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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 (25558 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 (4222 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 (11266 genes with cutoff value 6 normalized read counts), iv) genes whose biotype matched the following: rRNA, TR_V_pseudogene, TR_J_pseudogene, IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene (90 genes). The total number of genes excluded due to the application of gene filters was 4313. The total (unified) number of genes excluded due to the application of all filters was 38425. The resulting gene counts table was subjected to differential expression analysis for the contrasts Wt versus C_221_222, Wt versus Tg197, Tg197_C versus Tg197, Tg197_C versus C_221_222 using the Bioconductor package DESeq. The final numbers of differentially expressed genes were (per contrast): for the contrast Wt versus C_221_222, 178 (13) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 51 (0) were up-regulated, 112 (13) were down-regulated and 15 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log2 scale, for the contrast Wt versus Tg197, 550 (58) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 242 (34) were up-regulated, 250 (24) were down-regulated and 58 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log2 scale, for the contrast Tg197_C versus Tg197, 686 (20) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 225 (7) were up-regulated, 238 (13) were down-regulated and 223 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log2 scale, for the contrast Tg197_C versus C_221_222, 1081 (255) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 458 (102) were up-regulated, 456 (153) were down-regulated and 167 (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, C_221_222, Tg197, Tg197_C
Samples included: GK3R188-Wt1, GK3R189-Wt2, GK3R190-C1, GK3R191-C2, GK3R192-C3, GK3R193-Tg197-1, GK3R194-Tg197-2, GK3R195-Tg197-3, GK3R196-Tg197-C1, GK3R197-Tg197-C2, GK3R198-Tg197-C3
Samples excluded:
none
Requested contrasts: Wt_vs_C_221_222, Wt_vs_Tg197, Tg197_C_vs_Tg197, Tg197_C_vs_C_221_222
Library sizes:
- GK3R188-Wt1: 1825168
- GK3R189-Wt2: 5240467
- GK3R190-C1: 4965142
- GK3R191-C2: 5035527
- GK3R192-C3: 6160469
- GK3R193-Tg197-1: 6274376
- GK3R194-Tg197-2: 6842798
- GK3R195-Tg197-3: 6957832
- GK3R196-Tg197-C1: 6105555
- GK3R197-Tg197-C2: 1620166
- GK3R198-Tg197-C3: 4428560
Annotation: download
Organism: mouse ( Mus musculus), genome version alias mm10
Annotation source: Ensembl genomes
Count type: utr
3' UTR flanking :: 500
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
- lincRNA: FALSE
- protein_coding: FALSE
- antisense: FALSE
- processed_transcript: FALSE
- snRNA: FALSE
- sense_intronic: FALSE
- miRNA: FALSE
- misc_RNA: FALSE
- snoRNA: FALSE
- rRNA: TRUE
- polymorphic_pseudogene: FALSE
- sense_overlapping: FALSE
- three_prime_overlapping_ncrna: FALSE
- TR_V_gene: FALSE
- TR_V_pseudogene: TRUE
- TR_D_gene: FALSE
- TR_J_gene: FALSE
- TR_C_gene: FALSE
- TR_J_pseudogene: TRUE
- IG_C_gene: FALSE
- IG_C_pseudogene: TRUE
- IG_J_gene: FALSE
- IG_J_pseudogene: TRUE
- IG_D_gene: FALSE
- IG_V_gene: FALSE
- IG_V_pseudogene: TRUE
Filter application: after normalization
Normalization algorithm: DESeq
Normalization arguments:
locfunc - [[list(locfunc = function (x, na.rm = FALSE, ...)
standardGeneric("median"))locfunc
Statistical algorithm(s): DESeq
Statistical arguments for DESeq: method, sharingMode, fitType - method: blind
- sharingMode: fit-only
- fitType: local
Meta-analysis method: no meta-analysis, reported p-values from the first supplied statistical algorithm
Multiple testing correction: Benjamini-Hochberg FDR
p-value threshold: 0.05
Logarithmic tranformation offset: 1
Analysis preset: not available
Quality control plots: multidimensional scaling, biotype detection, biotype counts, sample and biotype saturation, filtered biotypes, correlation heatmap and correlogram, pairwise scatterplots between samples, boxplots, GC-content bias, transcript length bias, DEG biotype detection, volcano plot, DEG heatmap
Figure format: png, pdf
Output directory: /data/images/proton2/run403/www/metaseqr_GKlab_run403
Output data: Annotation, p-value, Adjusted p-value (FDR), Fold change, Read counts
Output scale(s): log2 scale, Reads per Gene Model
Output values: Normalized values
Output statistics: Mean, Median, Standard deviation, Median Absolute Deviation (MAD), Coefficient of Variation, Robust Coefficient of Variation
Total run time: 33 minutes 18 seconds
Filtered genes
Number of filtered genes: 38425 which is the union of
- Filtered because of zero reads: 25558
-
Filtered because of exon filters: 0
-
Filtered because of gene filters: 12867
which is the union of
- length: 4222 genes with filter cutoff value 500
- avg.reads: 0 genes with filter cutoff value 0
- expression: 11266 genes further decomposed to (filter name, filtered genes, filter cutoff):
- median: 11266 genes with filter cutoff value 6
- biotype: 90 genes with filter cutoff value rRNA, TR_V_pseudogene, TR_J_pseudogene, IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene
Differentially expressed genes
Number of differentially expressed genes per contrast:
- Wt_vs_C_221_222: 178 (13) statistically significant genes of which 51 (0) up regulated, 112 (13) down regulated and 15 (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_vs_Tg197: 550 (58) statistically significant genes of which 242 (34) up regulated, 250 (24) down regulated and 58 (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.
- Tg197_C_vs_Tg197: 686 (20) statistically significant genes of which 225 (7) up regulated, 238 (13) down regulated and 223 (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.
- Tg197_C_vs_C_221_222: 1081 (255) statistically significant genes of which 458 (102) up regulated, 456 (153) down regulated and 167 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log2 scale.
Run log[ 2018-06-14 11:40:07 ] INFO 2018-06-14 11:40:07: Data processing started... [ 2018-06-14 11:40:07 ] INFO Read counts file: imported sam/bam/bed files [ 2018-06-14 11:40:07 ] INFO Conditions: Wt, C_221_222, Tg197, Tg197_C [ 2018-06-14 11:40:07 ] INFO Samples to include: GK3R188-Wt1, GK3R189-Wt2, GK3R190-C1, GK3R191-C2, GK3R192-C3, GK3R193-Tg197-1, GK3R194-Tg197-2, GK3R195-Tg197-3, GK3R196-Tg197-C1, GK3R197-Tg197-C2, GK3R198-Tg197-C3 [ 2018-06-14 11:40:07 ] INFO Samples to exclude: none [ 2018-06-14 11:40:07 ] INFO Requested contrasts: Wt_vs_C_221_222, Wt_vs_Tg197, Tg197_C_vs_Tg197, Tg197_C_vs_C_221_222 [ 2018-06-14 11:40:07 ] INFO Annotation: download [ 2018-06-14 11:40:07 ] INFO Organism: mm10 [ 2018-06-14 11:40:07 ] INFO Reference source: ensembl [ 2018-06-14 11:40:07 ] INFO Count type: utr [ 2018-06-14 11:40:07 ] INFO Exon filters: none applied [ 2018-06-14 11:40:07 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2018-06-14 11:40:07 ] INFO length: [ 2018-06-14 11:40:07 ] INFO length: 500 [ 2018-06-14 11:40:07 ] INFO avg.reads: [ 2018-06-14 11:40:07 ] INFO average.per.bp: 100 [ 2018-06-14 11:40:07 ] INFO quantile: 0.25 [ 2018-06-14 11:40:07 ] INFO expression: [ 2018-06-14 11:40:07 ] INFO median: TRUE [ 2018-06-14 11:40:07 ] INFO mean: FALSE [ 2018-06-14 11:40:07 ] INFO quantile: NA [ 2018-06-14 11:40:07 ] INFO known: NA [ 2018-06-14 11:40:07 ] INFO custom: NA [ 2018-06-14 11:40:07 ] INFO biotype: [ 2018-06-14 11:40:07 ] INFO pseudogene: FALSE [ 2018-06-14 11:40:07 ] INFO lincRNA: FALSE [ 2018-06-14 11:40:07 ] INFO protein_coding: FALSE [ 2018-06-14 11:40:07 ] INFO antisense: FALSE [ 2018-06-14 11:40:07 ] INFO processed_transcript: FALSE [ 2018-06-14 11:40:07 ] INFO snRNA: FALSE [ 2018-06-14 11:40:07 ] INFO sense_intronic: FALSE [ 2018-06-14 11:40:07 ] INFO miRNA: FALSE [ 2018-06-14 11:40:07 ] INFO misc_RNA: FALSE [ 2018-06-14 11:40:07 ] INFO snoRNA: FALSE [ 2018-06-14 11:40:07 ] INFO rRNA: TRUE [ 2018-06-14 11:40:07 ] INFO polymorphic_pseudogene: FALSE [ 2018-06-14 11:40:07 ] INFO sense_overlapping: FALSE [ 2018-06-14 11:40:07 ] INFO three_prime_overlapping_ncrna: FALSE [ 2018-06-14 11:40:07 ] INFO TR_V_gene: FALSE [ 2018-06-14 11:40:07 ] INFO TR_V_pseudogene: TRUE [ 2018-06-14 11:40:07 ] INFO TR_D_gene: FALSE [ 2018-06-14 11:40:07 ] INFO TR_J_gene: FALSE [ 2018-06-14 11:40:07 ] INFO TR_C_gene: FALSE [ 2018-06-14 11:40:07 ] INFO TR_J_pseudogene: TRUE [ 2018-06-14 11:40:07 ] INFO IG_C_gene: FALSE [ 2018-06-14 11:40:07 ] INFO IG_C_pseudogene: TRUE [ 2018-06-14 11:40:07 ] INFO IG_J_gene: FALSE [ 2018-06-14 11:40:07 ] INFO IG_J_pseudogene: TRUE [ 2018-06-14 11:40:07 ] INFO IG_D_gene: FALSE [ 2018-06-14 11:40:07 ] INFO IG_V_gene: FALSE [ 2018-06-14 11:40:07 ] INFO IG_V_pseudogene: TRUE [ 2018-06-14 11:40:07 ] INFO Filter application: postnorm [ 2018-06-14 11:40:07 ] INFO Normalization algorithm: deseq [ 2018-06-14 11:40:07 ] INFO Normalization arguments: [ 2018-06-14 11:40:07 ] INFO locfunc: [ 2018-06-14 11:40:07 ] INFO [[ [ 2018-06-14 11:40:07 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2018-06-14 11:40:07 ] INFO locfunc [ 2018-06-14 11:40:07 ] INFO Statistical algorithm: deseq [ 2018-06-14 11:40:07 ] INFO Statistical arguments: [ 2018-06-14 11:40:07 ] INFO deseq: blind, fit-only, local [ 2018-06-14 11:40:07 ] INFO Meta-analysis method: none [ 2018-06-14 11:40:07 ] INFO Multiple testing correction: BH [ 2018-06-14 11:40:07 ] INFO p-value threshold: 0.05 [ 2018-06-14 11:40:07 ] INFO Logarithmic transformation offset: 1 [ 2018-06-14 11:40:07 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2018-06-14 11:40:07 ] INFO Figure format: png, pdf [ 2018-06-14 11:40:07 ] INFO Output directory: /data/images/proton2/run403/www/metaseqr_GKlab_run403 [ 2018-06-14 11:40:07 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2018-06-14 11:40:07 ] INFO Output scale(s): log2, rpgm [ 2018-06-14 11:40:07 ] INFO Output values: normalized [ 2018-06-14 11:40:07 ] INFO Downloading gene annotation for mm10... [ 2018-06-14 12:03:23 ] INFO 2018-06-14 12:03:23: Data processing started... [ 2018-06-14 12:03:23 ] INFO Read counts file: imported sam/bam/bed files [ 2018-06-14 12:03:23 ] INFO Conditions: Wt, C_221_222, Tg197, Tg197_C [ 2018-06-14 12:03:23 ] INFO Samples to include: GK3R188-Wt1, GK3R189-Wt2, GK3R190-C1, GK3R191-C2, GK3R192-C3, GK3R193-Tg197-1, GK3R194-Tg197-2, GK3R195-Tg197-3, GK3R196-Tg197-C1, GK3R197-Tg197-C2, GK3R198-Tg197-C3 [ 2018-06-14 12:03:23 ] INFO Samples to exclude: none [ 2018-06-14 12:03:23 ] INFO Requested contrasts: Wt_vs_C_221_222, Wt_vs_Tg197, Tg197_C_vs_Tg197, Tg197_C_vs_C_221_222 [ 2018-06-14 12:03:23 ] INFO Annotation: download [ 2018-06-14 12:03:23 ] INFO Organism: mm10 [ 2018-06-14 12:03:23 ] INFO Reference source: ensembl [ 2018-06-14 12:03:23 ] INFO Count type: utr [ 2018-06-14 12:03:23 ] INFO 3' UTR flanking: 500 [ 2018-06-14 12:03:23 ] INFO Exon filters: none applied [ 2018-06-14 12:03:23 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2018-06-14 12:03:23 ] INFO length: [ 2018-06-14 12:03:23 ] INFO length: 500 [ 2018-06-14 12:03:23 ] INFO avg.reads: [ 2018-06-14 12:03:23 ] INFO average.per.bp: 100 [ 2018-06-14 12:03:23 ] INFO quantile: 0.25 [ 2018-06-14 12:03:23 ] INFO expression: [ 2018-06-14 12:03:23 ] INFO median: TRUE [ 2018-06-14 12:03:23 ] INFO mean: FALSE [ 2018-06-14 12:03:23 ] INFO quantile: NA [ 2018-06-14 12:03:23 ] INFO known: NA [ 2018-06-14 12:03:23 ] INFO custom: NA [ 2018-06-14 12:03:23 ] INFO biotype: [ 2018-06-14 12:03:23 ] INFO pseudogene: FALSE [ 2018-06-14 12:03:23 ] INFO lincRNA: FALSE [ 2018-06-14 12:03:23 ] INFO protein_coding: FALSE [ 2018-06-14 12:03:23 ] INFO antisense: FALSE [ 2018-06-14 12:03:23 ] INFO processed_transcript: FALSE [ 2018-06-14 12:03:23 ] INFO snRNA: FALSE [ 2018-06-14 12:03:23 ] INFO sense_intronic: FALSE [ 2018-06-14 12:03:23 ] INFO miRNA: FALSE [ 2018-06-14 12:03:23 ] INFO misc_RNA: FALSE [ 2018-06-14 12:03:23 ] INFO snoRNA: FALSE [ 2018-06-14 12:03:23 ] INFO rRNA: TRUE [ 2018-06-14 12:03:23 ] INFO polymorphic_pseudogene: FALSE [ 2018-06-14 12:03:23 ] INFO sense_overlapping: FALSE [ 2018-06-14 12:03:23 ] INFO three_prime_overlapping_ncrna: FALSE [ 2018-06-14 12:03:23 ] INFO TR_V_gene: FALSE [ 2018-06-14 12:03:23 ] INFO TR_V_pseudogene: TRUE [ 2018-06-14 12:03:23 ] INFO TR_D_gene: FALSE [ 2018-06-14 12:03:23 ] INFO TR_J_gene: FALSE [ 2018-06-14 12:03:23 ] INFO TR_C_gene: FALSE [ 2018-06-14 12:03:23 ] INFO TR_J_pseudogene: TRUE [ 2018-06-14 12:03:23 ] INFO IG_C_gene: FALSE [ 2018-06-14 12:03:23 ] INFO IG_C_pseudogene: TRUE [ 2018-06-14 12:03:23 ] INFO IG_J_gene: FALSE [ 