00e-02 | 11.01 | 11.01 | 0.054729 | 0.057376 | 4.97e-03 | 5.21e-03 | 12.03 | 11.87 | 11.05 | 10.98 | | chr19 | 17400630 | 17431157 | NM_173442 | 0.4372 | - | Gcnt1 | protein_coding | 5.11e-18 | 5.57e-16 | -1.138974 | 11.60 | 11.60 | 0.277303 | 0.290712 | 2.39e-02 | 2.51e-02 | 10.48 | 10.48 | 0.053610 | 0.056202 | 5.12e-03 | 5.36e-03 | 11.80 | 11.41 | 10.44 | 10.52 | | chr15 | 89164903 | 89167438 | NM_019977 | 0.5599 | + | Miox | protein_coding | 5.59e-18 | 6.03e-16 | -2.588208 | 8.69 | 8.69 | 0.792385 | 0.830702 | 9.11e-02 | 9.55e-02 | 6.21 | 6.21 | 0.301415 | 0.315990 | 4.85e-02 | 5.09e-02 | 9.26 | 8.13 | 6.43 | 6.00 | | chr14 | 56983904 | 57007388 | NM_138652 | 0.4575 | + | Atp12a | protein_coding | 9.39e-18 | 1.00e-15 | 1.215949 | 8.09 | 8.09 | 0.078367 | 0.082157 | 9.68e-03 | 1.01e-02 | 9.30 | 9.30 | 0.187173 | 0.196225 | 2.01e-02 | 2.11e-02 | 8.15 | 8.04 | 9.43 | 9.17 | | chr16 | 38396202 | 38433225 | NM_134102 | 0.4527 | - | Pla1a | protein_coding | 9.72e-18 | 1.02e-15 | -1.345511 | 9.16 | 9.16 | 0.083943 | 0.088003 | 9.17e-03 | 9.61e-03 | 7.79 | 7.79 | 0.361112 | 0.378574 | 4.63e-02 | 4.86e-02 | 9.22 | 9.10 | 8.05 | 7.54 | | chr9 | 15087780 | 15110611 | NM_001199485 | 0.4231 | - | 4931406C07Rik | protein_coding | 1.39e-17 | 1.44e-15 | -1.220013 | 12.38 | 12.38 | 0.102233 | 0.107176 | 8.26e-03 | 8.65e-03 | 11.16 | 11.16 | 0.135567 | 0.142122 | 1.21e-02 | 1.27e-02 | 12.46 | 12.31 | 11.26 | 11.07 | | chr3 | 96633987 | 96674849 | NM_021517 | 0.4714 | + | Pdzk1 | protein_coding | 1.46e-17 | 1.50e-15 | -1.320207 | 12.91 | 12.91 | 0.187562 | 0.196632 | 1.45e-02 | 1.52e-02 | 11.60 | 11.60 | 0.170281 | 0.178515 | 1.47e-02 | 1.54e-02 | 13.05 | 12.78 | 11.72 | 11.47 | | chr2 | 69262391 | 69424124 | NM_001081088 | 0.4252 | - | Lrp2 | protein_coding | 2.11e-17 | 2.12e-15 | -1.407789 | 14.16 | 14.16 | 0.242244 | 0.253958 | 1.71e-02 | 1.79e-02 | 12.76 | 12.76 | 0.090207 | 0.094569 | 7.07e-03 | 7.41e-03 | 14.33 | 13.99 | 12.83 | 12.70 | | chr2 | 163372890 | 163398643 | NM_008261 | 0.4997 | + | Hnf4a | protein_coding | 2.11e-17 | 2.12e-15 | -1.042408 | 11.81 | 11.81 | 0.189674 | 0.198846 | 1.61e-02 | 1.68e-02 | 10.77 | 10.77 | 0.134662 | 0.141173 | 1.25e-02 | 1.31e-02 | 11.95 | 11.68 | 10.87 | 10.68 | | chr7 | 126606221 | 126622776 | NM_009470 | 0.4496 | - | Umod | protein_coding | 2.26e-17 | 2.25e-15 | -1.303567 | 10.03 | 10.03 | 0.307874 | 0.322762 | 3.07e-02 | 3.22e-02 | 8.74 | 8.74 | 0.057219 | 0.059986 | 6.55e-03 | 6.86e-03 | 10.24 | 9.81 | 8.70 | 8.78 | | chr10 | 75036239 | 75048936 | NM_008116 | 0.5072 | + | Ggt1 | protein_coding | 2.85e-17 | 2.81e-15 | -1.255690 | 12.63 | 12.63 | 0.069118 | 0.072460 | 5.47e-03 | 5.74e-03 | 11.37 | 11.37 | 0.181142 | 0.189902 | 1.59e-02 | 1.67e-02 | 12.68 | 12.58 | 11.50 | 11.24 | | chr14 | 32420411 | 32454151 | NM_019975 | 0.4312 | - | Hacl1 | protein_coding | 3.06e-17 | 2.99e-15 | -0.935578 | 10.34 | 10.34 | 0.014202 | 0.014888 | 1.37e-03 | 1.44e-03 | 9.40 | 9.40 | 0.086005 | 0.090164 | 9.15e-03 | 9.59e-03 | 10.33 | 10.35 | 9.46 | 9.34 | | chr9 | 106055190 | 106060469 | NM_001039586 | 0.5511 | - | Glyctk | protein_coding | 4.08e-17 | 3.94e-15 | -1.228233 | 9.17 | 9.17 | 0.185670 | 0.194648 | 2.02e-02 | 2.12e-02 | 7.95 | 7.95 | 0.103132 | 0.108119 | 1.30e-02 | 1.36e-02 | 9.30 | 9.04 | 8.02 | 7.88 | | chrX | 82947275 | 83022158 | NM_212444 | 0.3885 | - | Gk | protein_coding | 5.84e-17 | 5.58e-15 | -0.883534 | 12.11 | 12.11 | 0.041672 | 0.043687 | 3.44e-03 | 3.61e-03 | 11.23 | 11.23 | 0.026752 | 0.028046 | 2.38e-03 | 2.50e-03 | 12.14 | 12.08 | 11.25 | 11.21 | | chr5 | 114453743 | 114475684 | NM_010018 | 0.4896 | + | Dao | protein_coding | 6.34e-17 | 5.99e-15 | -0.967225 | 10.09 | 10.09 | 0.065596 | 0.068768 | 6.50e-03 | 6.82e-03 | 9.12 | 9.12 | 0.053078 | 0.055644 | 5.82e-03 | 6.10e-03 | 10.13 | 10.04 | 9.08 | 9.16 | | chr6 | 72305476 | 72309756 | NM_144916 | 0.5573 | + | Tmem150a | protein_coding | 1.19e-16 | 1.12e-14 | -1.009597 | 9.82 | 9.82 | 0.011260 | 0.011804 | 1.15e-03 | 1.20e-03 | 8.81 | 8.81 | 0.133795 | 0.140264 | 1.52e-02 | 1.59e-02 | 9.82 | 9.83 | 8.91 | 8.72 | | chr3 | 59835709 | 59844079 | NM_023383 | 0.3578 | + | Aadac | protein_coding | 1.30e-16 | 1.21e-14 | -1.322480 | 9.36 | 9.36 | 0.009345 | 0.009797 | 9.99e-04 | 1.05e-03 | 8.01 | 8.01 | 0.405541 | 0.425152 | 5.06e-02 | 5.31e-02 | 9.35 | 9.36 | 8.29 | 7.72 | | chr2 | 172978573 | 172984754 | NM_011044 | 0.5163 | + | Pck1 | protein_coding | 2.07e-16 | 1.90e-14 | -1.230500 | 10.42 | 10.42 | 0.043226 | 0.045317 | 4.15e-03 | 4.35e-03 | 9.16 | 9.16 | 0.381704 | 0.400161 | 4.16e-02 | 