2018-06-14 12:03:23 ] INFO IG_J_pseudogene: TRUE [ 2018-06-14 12:03:23 ] INFO IG_D_gene: FALSE [ 2018-06-14 12:03:23 ] INFO IG_V_gene: FALSE [ 2018-06-14 12:03:23 ] INFO IG_V_pseudogene: TRUE [ 2018-06-14 12:03:23 ] INFO Filter application: postnorm [ 2018-06-14 12:03:23 ] INFO Normalization algorithm: deseq [ 2018-06-14 12:03:23 ] INFO Normalization arguments: [ 2018-06-14 12:03:23 ] INFO locfunc: [ 2018-06-14 12:03:23 ] INFO [[ [ 2018-06-14 12:03:23 ] INFO list(locfunc = function (x, na.rm = FALSE, ...) standardGeneric("median")) [ 2018-06-14 12:03:23 ] INFO locfunc [ 2018-06-14 12:03:23 ] INFO Statistical algorithm: deseq [ 2018-06-14 12:03:23 ] INFO Statistical arguments: [ 2018-06-14 12:03:23 ] INFO deseq: blind, fit-only, local [ 2018-06-14 12:03:23 ] INFO Meta-analysis method: none [ 2018-06-14 12:03:23 ] INFO Multiple testing correction: BH [ 2018-06-14 12:03:23 ] INFO p-value threshold: 0.05 [ 2018-06-14 12:03:23 ] INFO Logarithmic transformation offset: 1 [ 2018-06-14 12:03:23 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2018-06-14 12:03:23 ] INFO Figure format: png, pdf [ 2018-06-14 12:03:23 ] INFO Output directory: /data/images/proton2/run403/www/metaseqr_GKlab_run403 [ 2018-06-14 12:03:23 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2018-06-14 12:03:23 ] INFO Output scale(s): log2, rpgm [ 2018-06-14 12:03:23 ] INFO Output values: normalized [ 2018-06-14 12:03:23 ] INFO Downloading gene annotation for mm10... [ 2018-06-14 12:03:31 ] INFO Downloading transcript annotation for mm10... [ 2018-06-14 12:05:31 ] INFO Converting annotation to GenomicRanges object... [ 2018-06-14 12:05:32 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2018-06-14 12:13:50 ] INFO Flanking merged transcript 3' UTRs per 500bp... [ 2018-06-14 12:13:54 ] INFO Reading bam file GK3R188-Wt1.bam for sample with name GK3R188-Wt1. This might take some time... [ 2018-06-14 12:13:54 ] INFO Reading bam file GK3R189-Wt2.bam for sample with name GK3R189-Wt2. This might take some time... [ 2018-06-14 12:13:54 ] INFO Reading bam file GK3R190-C1.bam for sample with name GK3R190-C1. This might take some time... [ 2018-06-14 12:13:54 ] INFO Reading bam file GK3R191-C2.bam for sample with name GK3R191-C2. This might take some time... [ 2018-06-14 12:13:54 ] INFO Reading bam file GK3R192-C3.bam for sample with name GK3R192-C3. This might take some time... [ 2018-06-14 12:13:54 ] INFO Reading bam file GK3R193-Tg197-1.bam for sample with name GK3R193-Tg197-1. This might take some time... [ 2018-06-14 12:14:11 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:14:11 ] INFO ...for single-end reads... [ 2018-06-14 12:14:11 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:14:27 ] INFO Reading bam file GK3R194-Tg197-2.bam for sample with name GK3R194-Tg197-2. This might take some time... [ 2018-06-14 12:14:41 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:14:41 ] INFO ...for single-end reads... [ 2018-06-14 12:14:41 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:14:41 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:14:41 ] INFO ...for single-end reads... [ 2018-06-14 12:14:41 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:14:42 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:14:42 ] INFO ...for single-end reads... [ 2018-06-14 12:14:42 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:14:45 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:14:45 ] INFO ...for single-end reads... [ 2018-06-14 12:14:45 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:14:45 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:14:45 ] INFO ...for single-end reads... [ 2018-06-14 12:14:45 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:14:55 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:14:55 ] INFO ...for single-end reads... [ 2018-06-14 12:14:55 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:15:31 ] INFO Reading bam file GK3R196-Tg197-C1.bam for sample with name GK3R196-Tg197-C1. This might take some time... [ 2018-06-14 12:15:32 ] INFO Reading bam file GK3R195-Tg197-3.bam for sample with name GK3R195-Tg197-3. This might take some time... [ 2018-06-14 12:15:32 ] INFO Reading bam file GK3R197-Tg197-C2.bam for sample with name GK3R197-Tg197-C2. This might take some time... [ 2018-06-14 12:15:39 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:15:39 ] INFO ...for single-end reads... [ 2018-06-14 12:15:39 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:15:39 ] INFO Reading bam file GK3R198-Tg197-C3.bam for sample with name GK3R198-Tg197-C3. This might take some time... [ 2018-06-14 12:16:00 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:16:00 ] INFO ...for single-end reads... [ 2018-06-14 12:16:00 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:16:01 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:16:01 ] INFO ...for single-end reads... [ 2018-06-14 12:16:01 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:16:03 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:16:03 ] INFO ...for single-end reads... [ 2018-06-14 12:16:03 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:16:48 ] INFO Exporting raw read counts table to /data/images/proton2/run403/www/metaseqr_GKlab_run403/lists/raw_counts_table.txt.gz [ 2018-06-14 12:16:51 ] INFO Checking chromosomes in transcript counts and gene annotation... [ 2018-06-14 12:16:51 ] INFO Processing transcripts... [ 2018-06-14 12:16:51 ] INFO Separating transcripts (UTR regions) per gene for GK3R188-Wt1... [ 2018-06-14 12:18:02 ] INFO Separating transcripts (UTR regions) per gene for GK3R189-Wt2... [ 2018-06-14 12:19:12 ] INFO Separating transcripts (UTR regions) per gene for GK3R190-C1... [ 2018-06-14 12:20:24 ] INFO Separating transcripts (UTR regions) per gene for GK3R191-C2... [ 2018-06-14 12:21:39 ] INFO Separating transcripts (UTR regions) per gene for GK3R192-C3... [ 2018-06-14 12:22:54 ] INFO Separating transcripts (UTR regions) per gene for GK3R193-Tg197-1... [ 2018-06-14 12:24:10 ] INFO Separating transcripts (UTR regions) per gene for GK3R194-Tg197-2... [ 2018-06-14 12:25:26 ] INFO Separating transcripts (UTR regions) per gene for GK3R195-Tg197-3... [ 2018-06-14 12:26:43 ] INFO Separating transcripts (UTR regions) per gene for GK3R196-Tg197-C1... [ 2018-06-14 12:28:00 ] INFO Separating transcripts (UTR regions) per gene for GK3R197-Tg197-C2... [ 2018-06-14 12:29:18 ] INFO Separating transcripts (UTR regions) per gene for GK3R198-Tg197-C3... [ 2018-06-14 12:30:36 ] INFO Saving gene model to /data/images/proton2/run403/www/metaseqr_GKlab_run403/data/gene_model.RData [ 2018-06-14 12:30:39 ] INFO Summarizing count data... [ 2018-06-14 12:30:46 ] INFO Removing genes with zero counts in all samples... [ 2018-06-14 12:30:46 ] INFO Normalizing with: deseq [ 2018-06-14 12:30:47 ] INFO Applying gene filter length... [ 2018-06-14 12:30:47 ] INFO Threshold below which ignored: 500 [ 2018-06-14 12:30:47 ] INFO Applying gene filter avg.reads... [ 2018-06-14 12:30:47 ] INFO Threshold below which ignored: 0 [ 2018-06-14 12:30:47 ] INFO Applying gene filter expression... [ 2018-06-14 12:30:47 ] INFO Threshold below which ignored: 6 [ 2018-06-14 12:30:47 ] INFO Applying gene filter biotype... [ 2018-06-14 12:30:47 ] INFO Biotypes ignored: rRNA, TR_V_pseudogene, TR_J_pseudogene, IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene [ 2018-06-14 12:30:47 ] INFO 38425 genes filtered out [ 2018-06-14 12:30:47 ] INFO 15253 genes remain after filtering [ 2018-06-14 12:30:47 ] INFO Running statistical tests with: deseq [ 2018-06-14 12:30:47 ] INFO Contrast: Wt_vs_C_221_222 [ 2018-06-14 12:31:01 ] INFO Contrast: Wt_vs_Tg197 [ 2018-06-14 12:31:16 ] INFO Contrast: Tg197_C_vs_Tg197 [ 2018-06-14 12:31:33 ] INFO Contrast: Tg197_C_vs_C_221_222 [ 2018-06-14 12:31:47 ] INFO Contrast Wt_vs_C_221_222: found 178 genes [ 2018-06-14 12:31:47 ] INFO Contrast Wt_vs_Tg197: found 550 genes [ 2018-06-14 12:31:47 ] INFO Contrast Tg197_C_vs_Tg197: found 686 genes [ 2018-06-14 12:31:47 ] INFO Contrast Tg197_C_vs_C_221_222: found 1081 genes [ 2018-06-14 12:31:47 ] INFO Exporting and compressing normalized read counts table to /data/images/proton2/run403/www/metaseqr_GKlab_run403/lists/normalized_counts_table.txt [ 2018-06-14 12:31:49 ] INFO Building output files... [ 2018-06-14 12:31:51 ] INFO Contrast: Wt_vs_C_221_222 [ 2018-06-14 12:31:51 ] INFO Adding non-filtered data... [ 2018-06-14 12:31:51 ] INFO binding annotation... [ 2018-06-14 12:31:52 ] INFO binding p-values... [ 2018-06-14 12:31:52 ] INFO binding FDRs... [ 2018-06-14 12:31:52 ] INFO binding log2 normalized fold changes... [ 2018-06-14 12:31:53 ] INFO binding all normalized counts for Wt... [ 2018-06-14 12:31:53 ] INFO binding all normalized counts for C_221_222... [ 2018-06-14 12:31:53 ] INFO binding filtering flags... [ 2018-06-14 12:31:55 ] INFO Writing output... [ 2018-06-14 12:31:55 ] INFO Adding filtered data... [ 2018-06-14 12:31:55 ] INFO binding annotation... [ 2018-06-14 12:31:55 ] INFO binding p-values... [ 2018-06-14 12:31:55 ] INFO binding FDRs... [ 2018-06-14 12:31:56 ] INFO binding log2 normalized fold changes... [ 2018-06-14 12:31:56 ] INFO binding all normalized counts for Wt... [ 2018-06-14 12:31:56 ] INFO binding all normalized counts for C_221_222... [ 2018-06-14 12:31:56 ] INFO binding filtering flags... [ 2018-06-14 12:31:57 ] INFO Writing output... [ 2018-06-14 12:31:58 ] INFO Contrast: Wt_vs_Tg197 [ 2018-06-14 12:31:58 ] INFO Adding non-filtered data... [ 2018-06-14 12:31:58 ] INFO binding annotation... [ 2018-06-14 12:31:59 ] INFO binding p-values... [ 2018-06-14 12:31:59 ] INFO binding FDRs... [ 2018-06-14 12:31:59 ] INFO binding log2 normalized fold changes... [ 2018-06-14 12:31:59 ] INFO binding all normalized counts for Wt... [ 2018-06-14 12:32:00 ] INFO binding all normalized counts for Tg197... [ 2018-06-14 12:32:00 ] INFO binding filtering flags... [ 2018-06-14 12:32:01 ] INFO Writing output... [ 2018-06-14 12:32:01 ] INFO Adding filtered data... [ 2018-06-14 12:32:01 ] INFO binding annotation... [ 2018-06-14 12:32:01 ] INFO binding p-values... [ 2018-06-14 12:32:01 ] INFO binding FDRs... [ 2018-06-14 12:32:02 ] INFO binding log2 normalized fold changes... [ 2018-06-14 12:32:02 ] INFO binding all normalized counts for Wt... [ 2018-06-14 12:32:02 ] INFO binding all normalized counts for Tg197... [ 2018-06-14 12:32:02 ] INFO binding filtering flags... [ 2018-06-14 12:32:03 ] INFO Writing output... [ 2018-06-14 12:32:05 ] INFO Contrast: Tg197_C_vs_Tg197 [ 2018-06-14 12:32:05 ] INFO Adding non-filtered data... [ 2018-06-14 12:32:05 ] INFO binding annotation... [ 2018-06-14 12:32:05 ] INFO binding p-values... [ 2018-06-14 12:32:05 ] INFO binding FDRs... [ 2018-06-14 12:32:06 ] INFO binding log2 normalized fold changes... [ 2018-06-14 12:32:06 ] INFO binding all normalized counts for Tg197_C... [ 2018-06-14 12:32:07 ] INFO binding all normalized counts for Tg197... [ 2018-06-14 12:32:07 ] INFO binding filtering flags... [ 2018-06-14 12:32:08 ] INFO Writing output... [ 2018-06-14 12:32:08 ] INFO Adding filtered data... [ 2018-06-14 12:32:08 ] INFO binding annotation... [ 2018-06-14 12:32:08 ] INFO binding p-values... [ 2018-06-14 12:32:08 ] INFO binding FDRs... [ 2018-06-14 12:32:09 ] INFO binding log2 normalized fold changes... [ 2018-06-14 12:32:09 ] INFO binding all normalized counts for Tg197_C... [ 2018-06-14 12:32:09 ] INFO binding all normalized counts for Tg197... [ 2018-06-14 12:32:09 ] INFO binding filtering flags... [ 2018-06-14 12:32:10 ] INFO Writing output... [ 2018-06-14 12:32:12 ] INFO Contrast: Tg197_C_vs_C_221_222 [ 2018-06-14 12:32:12 ] INFO Adding non-filtered data... [ 2018-06-14 12:32:12 ] INFO binding annotation... [ 2018-06-14 12:32:12 ] INFO binding p-values... [ 2018-06-14 12:32:12 ] INFO binding FDRs... [ 2018-06-14 12:32:13 ] INFO binding log2 normalized fold changes... [ 2018-06-14 12:32:13 ] INFO binding all normalized counts for Tg197_C... [ 2018-06-14 12:32:13 ] INFO binding all normalized counts for C_221_222... [ 2018-06-14 12:32:14 ] INFO binding filtering flags... [ 2018-06-14 12:32:15 ] INFO Writing output... [ 2018-06-14 12:32:15 ] INFO Adding filtered data... [ 2018-06-14 12:32:15 ] INFO binding annotation... [ 2018-06-14 12:32:15 ] INFO binding p-values... [ 2018-06-14 12:32:15 ] INFO binding FDRs... [ 2018-06-14 12:32:16 ] INFO binding log2 normalized fold changes... [ 2018-06-14 12:32:16 ] INFO binding all normalized counts for Tg197_C... [ 2018-06-14 12:32:16 ] INFO binding all normalized counts for C_221_222... [ 2018-06-14 12:32:16 ] INFO binding filtering flags... [ 2018-06-14 12:32:17 ] INFO Writing output... [ 2018-06-14 12:32:19 ] INFO Creating quality control graphs... [ 2018-06-14 12:32:19 ] INFO Plotting in png format... [ 2018-06-14 12:32:19 ] INFO Plotting mds... [ 2018-06-14 12:32:19 ] INFO Plotting biodetection... [ 2018-06-14 12:32:21 ] INFO Plotting countsbio... [ 2018-06-14 12:32:23 ] INFO Plotting saturation... [ 2018-06-14 12:32:33 ] INFO Plotting readnoise... [ 2018-06-14 12:32:35 ] INFO Plotting correl... [ 2018-06-14 12:32:35 ] INFO Plotting pairwise... [ 2018-06-14 12:33:27 ] INFO Plotting boxplot... [ 2018-06-14 12:33:27 ] INFO Plotting gcbias... [ 2018-06-14 12:33:28 ] INFO Plotting lengthbias... [ 2018-06-14 12:33:29 ] INFO Plotting meandiff... [ 2018-06-14 12:37:51 ] WARN "yes" and "no" for read strandedness have been deprecated. Please use "forward", "forward" or "no". Replacing "yes" with "forward"... [ 2018-06-14 12:37:52 ] INFO 2018-06-14 12:37:52: Data processing started... [ 2018-06-14 12:37:52 ] INFO Read counts file: imported sam/bam/bed files [ 2018-06-14 12:37:52 ] INFO Conditions: Wt, C_221_222, Tg197, Tg197_C [ 2018-06-14 12:37:52 ] INFO Samples to include: GK3R188-Wt1, GK3R189-Wt2, GK3R190-C1, GK3R191-C2, GK3R192-C3, GK3R193-Tg197-1, GK3R194-Tg197-2, GK3R195-Tg197-3, GK3R196-Tg197-C1, GK3R197-Tg197-C2, GK3R198-Tg197-C3 [ 2018-06-14 12:37:52 ] INFO Samples to exclude: none [ 2018-06-14 12:37:52 ] INFO Requested contrasts: Wt_vs_C_221_222, Wt_vs_Tg197, Tg197_C_vs_Tg197, Tg197_C_vs_C_221_222 [ 2018-06-14 12:37:52 ] INFO Annotation: download [ 2018-06-14 12:37:52 ] INFO Organism: mm10 [ 2018-06-14 12:37:52 ] INFO Reference source: ensembl [ 2018-06-14 12:37:52 ] INFO Count type: utr [ 2018-06-14 12:37:52 ] INFO 3' UTR flanking: 500 [ 2018-06-14 12:37:52 ] INFO Exon filters: none applied [ 2018-06-14 12:37:52 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2018-06-14 12:37:52 ] INFO length: [ 2018-06-14 12:37:52 ] INFO length: 500 [ 2018-06-14 12:37:52 ] INFO avg.reads: [ 2018-06-14 12:37:52 ] INFO average.per.bp: 100 [ 2018-06-14 12:37:52 ] INFO quantile: 0.25 [ 2018-06-14 12:37:52 ] INFO expression: [ 2018-06-14 12:37:52 ] INFO median: TRUE [ 2018-06-14 12:37:52 ] INFO mean: FALSE [ 2018-06-14 12:37:52 ] INFO quantile: NA [ 2018-06-14 12:37:52 ] INFO known: NA [ 2018-06-14 12:37:52 ] INFO custom: NA [ 2018-06-14 12:37:52 ] INFO biotype: [ 2018-06-14 12:37:52 ] INFO pseudogene: FALSE [ 2018-06-14 12:37:52 ] INFO lincRNA: FALSE [ 2018-06-14 12:37:52 ] INFO protein_coding: FALSE [ 2018-06-14 12:37:52 ] INFO antisense: FALSE [ 2018-06-14 12:37:52 ] INFO processed_transcript: FALSE [ 2018-06-14 12:37:52 ] INFO snRNA: FALSE [ 2018-06-14 12:37:52 ] INFO sense_intronic: FALSE [ 2018-06-14 12:37:52 ] INFO miRNA: FALSE [ 2018-06-14 12:37:52 ] INFO misc_RNA: FALSE [ 2018-06-14 12:37:52 ] INFO snoRNA: FALSE [ 2018-06-14 12:37:52 ] INFO rRNA: TRUE [ 2018-06-14 12:37:52 ] INFO polymorphic_pseudogene: FALSE [ 2018-06-14 12:37:52 ] INFO sense_overlapping: FALSE [ 2018-06-14 12:37:52 ] INFO three_prime_overlapping_ncrna: FALSE [ 2018-06-14 12:37:52 ] INFO TR_V_gene: FALSE [ 2018-06-14 12:37:52 ] INFO TR_V_pseudogene: TRUE [ 2018-06-14 12:37:52 ] INFO TR_D_gene: FALSE [ 2018-06-14 12:37:52 ] INFO TR_J_gene: FALSE [ 2018-06-14 12:37:52 ] INFO TR_C_gene: FALSE [ 2018-06-14 12:37:52 ] INFO TR_J_pseudogene: TRUE [ 2018-06-14 12:37:52 ] INFO IG_C_gene: FALSE [ 2018-06-14 12:37:52 ] INFO IG_C_pseudogene: TRUE [ 2018-06-14 12:37:52 ] INFO IG_J_gene: FALSE [ 2018-06-14 12:37:52 ] INFO IG_J_pseudogene: TRUE [ 2018-06-14 12:37:52 ] INFO IG_D_gene: FALSE [ 2018-06-14 12:37:52 ] INFO IG_V_gene: FALSE [ 2018-06-14 12:37:52 ] INFO IG_V_pseudogene: TRUE [ 2018-06-14 12:37:52 ] INFO Filter application: postnorm [ 2018-06-14 12:37:52 ] INFO Normalization algorithm: deseq [ 2018-06-14 12:37:52 ] INFO Normalization arguments: [ 2018-06-14 12:37:52 ] INFO locfunc: [ 2018-06-14 12:37:52 ] INFO [[ [ 2018-06-14 12:37:52 ] INFO list(locfunc = function (x, na.rm = FALSE, ...) standardGeneric("median")) [ 2018-06-14 12:37:52 ] INFO locfunc [ 2018-06-14 12:37:52 ] INFO Statistical algorithm: deseq [ 2018-06-14 12:37:52 ] INFO Statistical arguments: [ 2018-06-14 12:37:52 ] INFO deseq: blind, fit-only, local [ 2018-06-14 12:37:52 ] INFO Meta-analysis method: none [ 2018-06-14 12:37:52 ] INFO Multiple testing correction: BH [ 2018-06-14 12:37:52 ] INFO p-value threshold: 0.05 [ 2018-06-14 12:37:52 ] INFO Logarithmic transformation offset: 1 [ 2018-06-14 12:37:52 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meanvar, biodist, volcano, deheatmap [ 2018-06-14 12:37:52 ] INFO Figure format: png, pdf [ 2018-06-14 12:37:52 ] INFO Output directory: /data/images/proton2/run403/www/metaseqr_GKlab_run403 [ 2018-06-14 12:37:52 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2018-06-14 12:37:52 ] INFO Output scale(s): log2, rpgm [ 2018-06-14 12:37:52 ] INFO Output values: normalized [ 2018-06-14 12:37:52 ] INFO Downloading gene annotation for mm10... [ 2018-06-14 12:37:58 ] INFO Downloading transcript annotation for mm10... [ 2018-06-14 12:40:08 ] INFO Converting annotation to GenomicRanges object... [ 2018-06-14 12:40:08 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2018-06-14 12:47:46 ] INFO Flanking merged transcript 3' UTRs per 500bp... [ 2018-06-14 12:47:49 ] INFO Reading bam file GK3R188-Wt1.bam for sample with name GK3R188-Wt1. This might take some time... [ 2018-06-14 12:47:49 ] INFO Reading bam file GK3R189-Wt2.bam for sample with name GK3R189-Wt2. This might take some time... [ 2018-06-14 12:47:49 ] INFO Reading bam file GK3R190-C1.bam for sample with name GK3R190-C1. This might take some time... [ 2018-06-14 12:47:49 ] INFO Reading bam file GK3R191-C2.bam for sample with name GK3R191-C2. This might take some time... [ 2018-06-14 12:47:49 ] INFO Reading bam file GK3R192-C3.bam for sample with name GK3R192-C3. This might take some time... [ 2018-06-14 12:47:49 ] INFO Reading bam file GK3R193-Tg197-1.bam for sample with name GK3R193-Tg197-1. This might take some time... [ 2018-06-14 12:47:53 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:47:53 ] INFO ...for single-end reads... [ 2018-06-14 12:47:53 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:47:59 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:47:59 ] INFO ...for single-end reads... [ 2018-06-14 12:47:59 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:47:59 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:47:59 ] INFO ...for single-end reads... [ 2018-06-14 12:47:59 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:47:59 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:47:59 ] INFO ...for single-end reads... [ 2018-06-14 12:47:59 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:48:00 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:48:00 ] INFO ...for single-end reads... [ 2018-06-14 12:48:00 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:48:01 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:48:01 ] INFO ...for single-end reads... [ 2018-06-14 12:48:01 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:48:06 ] INFO Reading bam file GK3R194-Tg197-2.bam for sample with name GK3R194-Tg197-2. This might take some time... [ 2018-06-14 12:48:17 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:48:17 ] INFO ...for single-end reads... [ 2018-06-14 12:48:17 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:48:42 ] INFO Reading bam file GK3R196-Tg197-C1.bam for sample with name GK3R196-Tg197-C1. This might take some time... [ 2018-06-14 12:48:42 ] INFO Reading bam file GK3R197-Tg197-C2.bam for sample with name GK3R197-Tg197-C2. This might take some time... [ 2018-06-14 12:48:45 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:48:45 ] INFO ...for single-end reads... [ 2018-06-14 12:48:45 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:48:45 ] INFO Reading bam file GK3R195-Tg197-3.bam for sample with name GK3R195-Tg197-3. This might take some time... [ 2018-06-14 12:48:50 ] INFO Reading bam file GK3R198-Tg197-C3.bam for sample with name GK3R198-Tg197-C3. This might take some time... [ 2018-06-14 12:48:54 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:48:54 ] INFO ...for single-end reads... [ 2018-06-14 12:48:54 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:48:58 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:48:58 ] INFO ...for single-end reads... [ 2018-06-14 12:48:58 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:48:59 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 12:48:59 ] INFO ...for single-end reads... [ 2018-06-14 12:48:59 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 12:49:45 ] INFO Exporting raw read counts table to /data/images/proton2/run403/www/metaseqr_GKlab_run403/lists/raw_counts_table.txt.gz [ 2018-06-14 12:49:47 ] INFO Checking chromosomes in transcript counts and gene annotation... [ 2018-06-14 12:49:47 ] INFO Processing transcripts... [ 2018-06-14 12:49:47 ] INFO Separating transcripts (UTR regions) per gene for GK3R188-Wt1... [ 2018-06-14 12:50:55 ] INFO Separating transcripts (UTR regions) per gene for GK3R189-Wt2... [ 2018-06-14 12:52:04 ] INFO Separating transcripts (UTR regions) per gene for GK3R190-C1... [ 2018-06-14 12:53:15 ] INFO Separating transcripts (UTR regions) per gene for GK3R191-C2... [ 2018-06-14 12:54:29 ] INFO Separating transcripts (UTR regions) per gene for GK3R192-C3... [ 2018-06-14 12:55:43 ] INFO Separating transcripts (UTR regions) per gene for GK3R193-Tg197-1... [ 2018-06-14 12:56:59 ] INFO Separating transcripts (UTR regions) per gene for GK3R194-Tg197-2... [ 2018-06-14 12:58:14 ] INFO Separating transcripts (UTR regions) per gene for GK3R195-Tg197-3... [ 2018-06-14 12:59:29 ] INFO Separating transcripts (UTR regions) per gene for GK3R196-Tg197-C1... [ 2018-06-14 13:00:44 ] INFO Separating transcripts (UTR regions) per gene for GK3R197-Tg197-C2... [ 2018-06-14 13:01:57 ] INFO Separating transcripts (UTR regions) per gene for GK3R198-Tg197-C3... [ 2018-06-14 13:03:10 ] INFO Saving gene model to /data/images/proton2/run403/www/metaseqr_GKlab_run403/data/gene_model.RData [ 2018-06-14 13:03:13 ] INFO Summarizing count data... [ 2018-06-14 13:03:23 ] INFO Removing genes with zero counts in all samples... [ 2018-06-14 13:03:24 ] INFO Normalizing with: deseq [ 2018-06-14 13:03:24 ] INFO Applying gene filter length... [ 2018-06-14 13:03:24 ] INFO Threshold below which ignored: 500 [ 2018-06-14 13:03:24 ] INFO Applying gene filter avg.reads... [ 2018-06-14 13:03:25 ] INFO Threshold below which ignored: 0 [ 2018-06-14 13:03:25 ] INFO Applying gene filter expression... [ 2018-06-14 13:03:25 ] INFO Threshold below which ignored: 6 [ 2018-06-14 13:03:25 ] INFO Applying gene filter biotype... [ 2018-06-14 13:03:25 ] INFO Biotypes ignored: rRNA, TR_V_pseudogene, TR_J_pseudogene, IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene [ 2018-06-14 13:03:25 ] INFO 38425 genes filtered out [ 2018-06-14 13:03:25 ] INFO 15253 genes remain after filtering [ 2018-06-14 13:03:25 ] INFO Running statistical tests with: deseq [ 2018-06-14 13:03:25 ] INFO Contrast: Wt_vs_C_221_222 [ 2018-06-14 13:03:38 ] INFO Contrast: Wt_vs_Tg197 [ 2018-06-14 13:03:53 ] INFO Contrast: Tg197_C_vs_Tg197 [ 2018-06-14 13:04:09 ] INFO Contrast: Tg197_C_vs_C_221_222 [ 2018-06-14 13:04:24 ] INFO Contrast Wt_vs_C_221_222: found 178 genes [ 2018-06-14 13:04:24 ] INFO Contrast Wt_vs_Tg197: found 550 genes [ 2018-06-14 13:04:24 ] INFO Contrast Tg197_C_vs_Tg197: found 686 genes [ 2018-06-14 13:04:24 ] INFO Contrast Tg197_C_vs_C_221_222: found 1081 genes [ 2018-06-14 13:04:24 ] INFO Exporting and compressing normalized read counts table to /data/images/proton2/run403/www/metaseqr_GKlab_run403/lists/normalized_counts_table.txt [ 2018-06-14 13:04:25 ] INFO Building output files... [ 2018-06-14 13:04:28 ] INFO Contrast: Wt_vs_C_221_222 [ 2018-06-14 13:04:28 ] INFO Adding non-filtered data... [ 2018-06-14 13:04:28 ] INFO binding annotation... [ 2018-06-14 13:04:29 ] INFO binding p-values... [ 2018-06-14 13:04:29 ] INFO binding FDRs... [ 2018-06-14 13:04:29 ] INFO binding log2 normalized fold changes... [ 2018-06-14 13:04:29 ] INFO binding all normalized counts for Wt... [ 2018-06-14 13:04:30 ] INFO binding all normalized counts for C_221_222... [ 2018-06-14 13:04:30 ] INFO binding filtering flags... [ 2018-06-14 13:04:31 ] INFO Writing output... [ 2018-06-14 13:04:31 ] INFO Adding filtered data... [ 2018-06-14 13:04:31 ] INFO