4.37e-02 | 10.39 | 10.45 | 9.43 | 8.89 | | chr19 | 42120340 | 42145429 | NM_026152 | 0.4664 | + | Hoga1 | protein_coding | 2.94e-16 | 2.67e-14 | -0.978996 | 11.09 | 11.09 | 0.122583 | 0.128510 | 1.11e-02 | 1.16e-02 | 10.11 | 10.11 | 0.040516 | 0.042476 | 4.01e-03 | 4.20e-03 | 11.18 | 11.00 | 10.08 | 10.14 | | chr5 | 90947974 | 90982570 | NM_145146 | 0.4143 | + | Afm | protein_coding | 3.76e-16 | 3.38e-14 | -1.077537 | 9.74 | 9.74 | 0.182953 | 0.191800 | 1.88e-02 | 1.97e-02 | 8.67 | 8.67 | 0.012487 | 0.013090 | 1.44e-03 | 1.51e-03 | 9.87 | 9.61 | 8.68 | 8.67 | | chr4 | 139178808 | 139205606 | NM_175438 | 0.5286 | + | Aldh4a1 | protein_coding | 1.15e-15 | 1.02e-13 | -0.891143 | 11.79 | 11.79 | 0.119240 | 0.125006 | 1.01e-02 | 1.06e-02 | 10.90 | 10.90 | 0.101192 | 0.106085 | 9.28e-03 | 9.73e-03 | 11.88 | 11.71 | 10.97 | 10.83 | | chr2 | 12845667 | 12925081 | NM_008961 | 0.4008 | + | Pter | protein_coding | 1.44e-15 | 1.27e-13 | -1.059811 | 10.84 | 10.84 | 0.155363 | 0.162876 | 1.43e-02 | 1.50e-02 | 9.78 | 9.78 | 0.157793 | 0.165423 | 1.61e-02 | 1.69e-02 | 10.95 | 10.73 | 9.89 | 9.67 | | chr18 | 43887722 | 43896891 | NM_009258 | 0.3966 | - | Spink1 | protein_coding | 1.47e-15 | 1.29e-13 | -1.112841 | 9.32 | 9.32 | 0.019158 | 0.020085 | 2.06e-03 | 2.16e-03 | 8.20 | 8.20 | 0.228413 | 0.239458 | 2.79e-02 | 2.92e-02 | 9.33 | 9.31 | 8.36 | 8.04 | | chr16 | 36750249 | 36785048 | NM_021301 | 0.4114 | - | Slc15a2 | protein_coding | 1.53e-15 | 1.33e-13 | -1.001664 | 11.75 | 11.75 | 0.195101 | 0.204535 | 1.66e-02 | 1.74e-02 | 10.76 | 10.76 | 0.160897 | 0.168677 | 1.50e-02 | 1.57e-02 | 11.89 | 11.62 | 10.64 | 10.87 | | chr4 | 49548864 | 49562418 | NM_144903 | 0.4257 | - | Aldob | protein_coding | 1.77e-15 | 1.52e-13 | -1.321179 | 13.66 | 13.66 | 0.142811 | 0.149717 | 1.05e-02 | 1.10e-02 | 12.33 | 12.33 | 0.249234 | 0.261286 | 2.02e-02 | 2.12e-02 | 13.76 | 13.56 | 12.51 | 12.16 | | chr8 | 56040080 | 56146231 | NM_153581 | 0.3520 | + | Gpm6a | protein_coding | 2.40e-15 | 2.04e-13 | -1.178103 | 9.92 | 9.92 | 0.252653 | 0.264870 | 2.55e-02 | 2.67e-02 | 8.75 | 8.75 | 0.189900 | 0.199082 | 2.17e-02 | 2.28e-02 | 10.10 | 9.74 | 8.88 | 8.61 | | chr6 | 90500841 | 90549165 | NM_027406 | 0.5013 | + | Aldh1l1 | protein_coding | 2.47e-15 | 2.08e-13 | -1.245416 | 9.90 | 9.90 | 0.334416 | 0.350587 | 3.38e-02 | 3.54e-02 | 8.68 | 8.68 | 0.072275 | 0.075769 | 8.33e-03 | 8.73e-03 | 10.14 | 9.67 | 8.73 | 8.63 | | chr15 | 79088624 | 79115939 | NM_177580 | 0.5200 | - | Baiap2l2 | protein_coding | 2.67e-15 | 2.23e-13 | -0.935028 | 10.89 | 10.89 | 0.038115 | 0.039959 | 3.50e-03 | 3.67e-03 | 9.96 | 9.96 | 0.099580 | 0.104395 | 1.00e-02 | 1.05e-02 | 10.86 | 10.92 | 10.03 | 9.89 | | chr1 | 74455957 | 74482134 | NM_009509 | 0.4954 | + | Vil1 | protein_coding | 3.43e-15 | 2.84e-13 | -1.069550 | 9.88 | 9.88 | 0.128428 | 0.134638 | 1.30e-02 | 1.36e-02 | 8.81 | 8.81 | 0.224588 | 0.235448 | 2.55e-02 | 2.67e-02 | 9.97 | 9.79 | 8.97 | 8.65 | | chr9 | 44601861 | 44607299 | NM_027865 | 0.5216 | - | Tmem25 | protein_coding | 3.75e-15 | 3.07e-13 | -0.870591 | 10.16 | 10.16 | 0.020466 | 0.021455 | 2.01e-03 | 2.11e-03 | 9.29 | 9.29 | 0.040648 | 0.042614 | 4.37e-03 | 4.59e-03 | 10.18 | 10.15 | 9.26 | 9.32 | | chr15 | 54670455 | 54751701 | NM_015744 | 0.4043 | - | Enpp2 | protein_coding | 5.81e-15 | 4.72e-13 | -0.922991 | 12.17 | 12.17 | 0.172696 | 0.181047 | 1.42e-02 | 1.49e-02 | 11.25 | 11.25 | 0.008782 | 0.009206 | 7.80e-04 | 8.18e-04 | 12.29 | 12.05 | 11.25 | 11.26 | | chr10 | 51765731 | 51915050 | NM_011282 | 0.4046 | - | Ros1 | protein_coding | 6.28e-15 | 5.06e-13 | -1.015042 | 9.68 | 9.68 | 0.073387 | 0.076936 | 7.58e-03 | 7.95e-03 | 8.66 | 8.66 | 0.168523 | 0.176672 | 1.95e-02 | 2.04e-02 | 9.73 | 9.63 | 8.54 | 8.78 | | chr15 | 10288333 | 10339493 | NM_001031851 | 0.4084 | + | Agxt2 | protein_coding | 7.07e-15 | 5.64e-13 | -1.127904 | 9.48 | 9.48 | 0.204712 | 0.214611 | 2.16e-02 | 2.26e-02 | 8.36 | 8.36 | 0.148646 | 0.155834 | 1.78e-02 | 1.86e-02 | 9.63 | 9.34 | 8.47 | 8.26 | | chr9 | 32201569 | 32206779 | NM_001168354 | 0.4419 | + | Kcnj1 | protein_coding | 1.10e-14 | 8.68e-13 | -0.950484 | 10.21 | 10.21 | 0.177977 | 0.186584 | 1.74e-02 | 1.83e-02 | 9.27 | 9.27 | 0.046378 | 0.048621 | 5.00e-03 | 5.25e-03 | 10.34 | 10.08 | 9.30 | 9.23 | | chr9 | 78178826 | 78194952 | NM_008182 | 0.4604 | - | Gsta2 | protein_coding | 1.22e-14 | 9.60e-13 | -1.096463 | 11.17 | 11.17 | 0.079887 | 0.083750 | 7.15e-03 | 7.50e-03 | 10.07 | 10.07 | 0.284681 | 0.298448 | 2.83e-02 | 2.97e-02 | 11.23 | 11.12 | 10.27 | 9.86 | | chr19 | 12770279 | 12794386 | NM_029550 | 0.3814 | + | Keg1 | protein_coding | 2.49e-14 | 1.94e-12 | -0.935776 | 11.38 | 11.38 | 0.220021 | 0.230660 | 1.93e-02 | 2.03e-02 | 10.45 | 10.45 | 0.068423 | 0.071732 | 6.55e-03 | 6.86e-03 | 11.54 | 11.22 | 10.50 | 10.40 | | chr9 | 45214159 | 45218361 | NM_007503 | 0.5353 | + | Fxyd2 | protein_coding | 3.08e-14 | 2.38e-12 | -1.109408 | 12.31 | 12.31 | 0.054624 | 0.057265 | 4.44e-03 | 4.65e-03 | 11.19 | 11.19 | 0.199420 | 0.209063 | 1.78e-02 | 1.87e-02 | 12.27 | 12.35 | 11.34 | 11.05 | | chr10 | 39721378 | 39745074 | NM_144821 | 0.4511 | - | Mfsd4b1 | protein_coding | 3.13e-14 | 2.39e-12 | -0.968501 | 9.55 | 9.55 | 0.107770 | 0.112982 | 1.13e-02 | 1.18e-02 | 8.58 | 8.58 | 0.058614 | 0.061449 | 6.83e-03 | 7.16e-03 | 9.62 | 9.47 | 8.62 | 8.54 | | chr11 | 105829258 | 105851278 | NM_207624 | 0.5261 | + | Ace | protein_coding | 5.01e-14 | 3.80e-12 | -1.283430 | 10.93 | 10.93 | 0.394215 | 0.413278 | 3.61e-02 | 3.78e-02 | 9.67 | 9.67 | 0.101161 | 0.106053 | 1.05e-02 | 1.10e-02 | 11.21 | 10.65 | 9.74 | 9.60 | | chr5 | 87553971 | 87569365 | NM_009467 | 0.3576 | - | Ugt2b5 | protein_coding | 5.28e-14 | 3.98e-12 | -0.988720 | 9.32 | 9.32 | 0.057578 | 0.060362 | 6.18e-03 | 6.48e-03 | 8.33 | 8.33 | 0.107817 | 0.113030 | 1.29e-02 | 1.36e-02 | 9.36 | 9.28 | 8.25 | 8.41 | | chr1 | 20047859 | 20608138 | NM_153179 | 0.3968 | - | Pkhd1 | protein_coding | 7.40e-14 | 5.53e-12 | -0.977860 | 11.28 | 11.28 | 0.167085 | 0.175164 | 1.48e-02 | 1.55e-02 | 10.30 | 10.30 | 0.160001 | 0.167738 | 1.55e-02 | 1.63e-02 | 11.40 | 11.16 | 10.19 | 10.41 | | chr4 | 104702254 | 104782503 | NM_178143 | 0.4056 | - | Prkaa2 | protein_coding | 8.52e-14 | 6.32e-12 | -1.004155 | 10.44 | 10.44 | 0.110035 | 0.115356 | 1.05e-02 | 1.10e-02 | 9.44 | 9.44 | 0.163394 | 0.171296 | 1.73e-02 | 1.82e-02 | 10.52 | 10.36 | 9.32 | 9.55 | | chr12 | 85771670 | 85791974 | NM_134042 | 0.4184 | - | Aldh6a1 | protein_coding | 9.19e-14 | 6.76e-12 | -0.842402 | 12.10 | 12.10 | 0.127160 | 0.133309 | 1.05e-02 | 1.10e-02 | 11.26 | 11.26 | 0.068575 | 0.071891 | 6.09e-03 | 6.38e-03 | 12.19 | 12.01 | 11.31 | 11.21 | | chr9 | 66561492 | 66614652 | NM_178396 | 0.4667 | + | Car12 | protein_coding | 1.40e-13 | 1.02e-11 | -0.830361 | 11.71 | 11.71 | 0.161298 | 0.169098 | 1.38e-02 | 1.44e-02 | 10.88 | 10.88 | 