binding annotation... [ 2018-06-14 13:04:31 ] INFO binding p-values... [ 2018-06-14 13:04:31 ] INFO binding FDRs... [ 2018-06-14 13:04:31 ] INFO binding log2 normalized fold changes... [ 2018-06-14 13:04:31 ] INFO binding all normalized counts for Wt... [ 2018-06-14 13:04:31 ] INFO binding all normalized counts for C_221_222... [ 2018-06-14 13:04:31 ] INFO binding filtering flags... [ 2018-06-14 13:04:32 ] INFO Writing output... [ 2018-06-14 13:04:34 ] INFO Contrast: Wt_vs_Tg197 [ 2018-06-14 13:04:34 ] INFO Adding non-filtered data... [ 2018-06-14 13:04:34 ] INFO binding annotation... [ 2018-06-14 13:04:35 ] INFO binding p-values... [ 2018-06-14 13:04:35 ] INFO binding FDRs... [ 2018-06-14 13:04:35 ] INFO binding log2 normalized fold changes... [ 2018-06-14 13:04:35 ] INFO binding all normalized counts for Wt... [ 2018-06-14 13:04:36 ] INFO binding all normalized counts for Tg197... [ 2018-06-14 13:04:36 ] INFO binding filtering flags... [ 2018-06-14 13:04:37 ] INFO Writing output... [ 2018-06-14 13:04:37 ] INFO Adding filtered data... [ 2018-06-14 13:04:37 ] INFO binding annotation... [ 2018-06-14 13:04:37 ] INFO binding p-values... [ 2018-06-14 13:04:37 ] INFO binding FDRs... [ 2018-06-14 13:04:38 ] INFO binding log2 normalized fold changes... [ 2018-06-14 13:04:38 ] INFO binding all normalized counts for Wt... [ 2018-06-14 13:04:38 ] INFO binding all normalized counts for Tg197... [ 2018-06-14 13:04:38 ] INFO binding filtering flags... [ 2018-06-14 13:04:39 ] INFO Writing output... [ 2018-06-14 13:04:40 ] INFO Contrast: Tg197_C_vs_Tg197 [ 2018-06-14 13:04:40 ] INFO Adding non-filtered data... [ 2018-06-14 13:04:40 ] INFO binding annotation... [ 2018-06-14 13:04:41 ] INFO binding p-values... [ 2018-06-14 13:04:41 ] INFO binding FDRs... [ 2018-06-14 13:04:41 ] INFO binding log2 normalized fold changes... [ 2018-06-14 13:04:42 ] INFO binding all normalized counts for Tg197_C... [ 2018-06-14 13:04:42 ] INFO binding all normalized counts for Tg197... [ 2018-06-14 13:04:43 ] INFO binding filtering flags... [ 2018-06-14 13:04:43 ] INFO Writing output... [ 2018-06-14 13:04:43 ] INFO Adding filtered data... [ 2018-06-14 13:04:43 ] INFO binding annotation... [ 2018-06-14 13:04:43 ] INFO binding p-values... [ 2018-06-14 13:04:43 ] INFO binding FDRs... [ 2018-06-14 13:04:44 ] INFO binding log2 normalized fold changes... [ 2018-06-14 13:04:44 ] INFO binding all normalized counts for Tg197_C... [ 2018-06-14 13:04:44 ] INFO binding all normalized counts for Tg197... [ 2018-06-14 13:04:44 ] INFO binding filtering flags... [ 2018-06-14 13:04:45 ] INFO Writing output... [ 2018-06-14 13:04:47 ] INFO Contrast: Tg197_C_vs_C_221_222 [ 2018-06-14 13:04:47 ] INFO Adding non-filtered data... [ 2018-06-14 13:04:47 ] INFO binding annotation... [ 2018-06-14 13:04:48 ] INFO binding p-values... [ 2018-06-14 13:04:48 ] INFO binding FDRs... [ 2018-06-14 13:04:48 ] INFO binding log2 normalized fold changes... [ 2018-06-14 13:04:48 ] INFO binding all normalized counts for Tg197_C... [ 2018-06-14 13:04:49 ] INFO binding all normalized counts for C_221_222... [ 2018-06-14 13:04:49 ] INFO binding filtering flags... [ 2018-06-14 13:04:50 ] INFO Writing output... [ 2018-06-14 13:04:50 ] INFO Adding filtered data... [ 2018-06-14 13:04:50 ] INFO binding annotation... [ 2018-06-14 13:04:50 ] INFO binding p-values... [ 2018-06-14 13:04:50 ] INFO binding FDRs... [ 2018-06-14 13:04:51 ] INFO binding log2 normalized fold changes... [ 2018-06-14 13:04:51 ] INFO binding all normalized counts for Tg197_C... [ 2018-06-14 13:04:51 ] INFO binding all normalized counts for C_221_222... [ 2018-06-14 13:04:51 ] INFO binding filtering flags... [ 2018-06-14 13:04:52 ] INFO Writing output... [ 2018-06-14 13:04:54 ] INFO Creating quality control graphs... [ 2018-06-14 13:04:54 ] INFO Plotting in png format... [ 2018-06-14 13:04:54 ] INFO Plotting mds... [ 2018-06-14 13:04:54 ] INFO Plotting biodetection... [ 2018-06-14 13:04:55 ] INFO Plotting countsbio... [ 2018-06-14 13:04:58 ] INFO Plotting saturation... [ 2018-06-14 13:05:07 ] INFO Plotting readnoise... [ 2018-06-14 13:05:09 ] INFO Plotting correl... [ 2018-06-14 13:05:10 ] INFO Plotting pairwise... [ 2018-06-14 13:06:02 ] INFO Plotting boxplot... [ 2018-06-14 13:06:02 ] INFO Plotting gcbias... [ 2018-06-14 13:06:03 ] INFO Plotting lengthbias... [ 2018-06-14 13:06:04 ] INFO Plotting meanvar... [ 2018-06-14 14:02:27 ] WARN "yes" and "no" for read strandedness have been deprecated. Please use "forward", "forward" or "no". Replacing "yes" with "forward"... [ 2018-06-14 14:02:27 ] INFO 2018-06-14 14:02:27: Data processing started... [ 2018-06-14 14:02:27 ] INFO Read counts file: imported sam/bam/bed files [ 2018-06-14 14:02:27 ] INFO Conditions: Wt, C_221_222, Tg197, Tg197_C [ 2018-06-14 14:02:27 ] INFO Samples to include: GK3R188-Wt1, GK3R189-Wt2, GK3R190-C1, GK3R191-C2, GK3R192-C3, GK3R193-Tg197-1, GK3R194-Tg197-2, GK3R195-Tg197-3, GK3R196-Tg197-C1, GK3R197-Tg197-C2, GK3R198-Tg197-C3 [ 2018-06-14 14:02:27 ] INFO Samples to exclude: none [ 2018-06-14 14:02:27 ] INFO Requested contrasts: Wt_vs_C_221_222, Wt_vs_Tg197, Tg197_C_vs_Tg197, Tg197_C_vs_C_221_222 [ 2018-06-14 14:02:27 ] INFO Annotation: download [ 2018-06-14 14:02:27 ] INFO Organism: mm10 [ 2018-06-14 14:02:27 ] INFO Reference source: ensembl [ 2018-06-14 14:02:27 ] INFO Count type: utr [ 2018-06-14 14:02:27 ] INFO 3' UTR flanking: 500 [ 2018-06-14 14:02:27 ] INFO Exon filters: none applied [ 2018-06-14 14:02:27 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2018-06-14 14:02:27 ] INFO length: [ 2018-06-14 14:02:27 ] INFO length: 500 [ 2018-06-14 14:02:27 ] INFO avg.reads: [ 2018-06-14 14:02:27 ] INFO average.per.bp: 100 [ 2018-06-14 14:02:27 ] INFO quantile: 0.25 [ 2018-06-14 14:02:27 ] INFO expression: [ 2018-06-14 14:02:27 ] INFO median: TRUE [ 2018-06-14 14:02:27 ] INFO mean: FALSE [ 2018-06-14 14:02:27 ] INFO quantile: NA [ 2018-06-14 14:02:27 ] INFO known: NA [ 2018-06-14 14:02:27 ] INFO custom: NA [ 2018-06-14 14:02:27 ] INFO biotype: [ 2018-06-14 14:02:27 ] INFO pseudogene: FALSE [ 2018-06-14 14:02:27 ] INFO lincRNA: FALSE [ 2018-06-14 14:02:27 ] INFO protein_coding: FALSE [ 2018-06-14 14:02:27 ] INFO antisense: FALSE [ 2018-06-14 14:02:27 ] INFO processed_transcript: FALSE [ 2018-06-14 14:02:27 ] INFO snRNA: FALSE [ 2018-06-14 14:02:27 ] INFO sense_intronic: FALSE [ 2018-06-14 14:02:27 ] INFO miRNA: FALSE [ 2018-06-14 14:02:27 ] INFO misc_RNA: FALSE [ 2018-06-14 14:02:27 ] INFO snoRNA: FALSE [ 2018-06-14 14:02:27 ] INFO rRNA: TRUE [ 2018-06-14 14:02:27 ] INFO polymorphic_pseudogene: FALSE [ 2018-06-14 14:02:27 ] INFO sense_overlapping: FALSE [ 2018-06-14 14:02:27 ] INFO three_prime_overlapping_ncrna: FALSE [ 2018-06-14 14:02:27 ] INFO TR_V_gene: FALSE [ 2018-06-14 14:02:27 ] INFO TR_V_pseudogene: TRUE [ 2018-06-14 14:02:27 ] INFO TR_D_gene: FALSE [ 2018-06-14 14:02:27 ] INFO TR_J_gene: FALSE [ 2018-06-14 14:02:27 ] INFO TR_C_gene: FALSE [ 2018-06-14 14:02:27 ] INFO TR_J_pseudogene: TRUE [ 2018-06-14 14:02:27 ] INFO IG_C_gene: FALSE [ 2018-06-14 14:02:27 ] INFO IG_C_pseudogene: TRUE [ 2018-06-14 14:02:27 ] INFO IG_J_gene: FALSE [ 2018-06-14 14:02:27 ] INFO IG_J_pseudogene: TRUE [ 2018-06-14 14:02:27 ] INFO IG_D_gene: FALSE [ 2018-06-14 14:02:27 ] INFO IG_V_gene: FALSE [ 2018-06-14 14:02:27 ] INFO IG_V_pseudogene: TRUE [ 2018-06-14 14:02:27 ] INFO Filter application: postnorm [ 2018-06-14 14:02:27 ] INFO Normalization algorithm: deseq [ 2018-06-14 14:02:27 ] INFO Normalization arguments: [ 2018-06-14 14:02:27 ] INFO locfunc: [ 2018-06-14 14:02:27 ] INFO [[ [ 2018-06-14 14:02:27 ] INFO list(locfunc = function (x, na.rm = FALSE, ...) standardGeneric("median")) [ 2018-06-14 14:02:27 ] INFO locfunc [ 2018-06-14 14:02:27 ] INFO Statistical algorithm: deseq [ 2018-06-14 14:02:27 ] INFO Statistical arguments: [ 2018-06-14 14:02:27 ] INFO deseq: blind, fit-only, local [ 2018-06-14 14:02:27 ] INFO Meta-analysis method: none [ 2018-06-14 14:02:27 ] INFO Multiple testing correction: BH [ 2018-06-14 14:02:27 ] INFO p-value threshold: 0.05 [ 2018-06-14 14:02:27 ] INFO Logarithmic transformation offset: 1 [ 2018-06-14 14:02:27 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, biodist, volcano, deheatmap [ 2018-06-14 14:02:27 ] INFO Figure format: png, pdf [ 2018-06-14 14:02:27 ] INFO Output directory: /data/images/proton2/run403/www/metaseqr_GKlab_run403 [ 2018-06-14 14:02:27 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2018-06-14 14:02:27 ] INFO Output scale(s): log2, rpgm [ 2018-06-14 14:02:27 ] INFO Output values: normalized [ 2018-06-14 14:02:27 ] INFO Downloading gene annotation for mm10... [ 2018-06-14 14:02:36 ] INFO Downloading transcript annotation for mm10... [ 2018-06-14 14:04:30 ] INFO Converting annotation to GenomicRanges object... [ 2018-06-14 14:04:31 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2018-06-14 14:12:03 ] INFO Flanking merged transcript 3' UTRs per 500bp... [ 2018-06-14 14:12:06 ] INFO Reading bam file GK3R188-Wt1.bam for sample with name GK3R188-Wt1. This might take some time... [ 2018-06-14 14:12:06 ] INFO Reading bam file GK3R189-Wt2.bam for sample with name GK3R189-Wt2. This might take some time... [ 2018-06-14 14:12:06 ] INFO Reading bam file GK3R190-C1.bam for sample with name GK3R190-C1. This might take some time... [ 2018-06-14 14:12:06 ] INFO Reading bam file GK3R191-C2.bam for sample with name GK3R191-C2. This might take some time... [ 2018-06-14 14:12:06 ] INFO Reading bam file GK3R192-C3.bam for sample with name GK3R192-C3. This might take some time... [ 2018-06-14 14:12:06 ] INFO Reading bam file GK3R193-Tg197-1.bam for sample with name GK3R193-Tg197-1. This might take some time... [ 2018-06-14 14:12:09 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 14:12:09 ] INFO ...for single-end reads... [ 2018-06-14 14:12:09 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 14:12:16 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 14:12:16 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 14:12:16 ] INFO ...for single-end reads... [ 2018-06-14 14:12:16 ] INFO ...for single-end reads... [ 2018-06-14 14:12:16 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 14:12:16 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 14:12:16 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 14:12:16 ] INFO ...for single-end reads... [ 2018-06-14 14:12:16 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 14:12:17 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 14:12:17 ] INFO ...for single-end reads... [ 2018-06-14 14:12:17 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 14:12:17 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 14:12:17 ] INFO ...for single-end reads... [ 2018-06-14 14:12:18 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 14:12:22 ] INFO Reading bam file GK3R194-Tg197-2.bam for sample with name GK3R194-Tg197-2. This might take some time... [ 2018-06-14 14:12:34 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 14:12:34 ] INFO ...for single-end reads... [ 2018-06-14 14:12:34 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 14:12:59 ] INFO Reading bam file GK3R196-Tg197-C1.bam for sample with name GK3R196-Tg197-C1. This might take some time... [ 2018-06-14 14:13:01 ] INFO Reading bam file GK3R197-Tg197-C2.bam for sample with name GK3R197-Tg197-C2. This might take some time... [ 2018-06-14 14:13:02 ] INFO Reading bam file GK3R195-Tg197-3.bam for sample with name GK3R195-Tg197-3. This might take some time... [ 2018-06-14 14:13:03 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 14:13:03 ] INFO ...for single-end reads... [ 2018-06-14 14:13:03 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 14:13:06 ] INFO Reading bam file GK3R198-Tg197-C3.bam for sample with name GK3R198-Tg197-C3. This might take some time... [ 2018-06-14 14:13:11 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 14:13:11 ] INFO ...for single-end reads... [ 2018-06-14 14:13:11 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 14:13:15 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 14:13:15 ] INFO ...for single-end reads... [ 2018-06-14 14:13:15 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 14:13:15 ] INFO Counting reads overlapping with given annotation... [ 2018-06-14 14:13:15 ] INFO ...for single-end reads... [ 2018-06-14 14:13:15 ] INFO ...assuming forward sequenced reads... [ 2018-06-14 14:14:04 ] INFO Exporting raw read counts table to /data/images/proton2/run403/www/metaseqr_GKlab_run403/lists/raw_counts_table.txt.gz [ 2018-06-14 14:14:06 ] INFO Checking chromosomes in transcript counts and gene annotation... [ 2018-06-14 14:14:06 ] INFO Processing transcripts... [ 2018-06-14 14:14:06 ] INFO Separating transcripts (UTR regions) per gene for GK3R188-Wt1... [ 2018-06-14 14:15:17 ] INFO Separating transcripts (UTR regions) per gene for GK3R189-Wt2... [ 2018-06-14 14:16:27 ] INFO Separating transcripts (UTR regions) per gene for GK3R190-C1... [ 2018-06-14 14:17:38 ] INFO Separating transcripts (UTR regions) per gene for GK3R191-C2... [ 2018-06-14 14:18:49 ] INFO Separating transcripts (UTR regions) per gene for GK3R192-C3... [ 2018-06-14 14:20:02 ] INFO Separating transcripts (UTR regions) per gene for GK3R193-Tg197-1... [ 2018-06-14 14:21:15 ] INFO Separating transcripts (UTR regions) per gene for GK3R194-Tg197-2... [ 2018-06-14 14:22:27 ] INFO Separating transcripts (UTR regions) per gene for GK3R195-Tg197-3... [ 2018-06-14 14:23:41 ] INFO Separating transcripts (UTR regions) per gene for GK3R196-Tg197-C1... [ 2018-06-14 14:24:55 ] INFO Separating transcripts (UTR regions) per gene for GK3R197-Tg197-C2... [ 2018-06-14 14:26:10 ] INFO Separating transcripts (UTR regions) per gene for GK3R198-Tg197-C3... [ 2018-06-14 14:27:25 ] INFO Saving gene model to /data/images/proton2/run403/www/metaseqr_GKlab_run403/data/gene_model.RData [ 2018-06-14 14:27:29 ] INFO Summarizing count data... [ 2018-06-14 14:27:38 ] INFO Removing genes with zero counts in all samples... [ 2018-06-14 14:27:39 ] INFO Normalizing with: deseq [ 2018-06-14 14:27:39 ] INFO Applying gene filter length... [ 2018-06-14 14:27:39 ] INFO Threshold below which ignored: 500 [ 2018-06-14 14:27:39 ] INFO Applying gene filter avg.reads... [ 2018-06-14 14:27:39 ] INFO Threshold below which ignored: 0 [ 2018-06-14 14:27:39 ] INFO Applying gene filter expression... [ 2018-06-14 14:27:40 ] INFO Threshold below which ignored: 6 [ 2018-06-14 14:27:40 ] INFO Applying gene filter biotype... [ 2018-06-14 14:27:40 ] INFO Biotypes ignored: rRNA, TR_V_pseudogene, TR_J_pseudogene, IG_C_pseudogene, IG_J_pseudogene, IG_V_pseudogene [ 2018-06-14 14:27:40 ] INFO 38425 genes filtered out [ 2018-06-14 14:27:40 ] INFO 15253 genes remain after filtering [ 2018-06-14 14:27:40 ] INFO Running statistical tests with: deseq [ 2018-06-14 14:27:41 ] INFO Contrast: Wt_vs_C_221_222 [ 2018-06-14 14:27:54 ] INFO Contrast: Wt_vs_Tg197 [ 2018-06-14 14:28:09 ] INFO Contrast: Tg197_C_vs_Tg197 [ 2018-06-14 14:28:26 ] INFO Contrast: Tg197_C_vs_C_221_222 [ 2018-06-14 14:28:40 ] INFO Contrast Wt_vs_C_221_222: found 178 genes [ 2018-06-14 14:28:40 ] INFO Contrast Wt_vs_Tg197: found 550 genes [ 2018-06-14 14:28:40 ] INFO Contrast Tg197_C_vs_Tg197: found 686 genes [ 2018-06-14 14:28:40 ] INFO Contrast Tg197_C_vs_C_221_222: found 1081 genes [ 2018-06-14 14:28:40 ] INFO Exporting and compressing normalized read counts table to /data/images/proton2/run403/www/metaseqr_GKlab_run403/lists/normalized_counts_table.txt [ 2018-06-14 14:28:42 ] INFO Building output files... [ 2018-06-14 14:28:44 ] INFO Contrast: Wt_vs_C_221_222 [ 2018-06-14 14:28:44 ] INFO Adding non-filtered data... [ 2018-06-14 14:28:44 ] INFO binding annotation... [ 2018-06-14 14:28:45 ] INFO binding p-values... [ 2018-06-14 14:28:45 ] INFO binding FDRs... [ 2018-06-14 14:28:45 ] INFO binding log2 normalized fold changes... [ 2018-06-14 14:28:45 ] INFO binding all normalized counts for Wt... [ 2018-06-14 14:28:46 ] INFO binding all normalized counts for C_221_222... [ 2018-06-14 14:28:46 ] INFO binding filtering flags... [ 2018-06-14 14:28:47 ] INFO Writing output... [ 2018-06-14 14:28:47 ] INFO Adding filtered data... [ 2018-06-14 14:28:47 ] INFO binding annotation... [ 2018-06-14 14:28:47 ] INFO binding p-values... [ 2018-06-14 14:28:47 ] INFO binding FDRs... [ 2018-06-14 14:28:48 ] INFO binding log2 normalized fold changes... [ 2018-06-14 14:28:48 ] INFO binding all normalized counts for Wt... [ 2018-06-14 14:28:48 ] INFO binding all normalized counts for C_221_222... [ 2018-06-14 14:28:48 ] INFO binding filtering flags... [ 2018-06-14 14:28:49 ] INFO Writing output... [ 2018-06-14 14:28:50 ] INFO Contrast: Wt_vs_Tg197 [ 2018-06-14 14:28:50 ] INFO Adding non-filtered data... [ 2018-06-14 14:28:50 ] INFO binding annotation... [ 2018-06-14 14:28:51 ] INFO binding p-values... [ 2018-06-14 14:28:51 ] INFO binding FDRs... [ 2018-06-14 14:28:52 ] INFO binding log2 normalized fold changes... [ 2018-06-14 14:28:52 ] INFO binding all normalized counts for Wt... [ 2018-06-14 14:28:52 ] INFO binding all normalized counts for Tg197... [ 2018-06-14 14:28:53 ] INFO binding filtering flags... [ 2018-06-14 14:28:53 ] INFO Writing output... [ 2018-06-14 14:28:53 ] INFO Adding filtered data... [ 2018-06-14 14:28:53 ] INFO binding annotation... [ 2018-06-14 14:28:53 ] INFO binding p-values... [ 2018-06-14 14:28:53 ] INFO binding FDRs... [ 2018-06-14 14:28:54 ] INFO binding log2 normalized fold changes... [ 2018-06-14 14:28:54 ] INFO binding all normalized counts for Wt... [ 2018-06-14 14:28:54 ] INFO binding all normalized counts for Tg197... [ 2018-06-14 14:28:54 ] INFO binding filtering flags... [ 2018-06-14 14:28:55 ] INFO Writing output... [ 2018-06-14 14:28:57 ] INFO Contrast: Tg197_C_vs_Tg197 [ 2018-06-14 14:28:57 ] INFO Adding non-filtered data... [ 2018-06-14 14:28:57 ] INFO binding annotation... [ 2018-06-14 14:28:57 ] INFO binding p-values... [ 2018-06-14 14:28:57 ] INFO binding FDRs... [ 2018-06-14 14:28:58 ] INFO binding log2 normalized fold changes... [ 2018-06-14 14:28:58 ] INFO binding all normalized counts for Tg197_C... [ 2018-06-14 14:28:58 ] INFO binding all normalized counts for Tg197... [ 2018-06-14 14:28:59 ] INFO binding filtering flags... [ 2018-06-14 14:29:00 ] INFO Writing output... [ 2018-06-14 14:29:00 ] INFO Adding filtered data... [ 2018-06-14 14:29:00 ] INFO binding annotation... [ 2018-06-14 14:29:00 ] INFO binding p-values... [ 2018-06-14 14:29:00 ] INFO binding FDRs... [ 2018-06-14 14:29:01 ] INFO binding log2 normalized fold changes... [ 2018-06-14 14:29:01 ] INFO binding all normalized counts for Tg197_C... [ 2018-06-14 14:29:01 ] INFO binding all normalized counts for Tg197... [ 2018-06-14 14:29:01 ] INFO binding filtering flags... [ 2018-06-14 14:29:01 ] INFO Writing output... [ 2018-06-14 14:29:03 ] INFO Contrast: Tg197_C_vs_C_221_222 [ 2018-06-14 14:29:03 ] INFO Adding non-filtered data... [ 2018-06-14 14:29:03 ] INFO binding annotation... [ 2018-06-14 14:29:04 ] INFO binding p-values... [ 2018-06-14 14:29:04 ] INFO binding FDRs... [ 2018-06-14 14:29:04 ] INFO binding log2 normalized fold changes... [ 2018-06-14 14:29:05 ] INFO binding all normalized counts for Tg197_C... [ 2018-06-14 14:29:05 ] INFO binding all normalized counts for C_221_222... [ 2018-06-14 14:29:06 ] INFO binding filtering flags... [ 2018-06-14 14:29:06 ] INFO Writing output... [ 2018-06-14 14:29:06 ] INFO Adding filtered data... [ 2018-06-14 14:29:06 ] INFO binding annotation... [ 2018-06-14 14:29:06 ] INFO binding p-values... [ 2018-06-14 14:29:06 ] INFO binding FDRs... [ 2018-06-14 14:29:07 ] INFO binding log2 normalized fold changes... [ 2018-06-14 14:29:07 ] INFO binding all normalized counts for Tg197_C... [ 2018-06-14 14:29:07 ] INFO binding all normalized counts for C_221_222... [ 2018-06-14 14:29:07 ] INFO binding filtering flags... [ 2018-06-14 14:29:08 ] INFO Writing output... [ 2018-06-14 14:29:10 ] INFO Creating quality control graphs... [ 2018-06-14 14:29:10 ] INFO Plotting in png format... [ 2018-06-14 14:29:10 ] INFO Plotting mds... [ 2018-06-14 14:29:10 ] INFO Plotting biodetection... [ 2018-06-14 14:29:12 ] INFO Plotting countsbio... [ 2018-06-14 14:29:14 ] INFO Plotting saturation... [ 2018-06-14 14:29:24 ] INFO Plotting readnoise... [ 2018-06-14 14:29:25 ] INFO Plotting correl... [ 2018-06-14 14:29:25 ] INFO Plotting pairwise... [ 2018-06-14 14:30:17 ] INFO Plotting boxplot... [ 2018-06-14 14:30:17 ] INFO Plotting gcbias... [ 2018-06-14 14:30:18 ] INFO Plotting lengthbias... [ 2018-06-14 14:30:19 ] INFO Plotting boxplot... [ 2018-06-14 14:30:19 ] INFO Plotting gcbias... [ 2018-06-14 14:30:21 ] INFO Plotting lengthbias... [ 2018-06-14 14:30:22 ] INFO Plotting biodist... [ 2018-06-14 14:30:22 ] INFO Contrast: Wt_vs_C_221_222 [ 2018-06-14 14:30:22 ] INFO Contrast: Wt_vs_Tg197 [ 2018-06-14 14:30:23 ] INFO Contrast: Tg197_C_vs_Tg197 [ 2018-06-14 14:30:23 ] INFO Contrast: Tg197_C_vs_C_221_222 [ 2018-06-14 14:30:23 ] INFO Plotting volcano... [ 2018-06-14 14:30:23 ] INFO Contrast: Wt_vs_C_221_222 [ 2018-06-14 14:30:24 ] INFO Contrast: Wt_vs_Tg197 [ 2018-06-14 14:30:25 ] INFO Contrast: Tg197_C_vs_Tg197 [ 2018-06-14 14:30:25 ] INFO Contrast: Tg197_C_vs_C_221_222 [ 2018-06-14 14:30:26 ] INFO Plotting deheatmap... [ 2018-06-14 14:30:26 ] INFO Contrast: Wt_vs_C_221_222 [ 2018-06-14 14:31:01 ] INFO Contrast: Wt_vs_Tg197 [ 2018-06-14 14:31:34 ] INFO Contrast: Tg197_C_vs_Tg197 [ 2018-06-14 14:32:09 ] INFO Contrast: Tg197_C_vs_C_221_222 [ 2018-06-14 14:32:43 ] INFO Plotting filtered... [ 2018-06-14 14:32:43 ] INFO Plotting in pdf format... [ 2018-06-14 14:32:43 ] INFO Plotting mds... [ 2018-06-14 14:32:44 ] INFO Plotting biodetection... [ 2018-06-14 14:32:45 ] INFO Plotting countsbio... [ 2018-06-14 14:32:46 ] INFO Plotting saturation... [ 2018-06-14 14:32:53 ] INFO Plotting readnoise... [ 2018-06-14 14:32:55 ] INFO Plotting correl... [ 2018-06-14 14:32:55 ] INFO Plotting pairwise... [ 2018-06-14 14:33:19 ] INFO Plotting boxplot... [ 2018-06-14 14:33:20 ] INFO Plotting gcbias... [ 2018-06-14 14:33:21 ] INFO Plotting lengthbias... [ 2018-06-14 14:33:22 ] INFO Plotting boxplot... [ 2018-06-14 14:33:23 ] INFO Plotting gcbias... [ 2018-06-14 14:33:24 ] INFO Plotting lengthbias... [ 2018-06-14 14:33:25 ] INFO Plotting biodist... [ 2018-06-14 14:33:25 ] INFO Contrast: Wt_vs_C_221_222 [ 2018-06-14 14:33:26 ] INFO Contrast: Wt_vs_Tg197 [ 2018-06-14 14:33:26 ] INFO Contrast: Tg197_C_vs_Tg197 [ 2018-06-14 14:33:26 ] INFO Contrast: Tg197_C_vs_C_221_222 [ 2018-06-14 14:33:26 ] INFO Plotting volcano... [ 2018-06-14 14:33:26 ] INFO Contrast: Wt_vs_C_221_222 [ 2018-06-14 14:33:27 ] INFO Contrast: Wt_vs_Tg197 [ 2018-06-14 14:33:27 ] INFO Contrast: Tg197_C_vs_Tg197 [ 2018-06-14 14:33:27 ] INFO Contrast: Tg197_C_vs_C_221_222 [ 2018-06-14 14:33:28 ] INFO Plotting deheatmap... [ 2018-06-14 14:33:28 ] INFO Contrast: Wt_vs_C_221_222 [ 2018-06-14 14:34:01 ] INFO Contrast: Wt_vs_Tg197 [ 2018-06-14 14:34:34 ] INFO Contrast: Tg197_C_vs_Tg197 [ 2018-06-14 14:35:09 ] INFO Contrast: Tg197_C_vs_C_221_222 [ 2018-06-14 14:35:44 ] INFO Plotting filtered... [ 2018-06-14 14:35:44 ] INFO Creating HTML report... [ 2018-06-14 14:35:44 ] INFO Compressing figures...
Multidimensional scaling
Biotype detection
Biotype detection counts
Read and biotype saturation
RNA-Seq reads noise
Correlation plots
Pairwise scatterplots
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_vs_C_221_222The 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_vs_C_221_222. The fields of the table correspond to the requested features to be exported. The table can be searched using the search field on the top right. | chromosome | start | end | gene_id | gc_content | strand | gene_name | biotype | p-value_deseq | FDR_deseq | log2_normalized_fold_change_Wt_vs_C_221_222 | log2_normalized_counts_GK3R188-Wt1 | log2_normalized_counts_GK3R189-Wt2 | rpgm_normalized_counts_GK3R188-Wt1 | rpgm_normalized_counts_GK3R189-Wt2 | log2_normalized_counts_GK3R190-C1 | log2_normalized_counts_GK3R191-C2 | log2_normalized_counts_GK3R192-C3 | rpgm_normalized_counts_GK3R190-C1 | rpgm_normalized_counts_GK3R191-C2 | rpgm_normalized_counts_GK3R192-C3 | LN | AR | MD | MN | QN | KN | CM | BT | PR |
|---|