0.029697 | 0.031133 | 2.73e-03 | 2.86e-03 | 11.82 | 11.60 | 10.86 | 10.90 | | chr11 | 3817082 | 3832081 | NM_001130458 | 0.4971 | - | Tcn2 | protein_coding | 1.73e-13 | 1.25e-11 | -0.860755 | 12.04 | 12.04 | 0.137193 | 0.143827 | 1.14e-02 | 1.19e-02 | 11.18 | 11.18 | 0.130690 | 0.137009 | 1.17e-02 | 1.23e-02 | 12.14 | 11.94 | 11.27 | 11.09 | | chr5 | 5664828 | 5694089 | NM_001103156 | 0.4136 | - | Steap2 | protein_coding | 1.90e-13 | 1.36e-11 | -0.850622 | 11.07 | 11.07 | 0.069430 | 0.072788 | 6.27e-03 | 6.58e-03 | 10.22 | 10.22 | 0.053997 | 0.056608 | 5.29e-03 | 5.54e-03 | 11.12 | 11.02 | 10.26 | 10.18 | | chrX | 98572573 | 98580968 | NM_008124 | 0.4943 | + | Gjb1 | protein_coding | 2.45e-13 | 1.75e-11 | -1.072792 | 9.43 | 9.43 | 0.207095 | 0.217109 | 2.20e-02 | 2.30e-02 | 8.36 | 8.36 | 0.164444 | 0.172396 | 1.97e-02 | 2.06e-02 | 9.57 | 9.28 | 8.48 | 8.24 | | chr7 | 91733669 | 91754452 | NM_010176 | 0.4771 | - | Fah | protein_coding | 2.62e-13 | 1.85e-11 | -1.169260 | 9.65 | 9.65 | 0.336378 | 0.352644 | 3.49e-02 | 3.65e-02 | 8.50 | 8.50 | 0.047850 | 0.050164 | 5.63e-03 | 5.90e-03 | 9.89 | 9.41 | 8.54 | 8.47 | | chr3 | 27081925 | 27143833 | NM_178772 | 0.4613 | + | Nceh1 | protein_coding | 3.02e-13 | 2.12e-11 | -0.944907 | 10.54 | 10.54 | 0.117813 | 0.123510 | 1.12e-02 | 1.17e-02 | 9.60 | 9.60 | 0.055299 | 0.057973 | 5.76e-03 | 6.04e-03 | 10.62 | 10.46 | 9.64 | 9.56 | | chr4 | 101091893 | 101140376 | NM_001177602 | 0.4646 | + | Ak4 | protein_coding | 3.10e-13 | 2.16e-11 | -1.067487 | 10.61 | 10.61 | 0.069752 | 0.073125 | 6.57e-03 | 6.89e-03 | 9.53 | 9.53 | 0.267648 | 0.280591 | 2.81e-02 | 2.94e-02 | 10.66 | 10.56 | 9.72 | 9.34 | | chr19 | 28909655 | 28988450 | NM_009199 | 0.4425 | + | Slc1a1 | protein_coding | 3.62e-13 | 2.50e-11 | -1.149091 | 9.10 | 9.10 | 0.230554 | 0.241703 | 2.53e-02 | 2.66e-02 | 7.95 | 7.95 | 0.247017 | 0.258961 | 3.11e-02 | 3.26e-02 | 9.26 | 8.93 | 8.12 | 7.77 | | chr7 | 109006844 | 109019302 | NM_008034 | 0.4634 | - | Folr1 | protein_coding | 4.13e-13 | 2.83e-11 | -1.079241 | 10.66 | 10.66 | 0.109078 | 0.114353 | 1.02e-02 | 1.07e-02 | 9.57 | 9.57 | 0.267530 | 0.280467 | 2.80e-02 | 2.93e-02 | 10.74 | 10.58 | 9.76 | 9.38 | | chr15 | 34413776 | 34425001 | NM_008287 | 0.4074 | - | Rida | protein_coding | 6.49e-13 | 4.42e-11 | -0.818344 | 11.56 | 11.56 | 0.029434 | 0.030857 | 2.55e-03 | 2.67e-03 | 10.73 | 10.73 | 0.193212 | 0.202555 | 1.80e-02 | 1.89e-02 | 11.58 | 11.54 | 10.87 | 10.60 | | chr10 | 87935557 | 87966715 | NM_001146690 | 0.4049 | - | Chpt1 | protein_coding | 8.89e-13 | 6.01e-11 | -0.726099 | 11.87 | 11.87 | 0.019323 | 0.020257 | 1.63e-03 | 1.71e-03 | 11.15 | 11.15 | 0.000450 | 0.000472 | 4.04e-05 | 4.23e-05 | 11.89 | 11.86 | 11.15 | 11.15 | | chr3 | 125568260 | 125641468 | NM_011674 | 0.3786 | - | Ugt8a | protein_coding | 1.28e-12 | 8.60e-11 | -0.966421 | 9.31 | 9.31 | 0.160225 | 0.167973 | 1.72e-02 | 1.80e-02 | 8.35 | 8.35 | 0.037441 | 0.039251 | 4.48e-03 | 4.70e-03 | 9.43 | 9.20 | 8.38 | 8.33 | | chr7 | 53450720 | 53493860 | NM_153677 | 0.5146 | - | Ush1c | protein_coding | 1.65e-12 | 1.10e-10 | -0.960708 | 10.53 | 10.53 | 0.138887 | 0.145603 | 1.32e-02 | 1.38e-02 | 9.57 | 9.57 | 0.128354 | 0.134561 | 1.34e-02 | 1.41e-02 | 10.63 | 10.44 | 9.48 | 9.67 | | chr10 | 127832987 | 127837573 | NM_028092 | 0.5598 | - | Slc39a5 | protein_coding | 1.75e-12 | 1.16e-10 | -0.853753 | 9.94 | 9.94 | 0.057239 | 0.060006 | 5.76e-03 | 6.04e-03 | 9.08 | 9.08 | 0.120377 | 0.126198 | 1.33e-02 | 1.39e-02 | 9.98 | 9.90 | 9.17 | 9.00 | | chr1 | 90108533 | 90116577 | NM_201645 | 0.4326 | + | Ugt1a1 | protein_coding | 2.24e-12 | 1.47e-10 | -0.854093 | 11.52 | 11.52 | 0.012483 | 0.013087 | 1.08e-03 | 1.14e-03 | 10.66 | 10.66 | 0.248105 | 0.260102 | 2.33e-02 | 2.44e-02 | 11.53 | 11.51 | 10.83 | 10.48 | | chr13 | 47118911 | 47138586 | NM_016785 | 0.4348 | - | Tpmt | protein_coding | 2.41e-12 | 1.57e-10 | -0.847219 | 9.86 | 9.86 | 0.018698 | 0.019603 | 1.90e-03 | 1.99e-03 | 9.01 | 9.01 | 0.043501 | 0.045604 | 4.83e-03 | 5.06e-03 | 9.84 | 9.87 | 8.98 | 9.04 | | chr13 | 41277750 | 41315772 | NM_019423 | 0.4498 | - | Elovl2 | protein_coding | 3.24e-12 | 2.10e-10 | -0.869852 | 9.74 | 9.74 | 0.140357 | 0.147144 | 1.44e-02 | 1.51e-02 | 8.88 | 8.88 | 0.015178 | 0.015912 | 1.71e-03 | 1.79e-03 | 9.84 | 9.64 | 8.87 | 8.89 |
Download the DEG result list for WT_vs_HET.Download the whole result list for WT_vs_HET.Download the raw read counts table for the experiment.Download the normalized read counts table for the experiment.
References
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