| chr2 | 164940780 | 164955850 | ENSMUSG00000017737 | 0.5213 | + | Mmp9 | protein_coding | 1.75e-16 | 2.66e-12 | -5.207400 | 8.65e+00 | 6.02e+00 | 8.56e-02 | 1.36e-02 | 2.81e+00 | 3.32e+00 | 1.00e+00 | 1.28e-03 | 1.92e-03 | 2.13e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 130913125 | 130936141 | ENSMUSG00000028581 | 0.5309 | + | Laptm5 | protein_coding | 1.42e-10 | 1.08e-06 | -4.023536 | 6.99e+00 | 6.30e+00 | 1.22e-02 | 7.52e-03 | 2.00e+00 | 3.32e+00 | 2.32e+00 | 2.89e-04 | 8.68e-04 | 3.86e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 39581685 | 39642673 | ENSMUSG00000025044 | 0.3639 | - | Msr1 | protein_coding | 5.77e-09 | 2.93e-05 | -4.977280 | 6.30e+00 | 4.70e+00 | 8.84e-03 | 2.83e-03 | 1.00e+00 | 1.00e+00 | 0.00e+00 | 1.13e-04 | 1.13e-04 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 117277331 | 117282321 | ENSMUSG00000069516 | 0.4708 | - | Lyz2 | protein_coding | 1.05e-08 | 4.01e-05 | -3.139551 | 7.76e+00 | 7.69e+00 | 1.06e-01 | 1.00e-01 | 3.81e+00 | 3.32e+00 | 5.58e+00 | 6.37e-03 | 4.41e-03 | 2.30e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr15 | 77583819 | 77596125 | ENSMUSG00000050014 | 0.4661 | - | Apol10b | protein_coding | 1.10e-07 | 3.35e-04 | -3.584963 | 5.36e+00 | 5.55e+00 | 1.66e-02 | 1.91e-02 | 1.00e+00 | 2.00e+00 | 2.32e+00 | 4.16e-04 | 1.25e-03 | 1.66e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 91082390 | 91115756 | ENSMUSG00000002111 | 0.4989 | + | Spi1 | protein_coding | 1.74e-07 | 4.41e-04 | -4.321928 | 6.48e+00 | 4.95e+00 | 1.64e-02 | 5.59e-03 | 1.00e+00 | 1.00e+00 | 2.32e+00 | 1.86e-04 | 1.86e-04 | 7.45e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 30413760 | 30417585 | ENSMUSG00000030579 | 0.4851 | + | Tyrobp | protein_coding | 1.27e-06 | 2.78e-03 | -4.312883 | 4.86e+00 | 4.58e+00 | 7.90e-03 | 6.49e-03 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 2.82e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 22126727 | 22135711 | ENSMUSG00000001348 | 0.5233 | - | Acp5 | protein_coding | 1.84e-06 | 3.51e-03 | -3.260123 | 7.12e+00 | 5.88e+00 | 4.94e-02 | 2.08e-02 | 2.58e+00 | 4.17e+00 | 2.81e+00 | 1.79e-03 | 6.08e-03 | 2.15e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 134082448 | 134095082 | ENSMUSG00000000682 | 0.4953 | - | Cd52 | protein_coding | 5.01e-06 | 8.50e-03 | -3.584963 | 3.46e+00 | 3.70e+00 | 2.54e-03 | 3.04e-03 | 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 | 0 |
Download the DEG result list for Wt_vs_C_221_222.Download the whole result list for Wt_vs_C_221_222.DEG table for the contrast Wt_vs_Tg197The 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_vs_Tg197. The fields of the table correspond to the requested features to be exported. The table can be searched using the search field on the top right. | chromosome | start | end | gene_id | gc_content | strand | gene_name | biotype | p-value_deseq | FDR_deseq | log2_normalized_fold_change_Wt_vs_Tg197 | log2_normalized_counts_GK3R188-Wt1 | log2_normalized_counts_GK3R189-Wt2 | rpgm_normalized_counts_GK3R188-Wt1 | rpgm_normalized_counts_GK3R189-Wt2 | log2_normalized_counts_GK3R193-Tg197-1 | log2_normalized_counts_GK3R194-Tg197-2 | log2_normalized_counts_GK3R195-Tg197-3 | rpgm_normalized_counts_GK3R193-Tg197-1 | rpgm_normalized_counts_GK3R194-Tg197-2 | rpgm_normalized_counts_GK3R195-Tg197-3 | LN | AR | MD | MN | QN | KN | CM | BT | PR |
|---|
| chr7 | 46711998 | 46715700 | ENSMUSG00000040026 | 0.4807 | - | Saa3 | protein_coding | 1.24e-26 | 1.90e-22 | 8.113102 | 3.81e+00 | 2.32e+00 | 2.83e-03 | 8.72e-04 | 1.11e+01 | 1.11e+01 | 1.18e+01 | 4.70e-01 | 4.78e-01 | 7.73e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 83116766 | 83119167 | ENSMUSG00000026166 | 0.3926 | + | Ccl20 | protein_coding | 2.45e-20 | 1.87e-16 | 6.130091 | 5.61e+00 | 4.25e+00 | 2.09e-02 | 7.82e-03 | 1.08e+01 | 1.12e+01 | 1.16e+01 | 7.58e-01 | 1.01e+00 | 1.33e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr19 | 34473786 | 34475135 | ENSMUSG00000050370 | 0.4985 | - | Ch25h | protein_coding | 1.91e-15 | 9.69e-12 | 5.680304 | 2.58e+00 | 4.95e+00 | 3.47e-03 | 2.08e-02 | 9.38e+00 | 9.68e+00 | 1.04e+01 | 4.61e-01 | 5.70e-01 | 9.40e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 57203970 | 57228136 | ENSMUSG00000024164 | 0.5201 | - | C3 | protein_coding | 2.32e-11 | 8.85e-08 | 3.755054 | 6.30e+00 | 4.81e+00 | 2.05e-02 | 7.11e-03 | 9.04e+00 | 9.70e+00 | 9.66e+00 | 1.38e-01 | 2.19e-01 | 2.13e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 7445822 | 7455975 | ENSMUSG00000043613 | 0.4079 | + | Mmp3 | protein_coding | 3.46e-11 | 1.06e-07 | 3.883325 | 7.31e+00 | 6.52e+00 | 1.03e-01 | 5.92e-02 | 1.08e+01 | 1.11e+01 | 1.06e+01 | 1.15e+00 | 1.45e+00 | 1.01e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 45370185 | 45396159 | ENSMUSG00000066705 | 0.4943 | + | Fxyd6 | protein_coding | 2.64e-10 | 6.72e-07 | -3.941106 | 7.17e+00 | 6.81e+00 | 3.04e-02 | 2.36e-02 | 3.58e+00 | 2.81e+00 | 2.58e+00 | 2.34e-03 | 1.28e-03 | 1.06e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 30723547 | 30748465 | ENSMUSG00000051855 | 0.4545 | + | Mest | protein_coding | 6.46e-10 | 1.41e-06 | -3.230329 | 9.46e+00 | 8.94e+00 | 7.97e-02 | 5.56e-02 | 5.52e+00 | 5.46e+00 | 6.66e+00 | 5.10e-03 | 4.88e-03 | 1.13e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr18 | 35713086 | 35722356 | ENSMUSG00000073599 | 0.4990 | - | Ecscr | protein_coding | 1.34e-09 | 2.55e-06 | 3.639898 | 5.36e+00 | 5.00e+00 | 7.40e-03 | 5.74e-03 | 8.80e+00 | 9.08e+00 | 8.55e+00 | 8.26e-02 | 1.00e-01 | 6.92e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 19696109 | 19699188 | ENSMUSG00000002985 | 0.5464 | - | Apoe | protein_coding | 2.72e-09 | 4.62e-06 | -4.179909 | 9.00e+00 | 6.07e+00 | 1.47e-01 | 1.90e-02 | 4.75e+00 | 3.00e+00 | 3.70e+00 | 7.49e-03 | 2.02e-03 | 3.46e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 79434669 | 79440120 | ENSMUSG00000050711 | 0.3955 | - | Scg2 | protein_coding | 3.40e-09 | 4.84e-06 | -3.476586 | 6.00e+00 | 6.27e+00 | 3.64e-02 | 4.39e-02 | 3.00e+00 | 3.00e+00 | 1.58e+00 | 4.04e-03 | 4.04e-03 | 1.15e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 104247905 | 104253669 | ENSMUSG00000041449 | 0.4772 | + | Serpina3h | transcribed_unprocessed_pseudogene | 3.49e-09 | 4.84e-06 | 3.258016 | 5.67e+00 | 3.17e+00 | 2.00e-02 | 3.20e-03 | 7.91e+00 | 7.99e+00 | 8.52e+00 | 9.55e-02 | 1.02e-01 | 1.46e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 112106679 | 112127559 | ENSMUSG00000037686 | 0.5676 | + | Aspg | protein_coding | 4.66e-09 | 5.93e-06 | -3.227536 | 6.93e+00 | 7.31e+00 | 9.10e-03 | 1.19e-02 | 3.70e+00 | 2.32e+00 | 4.75e+00 | 9.02e-04 | 3.01e-04 | 1.95e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 31470207 | 31520672 | ENSMUSG00000076441 | 0.5281 | + | Ass1 | protein_coding | 7.35e-09 | 8.62e-06 | 3.722466 | 4.58e+00 | 4.00e+00 | 5.74e-03 | 3.74e-03 | 8.08e+00 | 8.17e+00 | 7.87e+00 | 6.71e-02 | 7.16e-02 | 5.81e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 109575128 | 109579172 | ENSMUSG00000031722 | 0.5125 | - | Hp | protein_coding | 1.47e-08 | 1.60e-05 | 3.339096 | 7.29e+00 | 7.38e+00 | 5.50e-02 | 5.82e-02 | 1.01e+01 | 1.06e+01 | 1.11e+01 | 3.80e-01 | 5.62e-01 | 7.85e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 82035571 | 82037453 | ENSMUSG00000035385 | 0.4376 | + | Ccl2 | protein_coding | 1.89e-08 | 1.92e-05 | 3.744269 | 9.85e+00 | 9.96e+00 | 6.04e-01 | 6.53e-01 | 1.34e+01 | 1.38e+01 | 1.37e+01 | 7.11e+00 | 9.35e+00 | 8.84e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 68723646 | 68782650 | ENSMUSG00000060044 | 0.4056 | + | Tmem26 | protein_coding | 2.86e-08 | 2.73e-05 | -2.691878 | 7.94e+00 | 8.30e+00 | 2.17e-02 | 2.80e-02 | 5.32e+00 | 5.46e+00 | 5.52e+00 | 3.47e-03 | 3.83e-03 | 4.01e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 31086106 | 31108237 | ENSMUSG00000029151 | 0.4999 | - | Slc30a3 | protein_coding | 4.51e-08 | 4.04e-05 | -3.447459 | 4.00e+00 | 7.17e+00 | 2.55e-03 | 2.43e-02 | 3.17e+00 | 3.32e+00 | 1.58e+00 | 1.36e-03 | 1.53e-03 | 3.40e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 128862981 | 128897034 | ENSMUSG00000027386 | 0.4755 | + | Fbln7 | protein_coding | 1.18e-07 | 9.96e-05 | -2.850465 | 7.31e+00 | 7.58e+00 | 5.86e-02 | 7.08e-02 | 4.58e+00 | 3.17e+00 | 5.32e+00 | 8.53e-03 | 2.97e-03 | 1.45e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 62071123 | 62072362 | ENSMUSG00000046687 | 0.5395 | + | Gm5424 | processed_pseudogene | 1.45e-07 | 1.16e-04 | 2.984146 | 5.61e+00 | 3.58e+00 | 3.84e-02 | 8.79e-03 | 7.95e+00 | 8.09e+00 | 7.68e+00 | 1.97e-01 | 2.17e-01 | 1.63e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 70373558 | 70382066 | ENSMUSG00000031849 | 0.5643 | + | Comp | protein_coding | 3.50e-07 | 2.67e-04 | -3.347271 | 1.39e+01 | 1.15e+01 | 2.47e+00 | 4.75e-01 | 1.01e+01 | 9.46e+00 | 9.83e+00 | 1.73e-01 | 1.14e-01 | 1.47e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 45555716 | 45563169 | ENSMUSG00000023947 | 0.5346 | + | Nfkbie | protein_coding | 4.38e-07 | 3.16e-04 | 3.415037 | 4.25e+00 | 2.00e+00 | 7.65e-03 | 1.27e-03 | 6.48e+00 | 6.98e+00 | 7.26e+00 | 3.74e-02 | 5.31e-02 | 6.46e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr19 | 6418731 | 6544169 | ENSMUSG00000033768 | 0.5368 | + | Nrxn2 | protein_coding | 4.56e-07 | 3.16e-04 | -3.748709 | 7.40e+00 | 6.00e+00 | 1.43e-02 | 5.38e-03 | 3.32e+00 | 1.00e+00 | 3.81e+00 | 7.68e-04 | 8.53e-05 | 1.11e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 66673425 | 66784914 | ENSMUSG00000034810 | 0.3734 | - | Scn7a | protein_coding | 6.19e-07 | 4.11e-04 | -3.002815 | 5.88e+00 | 6.81e+00 | 1.74e-02 | 3.34e-02 | 2.81e+00 | 3.81e+00 | 3.46e+00 | 1.81e-03 | 3.91e-03 | 3.01e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr15 | 54838901 | 54952892 | ENSMUSG00000022425 | 0.4130 | - | Enpp2 | protein_coding | 6.84e-07 | 4.35e-04 | 2.729146 | 6.51e+00 | 5.83e+00 | 1.13e-02 | 7.03e-03 | 8.76e+00 | 8.75e+00 | 9.25e+00 | 5.42e-02 | 5.39e-02 | 7.62e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr18 | 60911780 | 60918561 | ENSMUSG00000036412 | 0.5268 | + | Arsi | protein_coding | 7.99e-07 | 4.79e-04 | -2.598509 | 7.83e+00 | 7.65e+00 | 1.11e-01 | 9.78e-02 | 5.67e+00 | 4.09e+00 | 5.25e+00 | 2.45e-02 | 7.83e-03 | 1.81e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 134702593 | 134747323 | ENSMUSG00000029675 | 0.4978 | - | Eln | protein_coding | 8.17e-07 | 4.79e-04 | -2.668598 | 9.24e+00 | 8.39e+00 | 3.62e-02 | 2.00e-02 | 6.83e+00 | 5.49e+00 | 5.98e+00 | 6.75e-03 | 2.63e-03 | 3.71e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 102988712 | 103096002 | ENSMUSG00000032548 | 0.4822 | + | Slco2a1 | protein_coding | 1.31e-06 | 7.38e-04 | 3.300395 | 4.00e+00 | 4.86e+00 | 1.05e-03 | 1.95e-03 | 7.67e+00 | 7.86e+00 | 7.84e+00 | 1.41e-02 | 1.62e-02 | 1.59e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 70453983 | 70459984 | ENSMUSG00000018920 | 0.4742 | - | Cxcl16 | protein_coding | 1.43e-06 | 7.54e-04 | 2.934217 | 4.95e+00 | 3.58e+00 | 1.12e-02 | 4.12e-03 | 7.29e+00 | 7.52e+00 | 7.26e+00 | 5.80e-02 | 6.85e-02 | 5.69e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for Wt_vs_Tg197.Download the whole result list for Wt_vs_Tg197.DEG table for the contrast Tg197_C_vs_Tg197The following table presents the top 5% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Tg197_C_vs_Tg197. The fields of the table correspond to the requested features to be exported. The table can be searched using the search field on the top right. | chromosome | start | end | gene_id | gc_content | strand | gene_name | biotype | p-value_deseq | FDR_deseq | log2_normalized_fold_change_Tg197_C_vs_Tg197 | log2_normalized_counts_GK3R196-Tg197-C1 | log2_normalized_counts_GK3R197-Tg197-C2 | log2_normalized_counts_GK3R198-Tg197-C3 | rpgm_normalized_counts_GK3R196-Tg197-C1 | rpgm_normalized_counts_GK3R197-Tg197-C2 | rpgm_normalized_counts_GK3R198-Tg197-C3 | log2_normalized_counts_GK3R193-Tg197-1 | log2_normalized_counts_GK3R194-Tg197-2 | log2_normalized_counts_GK3R195-Tg197-3 | rpgm_normalized_counts_GK3R193-Tg197-1 | rpgm_normalized_counts_GK3R194-Tg197-2 | rpgm_normalized_counts_GK3R195-Tg197-3 | LN | AR | MD | MN | QN | KN | CM | BT | PR |
|---|
| chr6 | 70726435 | 70726966 | ENSMUSG00000076609 | 0.4925 | + | Igkc | IG_C_gene | 3.30e-17 | 5.03e-13 | -7.194757 | 0.00e+00 | 9.16e+00 | 3.70e+00 | 0.00e+00 | 4.73e-01 | 9.93e-03 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 8.28e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 4772373 | 4782857 | ENSMUSG00000004371 | 0.5362 | - | Il11 | protein_coding | 2.99e-13 | 2.28e-09 | -2.860480 | 9.94e+00 | 4.52e+00 | 8.22e+00 | 4.00e-01 | 9.00e-03 | 1.21e-01 | 6.29e+00 | 6.00e+00 | 5.21e+00 | 3.15e-02 | 2.58e-02 | 1.47e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 113254830 | 113260236 | ENSMUSG00000095079 | 0.5130 | - | Igha | IG_C_gene | 6.80e-11 | 3.46e-07 | -6.290019 | 0.00e+00 | 8.27e+00 | 1.58e+00 | 0.00e+00 | 7.82e-02 | 5.08e-04 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 2.54e-04 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 88519809 | 88527891 | ENSMUSG00000067149 | 0.3678 | - | Jchain | protein_coding | 5.93e-09 | 2.26e-05 | -6.087463 | 1.00e+00 | 7.65e+00 | 0.00e+00 | 3.03e-04 | 6.06e-02 | 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 | 0 | | chr6 | 124996694 | 125003096 | ENSMUSG00000030329 | 0.5627 | + | Pianp | protein_coding | 1.83e-06 | 5.28e-03 | 2.005853 | 0.00e+00 | 5.86e+00 | 6.00e+00 | 0.00e+00 | 8.84e-03 | 9.77e-03 | 8.04e+00 | 7.80e+00 | 3.00e+00 | 4.06e-02 | 3.44e-02 | 1.09e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 19696109 | 19699188 | ENSMUSG00000002985 | 0.5464 | - | Apoe | protein_coding | 2.08e-06 | 5.28e-03 | -2.066089 | 6.19e+00 | 3.46e+00 | 6.87e+00 | 2.07e-02 | 2.88e-03 | 3.34e-02 | 4.75e+00 | 3.00e+00 | 3.70e+00 | 7.49e-03 | 2.02e-03 | 3.46e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 143999338 | 144004161 | ENSMUSG00000026360 | 0.4362 | - | Rgs2 | protein_coding | 2.96e-06 | 6.46e-03 | -1.830562 | 8.73e+00 | 6.54e+00 | 7.12e+00 | 6.49e-02 | 1.41e-02 | 2.11e-02 | 5.98e+00 | 5.86e+00 | 6.00e+00 | 9.47e-03 | 8.70e-03 | 9.62e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 134182176 | 134190181 | ENSMUSG00000064246 | 0.5034 | + | Chil1 | protein_coding | 3.64e-06 | 6.93e-03 | -2.474404 | 6.43e+00 | 6.00e+00 | 7.56e+00 | 2.53e-02 | 1.88e-02 | 5.60e-02 | 4.09e+00 | 4.86e+00 | 3.91e+00 | 4.76e-03 | 8.34e-03 | 4.17e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 60223290 | 60592698 | ENSMUSG00000062949 | 0.3852 | - | Atp11c | protein_coding | 4.31e-06 | 6.93e-03 | -2.519286 | 8.68e+00 | 1.08e+01 | 1.00e+01 | 6.81e-02 | 3.04e-01 | 1.75e-01 | 8.05e+00 | 7.81e+00 | 6.39e+00 | 4.39e-02 | 3.71e-02 | 1.38e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr15 | 97854425 | 97910630 | ENSMUSG00000022479 | 0.4995 | - | Vdr | protein_coding | 4.72e-06 | 6.93e-03 | -1.657677 | 8.69e+00 | 5.78e+00 | 6.92e+00 | 5.94e-02 | 7.77e-03 | 1.73e-02 | 6.61e+00 | 5.64e+00 | 5.29e+00 | 1.40e-02 | 7.05e-03 | 5.47e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 16356304 | 16755839 | ENSMUSG00000026748 | 0.3807 | + | Plxdc2 | protein_coding | 5.00e-06 | 6.93e-03 | 2.007184 | 7.44e+00 | 7.88e+00 | 7.58e+00 | 2.99e-02 | 4.06e-02 | 3.29e-02 | 8.40e+00 | 1.05e+01 | 9.19e+00 | 5.83e-02 | 2.58e-01 | 1.01e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 117277331 | 117282321 | ENSMUSG00000069516 | 0.4708 | - | Lyz2 | protein_coding | 5.53e-06 | 7.02e-03 | 1.656347 | 4.86e+00 | 7.03e+00 | 4.58e+00 | 1.37e-02 | 6.37e-02 | 1.13e-02 | 7.59e+00 | 7.86e+00 | 7.28e+00 | 9.41e-02 | 1.13e-01 | 7.55e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 80798198 | 80804924 | ENSMUSG00000020211 | 0.5664 | + | Sf3a2 | protein_coding | 6.83e-06 | 7.73e-03 | -1.706233 | 9.21e+00 | 7.88e+00 | 1.03e+01 | 1.19e-01 | 4.74e-02 | 2.60e-01 | 8.54e+00 | 7.19e+00 | 7.04e+00 | 7.48e-02 | 2.93e-02 | 2.64e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr14 | 46383520 | 46390669 | ENSMUSG00000021835 | 0.5305 | - | Bmp4 | protein_coding | 7.09e-06 | 7.73e-03 | 1.233760 | 4.91e+00 | 7.92e+00 | 5.13e+00 | 7.09e-03 | 5.89e-02 | 8.31e-03 | 6.32e+00 | 7.88e+00 | 8.67e+00 | 1.93e-02 | 5.72e-02 | 9.92e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr13 | 30336441 | 30382867 | ENSMUSG00000049115 | 0.4305 | + | Agtr1a | protein_coding | 1.46e-05 | 1.49e-02 | 3.184425 | 3.00e+00 | 2.81e+00 | 2.81e+00 | 1.48e-03 | 1.27e-03 | 1.27e-03 | 5.21e+00 | 6.17e+00 | 6.51e+00 | 7.62e-03 | 1.50e-02 | 1.91e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr14 | 56082166 | 56085273 | ENSMUSG00000022157 | 0.4569 | - | Mcpt8 | protein_coding | 4.24e-05 | 3.98e-02 | -1.607330 | 8.34e+00 | 5.93e+00 | 7.64e+00 | 6.54e-02 | 1.21e-02 | 4.00e-02 | 5.64e+00 | 6.34e+00 | 5.93e+00 | 9.89e-03 | 1.62e-02 | 1.21e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 56294585 | 56321043 | ENSMUSG00000031613 | 0.3691 | + | Hpgd | protein_coding | 4.44e-05 | 3.98e-02 | 2.070912 | 6.23e+00 | 5.17e+00 | 7.25e+00 | 3.54e-02 | 1.68e-02 | 7.23e-02 | 7.99e+00 | 7.80e+00 | 9.29e+00 | 1.21e-01 | 1.06e-01 | 3.00e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 78816758 | 78820028 | ENSMUSG00000047330 | 0.4720 | + | Kcne4 | protein_coding | 6.07e-05 | 4.91e-02 | -1.467126 | 7.16e+00 | 2.81e+00 | 6.41e+00 | 4.54e-02 | 1.92e-03 | 2.68e-02 | 5.58e+00 | 4.09e+00 | 4.32e+00 | 1.50e-02 | 5.11e-03 | 6.07e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 149614287 | 149636376 | ENSMUSG00000029657 | 0.4550 | - | Hsph1 | protein_coding | 6.29e-05 | 4.91e-02 | -1.215096 | 1.18e+01 | 6.81e+00 | 1.10e+01 | 3.41e-01 | 1.09e-02 | 1.96e-01 | 1.02e+01 | 8.56e+00 | 9.75e+00 | 1.14e-01 | 3.70e-02 | 8.44e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 142851146 | 142966728 | ENSMUSG00000042225 | 0.3787 | - | Ammecr1 | protein_coding | 6.43e-05 | 4.91e-02 | 1.847517 | 5.67e+00 | 6.21e+00 | 5.39e+00 | 8.87e-03 | 1.29e-02 | 7.27e-03 | 7.48e+00 | 7.86e+00 | 7.57e+00 | 3.16e-02 | 4.10e-02 | 3.35e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 155398763 | 155421704 | ENSMUSG00000084803 | 0.4660 | - | 5830444B04Rik | processed_transcript | 7.06e-05 | 5.13e-02 | 4.196397 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 3.00e+00 | 4.00e+00 | 4.95e+00 | 1.86e-03 | 4.00e-03 | 7.99e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr14 | 47240944 | 47276857 | ENSMUSG00000037572 | 0.4054 | - | Wdhd1 | protein_coding | 8.01e-05 | 5.55e-02 | -1.882997 | 7.65e+00 | 7.40e+00 | 7.12e+00 | 3.09e-02 | 2.60e-02 | 2.13e-02 | 5.75e+00 | 5.21e+00 | 5.55e+00 | 8.19e-03 | 5.56e-03 | 7.11e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 25626654 | 25635100 | ENSMUSG00000059479 | 0.5666 | + | B3gnt8 | protein_coding | 1.18e-04 | 7.81e-02 | 3.369234 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 3.70e+00 | 3.32e+00 | 3.00e+00 | 1.51e-03 | 1.13e-03 | 8.78e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr19 | 4611785 | 4615667 | ENSMUSG00000045045 | 0.6467 | - | Lrfn4 | protein_coding | 1.32e-04 | 8.05e-02 | -1.473727 | 7.88e+00 | 6.58e+00 | 8.83e+00 | 1.52e-01 | 6.16e-02 | 2.94e-01 | 7.27e+00 | 5.64e+00 | 6.30e+00 | 9.92e-02 | 3.18e-02 | 5.06e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 159495433 | 159529955 | ENSMUSG00000028175 | 0.3469 | + | Depdc1a | protein_coding | 1.34e-04 | 8.05e-02 | -1.869106 | 6.21e+00 | 2.00e+00 | 6.66e+00 | 3.53e-02 | 1.45e-03 | 4.84e-02 | 4.09e+00 | 4.00e+00 | 4.00e+00 | 7.74e-03 | 7.26e-03 | 7.26e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr13 | 4590750 | 4609174 | ENSMUSG00000045410 | 0.4343 | - | Akr1e1 | protein_coding | 1.42e-04 | 8.05e-02 | 1.994171 | 4.09e+00 | 5.17e+00 | 3.17e+00 | 2.56e-03 | 5.59e-03 | 1.28e-03 | 5.21e+00 | 6.83e+00 | 6.58e+00 | 5.75e-03 | 1.81e-02 | 1.52e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 21543559 | 21575904 | ENSMUSG00000039883 | 0.4349 | + | Lrrc17 | protein_coding | 1.43e-04 | 8.05e-02 | -2.598599 | 1.45e+01 | 1.65e+01 | 1.58e+01 | 7.54e+00 | 2.99e+01 | 1.86e+01 | 1.36e+01 | 1.36e+01 | 1.19e+01 | 4.07e+00 | 3.96e+00 | 1.22e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 127336159 | 127338376 | ENSMUSG00000027368 | 0.5762 | + | Dusp2 | protein_coding | 1.55e-04 | 8.42e-02 | -2.361188 | 6.23e+00 | 5.29e+00 | 5.13e+00 | 2.40e-02 | 1.23e-02 | 1.10e-02 | 4.09e+00 | 1.00e+00 | 3.32e+00 | 5.19e-03 | 3.24e-04 | 2.92e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 6916559 | 6923588 | ENSMUSG00000102135 | 0.4255 | + | Gm37108 | processed_pseudogene | 1.70e-04 | 8.95e-02 | 2.301170 | 4.17e+00 | 4.52e+00 | 3.91e+00 | 1.36e-02 | 1.76e-02 | 1.12e-02 | 4.86e+00 | 7.64e+00 | 5.58e+00 | 2.24e-02 | 1.58e-01 | 3.76e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 72626858 | 72628028 | ENSMUSG00000105124 | 0.4851 | - | Gm5297 | transcribed_processed_pseudogene | 2.16e-04 | 1.10e-01 | -1.871992 | 6.52e+00 | 4.52e+00 | 6.30e+00 | 7.27e-02 | 1.76e-02 | 6.24e-02 | 5.09e+00 | 2.00e+00 | 3.91e+00 | 2.64e-02 | 2.40e-03 | 1.12e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 63444751 | 63759028 | ENSMUSG00000033510 | 0.4307 | + | Otud7a | protein_coding | 2.43e-04 | 1.19e-01 | -2.641106 | 4.52e+00 | 4.32e+00 | 6.46e+00 | 4.89e-03 | 4.23e-03 | 1.94e-02 | 2.00e+00 | 3.70e+00 | 2.00e+00 | 6.67e-04 | 2.67e-03 | 6.67e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr14 | 56258838 | 56262260 | ENSMUSG00000015437 | 0.4969 | - | Gzmb | protein_coding | 2.66e-04 | 1.27e-01 | -2.197939 | 5.91e+00 | 0.00e+00 | 4.09e+00 | 3.22e-02 | 0.00e+00 | 8.73e-03 | 2.00e+00 | 3.58e+00 | 0.00e+00 | 1.64e-03 | 6.00e-03 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 51480612 | 51496613 | ENSMUSG00000062593 | 0.4044 | + | Lilrb4a | protein_coding | 2.84e-04 | 1.27e-01 | 3.432959 | 1.58e+00 | 0.00e+00 | 0.00e+00 | 4.72e-04 | 0.00e+00 | 0.00e+00 | 3.17e+00 | 4.95e+00 | 3.81e+00 | 1.89e-03 | 7.08e-03 | 3.07e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 51490956 | 51496611 | ENSMUSG00000112148 | 0.4203 | + | Lilrb4 | protein_coding | 2.84e-04 | 1.27e-01 | 3.432959 | 1.58e+00 | 0.00e+00 | 0.00e+00 | 1.99e-04 | 0.00e+00 | 0.00e+00 | 3.17e+00 | 4.95e+00 | 3.81e+00 | 7.96e-04 | 2.98e-03 | 1.29e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 104299171 | 104311469 | ENSMUSG00000029306 | 0.4065 | + | Ibsp | protein_coding | 3.10e-04 | 1.32e-01 | 2.754888 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 4.66e-04 | 1.58e+00 | 3.32e+00 | 3.81e+00 | 9.32e-04 | 4.19e-03 | 6.05e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for Tg197_C_vs_Tg197.Download the whole result list for Tg197_C_vs_Tg197.DEG table for the contrast Tg197_C_vs_C_221_222The following table presents the top 5% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast Tg197_C_vs_C_221_222. The fields of the table correspond to the requested features to be exported. The table can be searched using the search field on the top right. | chromosome | start | end | gene_id | gc_content | strand | gene_name | biotype | p-value_deseq | FDR_deseq | log2_normalized_fold_change_Tg197_C_vs_C_221_222 | log2_normalized_counts_GK3R196-Tg197-C1 | log2_normalized_counts_GK3R197-Tg197-C2 | log2_normalized_counts_GK3R198-Tg197-C3 | rpgm_normalized_counts_GK3R196-Tg197-C1 | rpgm_normalized_counts_GK3R197-Tg197-C2 | rpgm_normalized_counts_GK3R198-Tg197-C3 | log2_normalized_counts_GK3R190-C1 | log2_normalized_counts_GK3R191-C2 | log2_normalized_counts_GK3R192-C3 | rpgm_normalized_counts_GK3R190-C1 | rpgm_normalized_counts_GK3R191-C2 | rpgm_normalized_counts_GK3R192-C3 | LN | AR | MD | MN | QN | KN | CM | BT | PR |
|---|
| chr7 | 46711998 | 46715700 | ENSMUSG00000040026 | 0.4807 | - | Saa3 | protein_coding | 1.83e-48 | 2.78e-44 | -9.118768 | 1.05e+01 | 1.19e+01 | 1.16e+01 | 3.15e-01 | 8.22e-01 | 6.81e-01 | 0.00e+00 | 2.00e+00 | 3.32e+00 | 0.00e+00 | 6.54e-04 | 1.96e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 164940780 | 164955850 | ENSMUSG00000017737 | 0.5213 | + | Mmp9 | protein_coding | 4.06e-31 | 3.10e-27 | -6.806677 | 8.77e+00 | 1.04e+01 | 8.46e+00 | 9.30e-02 | 2.84e-01 | 7.49e-02 | 2.81e+00 | 3.32e+00 | 1.00e+00 | 1.28e-03 | 1.92e-03 | 2.13e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 83116766 | 83119167 | ENSMUSG00000026166 | 0.3926 | + | Ccl20 | protein_coding | 1.04e-30 | 5.27e-27 | -6.042475 | 1.00e+01 | 1.05e+01 | 1.03e+01 | 4.57e-01 | 6.22e-01 | 5.52e-01 | 4.70e+00 | 4.39e+00 | 3.32e+00 | 1.09e-02 | 8.69e-03 | 3.91e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr19 | 34473786 | 34475135 | ENSMUSG00000050370 | 0.4985 | - | Ch25h | protein_coding | 6.03e-30 | 2.30e-26 | -5.836050 | 8.96e+00 | 7.88e+00 | 9.31e+00 | 3.45e-01 | 1.63e-01 | 4.40e-01 | 3.46e+00 | 1.58e+00 | 3.32e+00 | 6.93e-03 | 1.39e-03 | 6.24e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 57203970 | 57228136 | ENSMUSG00000024164 | 0.5201 | - | C3 | protein_coding | 4.05e-19 | 1.24e-15 | -4.710937 | 8.52e+00 | 1.03e+01 | 8.89e+00 | 9.67e-02 | 3.22e-01 | 1.25e-01 | 5.25e+00 | 5.00e+00 | 3.17e+00 | 9.75e-03 | 8.17e-03 | 2.11e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 7445822 | 7455975 | ENSMUSG00000043613 | 0.4079 | + | Mmp3 | protein_coding | 5.77e-19 | 1.47e-15 | -4.494301 | 1.04e+01 | 1.17e+01 | 1.12e+01 | 8.75e-01 | 2.22e+00 | 1.51e+00 | 7.30e+00 | 6.32e+00 | 6.25e+00 | 1.02e-01 | 5.14e-02 | 4.88e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 4772373 | 4782857 | ENSMUSG00000004371 | 0.5362 | - | Il11 | protein_coding | 6.24e-18 | 1.36e-14 | -3.744383 | 9.94e+00 | 4.52e+00 | 8.22e+00 | 4.00e-01 | 9.00e-03 | 1.21e-01 | 4.91e+00 | 4.64e+00 | 5.39e+00 | 1.19e-02 | 9.82e-03 | 1.68e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr18 | 35713086 | 35722356 | ENSMUSG00000073599 | 0.4990 | - | Ecscr | protein_coding | 5.17e-16 | 9.85e-13 | -4.060912 | 8.31e+00 | 9.53e+00 | 9.26e+00 | 5.85e-02 | 1.36e-01 | 1.14e-01 | 5.43e+00 | 4.81e+00 | 4.86e+00 | 7.77e-03 | 5.00e-03 | 5.18e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 104299171 | 104311469 | ENSMUSG00000029306 | 0.4065 | + | Ibsp | protein_coding | 1.08e-15 | 1.83e-12 | 6.417853 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 4.66e-04 | 6.13e+00 | 7.61e+00 | 6.25e+00 | 3.21e-02 | 9.08e-02 | 3.49e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 79434669 | 79440120 | ENSMUSG00000050711 | 0.3955 | - | Scg2 | protein_coding | 3.48e-15 | 5.31e-12 | 5.450033 | 3.00e+00 | 0.00e+00 | 2.32e+00 | 4.04e-03 | 0.00e+00 | 2.31e-03 | 7.57e+00 | 7.34e+00 | 8.02e+00 | 1.09e-01 | 9.29e-02 | 1.49e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 30723547 | 30748465 | ENSMUSG00000051855 | 0.4545 | + | Mest | protein_coding | 1.13e-14 | 1.57e-11 | 4.075931 | 5.78e+00 | 4.91e+00 | 5.58e+00 | 6.13e-03 | 3.29e-03 | 5.33e-03 | 9.92e+00 | 9.76e+00 | 8.68e+00 | 1.09e-01 | 9.81e-02 | 4.65e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr15 | 77583819 | 77596125 | ENSMUSG00000050014 | 0.4661 | - | Apol10b | protein_coding | 3.39e-14 | 4.31e-11 | -4.529253 | 7.69e+00 | 4.52e+00 | 4.58e+00 | 8.57e-02 | 9.16e-03 | 9.57e-03 | 1.00e+00 | 2.00e+00 | 2.32e+00 | 4.16e-04 | 1.25e-03 | 1.66e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 109575128 | 109579172 | ENSMUSG00000031722 | 0.5125 | - | Hp | protein_coding | 1.71e-13 | 2.01e-10 | -3.884691 | 8.96e+00 | 1.08e+01 | 8.71e+00 | 1.75e-01 | 6.08e-01 | 1.48e-01 | 6.38e+00 | 6.30e+00 | 4.09e+00 | 2.89e-02 | 2.75e-02 | 5.64e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 98422961 | 98446575 | ENSMUSG00000046402 | 0.4941 | + | Rbp1 | protein_coding | 2.15e-13 | 2.34e-10 | -3.494952 | 8.58e+00 | 9.02e+00 | 8.96e+00 | 2.58e-01 | 3.50e-01 | 3.36e-01 | 5.70e+00 | 5.83e+00 | 3.91e+00 | 3.45e-02 | 3.79e-02 | 9.48e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 82035571 | 82037453 | ENSMUSG00000035385 | 0.4376 | + | Ccl2 | protein_coding | 5.93e-13 | 6.03e-10 | -3.437865 | 1.34e+01 | 1.22e+01 | 1.37e+01 | 7.03e+00 | 2.98e+00 | 8.83e+00 | 9.75e+00 | 9.70e+00 | 9.90e+00 | 5.64e-01 | 5.46e-01 | 6.27e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 31470207 | 31520672 | ENSMUSG00000076441 | 0.5281 | + | Ass1 | protein_coding | 7.07e-13 | 6.40e-10 | -3.931613 | 6.58e+00 | 7.35e+00 | 7.26e+00 | 2.37e-02 | 4.04e-02 | 3.79e-02 | 2.81e+00 | 3.32e+00 | 3.32e+00 | 1.50e-03 | 2.25e-03 | 2.25e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 130913125 | 130936141 | ENSMUSG00000028581 | 0.5309 | + | Laptm5 | protein_coding | 7.14e-13 | 6.40e-10 | -4.462879 | 7.14e+00 | 8.06e+00 | 3.46e+00 | 1.35e-02 | 2.57e-02 | 9.64e-04 | 2.00e+00 | 3.32e+00 | 2.32e+00 | 2.89e-04 | 8.68e-04 | 3.86e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 134702593 | 134747323 | ENSMUSG00000029675 | 0.4978 | - | Eln | protein_coding | 9.92e-12 | 8.41e-09 | 2.674634 | 6.19e+00 | 8.44e+00 | 6.52e+00 | 4.30e-03 | 2.07e-02 | 5.44e-03 | 9.73e+00 | 1.02e+01 | 1.03e+01 | 5.09e-02 | 7.16e-02 | 7.28e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 113254830 | 113260236 | ENSMUSG00000095079 | 0.5130 | - | Igha | IG_C_gene | 1.25e-11 | 1.00e-08 | -6.705056 | 0.00e+00 | 8.27e+00 | 1.58e+00 | 0.00e+00 | 7.82e-02 | 5.08e-04 | 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 | 0 | | chr5 | 90786103 | 90789600 | ENSMUSG00000029379 | 0.4294 | + | Cxcl3 | protein_coding | 1.40e-11 | 1.07e-08 | -2.703562 | 9.09e+00 | 4.52e+00 | 8.48e+00 | 1.73e-01 | 6.99e-03 | 1.13e-01 | 6.02e+00 | 5.39e+00 | 5.13e+00 | 2.03e-02 | 1.30e-02 | 1.08e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 45370185 | 45396159 | ENSMUSG00000066705 | 0.4943 | + | Fxyd6 | protein_coding | 4.40e-11 | 3.17e-08 | 3.714246 | 3.00e+00 | 4.32e+00 | 2.00e+00 | 1.49e-03 | 4.04e-03 | 6.38e-04 | 7.37e+00 | 7.27e+00 | 6.66e+00 | 3.49e-02 | 3.26e-02 | 2.13e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 111669361 | 111672338 | ENSMUSG00000001270 | 0.6192 | - | Ckb | protein_coding | 4.57e-11 | 3.17e-08 | -3.414693 | 8.59e+00 | 9.63e+00 | 7.76e+00 | 7.40e-02 | 1.52e-01 | 4.15e-02 | 5.73e+00 | 5.46e+00 | 5.09e+00 | 9.99e-03 | 8.26e-03 | 6.34e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 66673425 | 66784914 | ENSMUSG00000034810 | 0.3734 | - | Scn7a | protein_coding | 5.72e-11 | 3.79e-08 | 4.398031 | 1.58e+00 | 2.81e+00 | 1.00e+00 | 6.02e-04 | 1.81e-03 | 3.01e-04 | 6.30e+00 | 6.81e+00 | 5.95e+00 | 2.35e-02 | 3.34e-02 | 1.84e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 19000910 | 19015657 | ENSMUSG00000019850 | 0.4554 | - | Tnfaip3 | protein_coding | 8.61e-11 | 5.47e-08 | -4.643856 | 5.29e+00 | 4.91e+00 | 5.81e+00 | 5.57e-03 | 4.25e-03 | 8.06e-03 | 0.00e+00 | 1.58e+00 | 0.00e+00 | 0.00e+00 | 2.93e-04 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 102988712 | 103096002 | ENSMUSG00000032548 | 0.4822 | + | Slco2a1 | protein_coding | 1.67e-10 | 1.02e-07 | -2.959923 | 7.45e+00 | 6.58e+00 | 8.21e+00 | 1.21e-02 | 6.63e-03 | 2.07e-02 | 4.95e+00 | 4.09e+00 | 4.64e+00 | 2.09e-03 | 1.12e-03 | 1.68e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 92209893 | 92215408 | ENSMUSG00000029409 | 0.4329 | - | U90926 | protein_coding | 2.42e-10 | 1.42e-07 | -4.066089 | 6.66e+00 | 6.27e+00 | 6.49e+00 | 6.79e-02 | 5.16e-02 | 6.05e-02 | 3.17e+00 | 1.00e+00 | 2.32e+00 | 5.43e-03 | 6.79e-04 | 2.72e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 124996694 | 125003096 | ENSMUSG00000030329 | 0.5627 | + | Pianp | protein_coding | 2.89e-10 | 1.63e-07 | 2.798952 | 0.00e+00 | 5.86e+00 | 6.00e+00 | 0.00e+00 | 8.84e-03 | 9.77e-03 | 8.23e+00 | 7.68e+00 | 8.45e+00 | 4.65e-02 | 3.16e-02 | 5.41e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 68723646 | 68782650 | ENSMUSG00000060044 | 0.4056 | + | Tmem26 | protein_coding | 6.77e-10 | 3.69e-07 | 3.176589 | 5.86e+00 | 5.17e+00 | 5.64e+00 | 5.08e-03 | 3.12e-03 | 4.36e-03 | 8.67e+00 | 9.11e+00 | 8.42e+00 | 3.62e-02 | 4.92e-02 | 3.04e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 113746164 | 113758646 | ENSMUSG00000074934 | 0.4358 | - | Grem1 | protein_coding | 7.38e-10 | 3.88e-07 | -3.463947 | 7.18e+00 | 6.54e+00 | 6.36e+00 | 3.07e-02 | 1.96e-02 | 1.73e-02 | 3.46e+00 | 2.58e+00 | 3.58e+00 | 2.13e-03 | 1.07e-03 | 2.35e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 70373558 | 70382066 | ENSMUSG00000031849 | 0.5643 | + | Comp | protein_coding | 8.28e-10 | 4.21e-07 | 2.728209 | 9.01e+00 | 1.04e+01 | 9.54e+00 | 8.31e-02 | 2.24e-01 | 1.20e-01 | 1.24e+01 | 1.14e+01 | 1.32e+01 | 8.48e-01 | 4.37e-01 | 1.55e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 55489410 | 55492647 | ENSMUSG00000021025 | 0.5435 | - | Nfkbia | protein_coding | 9.02e-10 | 4.39e-07 | -2.722512 | 1.11e+01 | 1.10e+01 | 1.11e+01 | 7.20e-01 | 6.58e-01 | 7.19e-01 | 8.15e+00 | 8.44e+00 | 8.34e+00 | 9.42e-02 | 1.15e-01 | 1.07e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 128862981 | 128897034 | ENSMUSG00000027386 | 0.4755 | + | Fbln7 | protein_coding | 9.21e-10 | 4.39e-07 | 3.682260 | 4.39e+00 | 2.81e+00 | 3.91e+00 | 7.42e-03 | 2.23e-03 | 5.19e-03 | 7.73e+00 | 7.55e+00 | 7.25e+00 | 7.83e-02 | 6.94e-02 | 5.60e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 4133531 | 4138819 | ENSMUSG00000045573 | 0.4386 | - | Penk | protein_coding | 1.12e-09 | 5.17e-07 | 2.975033 | 8.41e+00 | 8.19e+00 | 8.77e+00 | 1.21e-01 | 1.04e-01 | 1.56e-01 | 1.11e+01 | 1.20e+01 | 1.11e+01 | 7.63e-01 | 1.47e+00 | 7.63e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 112106679 | 112127559 | ENSMUSG00000037686 | 0.5676 | + | Aspg | protein_coding | 1.39e-09 | 6.25e-07 | 3.273018 | 3.91e+00 | 4.70e+00 | 4.00e+00 | 1.05e-03 | 1.88e-03 | 1.13e-03 | 7.68e+00 | 7.40e+00 | 7.47e+00 | 1.53e-02 | 1.26e-02 | 1.32e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 124530345 | 124542359 | ENSMUSG00000038521 | 0.4617 | - | C1s1 | protein_coding | 1.95e-09 | 8.48e-07 | -2.109546 | 9.71e+00 | 6.93e+00 | 3.46e+00 | 1.49e-01 | 2.16e-02 | 1.78e-03 | 0.00e+00 | 7.79e+00 | 1.00e+00 | 0.00e+00 | 3.94e-02 | 1.78e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 45555716 | 45563169 | ENSMUSG00000023947 | 0.5346 | + | Nfkbie | protein_coding | 2.53e-09 | 1.07e-06 | -3.746426 | 5.78e+00 | 7.07e+00 | 6.04e+00 | 2.29e-02 | 5.65e-02 | 2.76e-02 | 3.46e+00 | 2.00e+00 | 2.00e+00 | 4.25e-03 | 1.27e-03 | 1.27e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 22126727 | 22135711 | ENSMUSG00000001348 | 0.5233 | - | Acp5 | protein_coding | 2.91e-09 | 1.20e-06 | -3.260123 | 7.26e+00 | 6.63e+00 | 5.49e+00 | 5.44e-02 | 3.51e-02 | 1.57e-02 | 2.58e+00 | 4.17e+00 | 2.81e+00 | 1.79e-03 | 6.08e-03 | 2.15e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 134082448 | 134095082 | ENSMUSG00000000682 | 0.4953 | - | Cd52 | protein_coding | 3.92e-09 | 1.55e-06 | -5.866249 | 2.58e+00 | 7.38e+00 | 1.58e+00 | 1.27e-03 | 4.18e-02 | 5.07e-04 | 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 | 0 | | chr9 | 65265180 | 65280605 | ENSMUSG00000042254 | 0.4935 | + | Cilp | protein_coding | 3.97e-09 | 1.55e-06 | 2.744927 | 7.92e+00 | 8.11e+00 | 7.90e+00 | 2.18e-02 | 2.49e-02 | 2.14e-02 | 1.05e+01 | 1.11e+01 | 1.05e+01 | 1.26e-01 | 2.03e-01 | 1.29e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 166523007 | 166585720 | ENSMUSG00000000402 | 0.4254 | - | Egfl6 | protein_coding | 5.14e-09 | 1.96e-06 | 4.794416 | 1.00e+00 | 0.00e+00 | 2.32e+00 | 4.75e-04 | 0.00e+00 | 1.90e-03 | 5.49e+00 | 6.71e+00 | 6.17e+00 | 2.09e-02 | 4.94e-02 | 3.37e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 62071123 | 62072362 | ENSMUSG00000046687 | 0.5395 | + | Gm5424 | processed_pseudogene | 6.24e-09 | 2.32e-06 | -3.141596 | 6.55e+00 | 7.03e+00 | 7.00e+00 | 7.43e-02 | 1.04e-01 | 1.02e-01 | 3.17e+00 | 2.58e+00 | 4.64e+00 | 6.39e-03 | 4.00e-03 | 1.92e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr15 | 54838901 | 54952892 | ENSMUSG00000022425 | 0.4130 | - | Enpp2 | protein_coding | 7.85e-09 | 2.85e-06 | -2.414030 | 8.04e+00 | 7.23e+00 | 9.08e+00 | 3.29e-02 | 1.87e-02 | 6.77e-02 | 5.17e+00 | 6.58e+00 | 5.55e+00 | 4.39e-03 | 1.19e-02 | 5.77e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 56294585 | 56321043 | ENSMUSG00000031613 | 0.3691 | + | Hpgd | protein_coding | 8.72e-09 | 3.09e-06 | 2.898455 | 6.23e+00 | 5.17e+00 | 7.25e+00 | 3.54e-02 | 1.68e-02 | 7.23e-02 | 8.74e+00 | 9.79e+00 | 9.34e+00 | 2.04e-01 | 4.24e-01 | 3.10e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 57784881 | 57788450 | ENSMUSG00000019874 | 0.3838 | + | Fabp7 | protein_coding | 9.12e-09 | 3.16e-06 | -2.921997 | 6.48e+00 | 6.27e+00 | 6.93e+00 | 2.93e-02 | 2.53e-02 | 4.03e-02 | 3.46e+00 | 4.09e+00 | 3.32e+00 | 3.33e-03 | 5.32e-03 | 2.99e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 35552128 | 35557180 | ENSMUSG00000039518 | 0.5375 | + | Cdsn | protein_coding | 1.62e-08 | 5.50e-06 | 1.942165 | 6.21e+00 | 8.98e+00 | 7.31e+00 | 3.36e-02 | 2.32e-01 | 7.28e-02 | 9.28e+00 | 9.51e+00 | 1.05e+01 | 2.85e-01 | 3.36e-01 | 6.84e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 4257557 | 4272514 | ENSMUSG00000034394 | 0.5519 | + | Lif | protein_coding | 1.91e-08 | 6.34e-06 | -3.328471 | 6.93e+00 | 4.52e+00 | 6.25e+00 | 2.13e-02 | 3.87e-03 | 1.32e-02 | 3.17e+00 | 1.58e+00 | 3.32e+00 | 1.41e-03 | 3.52e-04 | 1.58e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 91074622 | 91093646 | ENSMUSG00000029377 | 0.3961 | + | Ereg | protein_coding | 3.62e-08 | 1.17e-05 | -3.164189 | 6.64e+00 | 6.00e+00 | 6.44e+00 | 2.08e-02 | 1.33e-02 | 1.81e-02 | 1.58e+00 | 3.46e+00 | 3.81e+00 | 4.21e-04 | 2.10e-03 | 2.74e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 22288227 | 22298522 | ENSMUSG00000029671 | 0.4153 | + | Wnt16 | protein_coding | 7.45e-08 | 2.31e-05 | 2.766001 | 4.39e+00 | 5.17e+00 | 5.09e+00 | 2.53e-03 | 4.43e-03 | 4.18e-03 | 7.63e+00 | 7.97e+00 | 7.41e+00 | 2.50e-02 | 3.17e-02 | 2.14e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 173962568 | 173982744 | ENSMUSG00000026535 | 0.3715 | - | Ifi202b | protein_coding | 7.49e-08 | 2.31e-05 | -2.319040 | 8.24e+00 | 4.70e+00 | 7.41e+00 | 2.03e-01 | 1.68e-02 | 1.14e-01 | 0.00e+00 | 5.55e+00 | 5.70e+00 | 0.00e+00 | 3.10e-02 | 3.43e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 70726435 | 70726966 | ENSMUSG00000076609 | 0.4925 | + | Igkc | IG_C_gene | 7.56e-08 | 2.31e-05 | -4.735325 | 0.00e+00 | 9.16e+00 | 3.70e+00 | 0.00e+00 | 4.73e-01 | 9.93e-03 | 1.00e+00 | 1.58e+00 | 4.09e+00 | 8.28e-04 | 1.66e-03 | 1.32e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 66016549 | 66173118 | ENSMUSG00000070780 | 0.4485 | - | Rbm47 | protein_coding | 9.58e-08 | 2.86e-05 | -4.357552 | 5.36e+00 | 3.46e+00 | 4.91e+00 | 4.86e-03 | 1.21e-03 | 3.52e-03 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 1.21e-04 | 0.00e+00 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 25626654 | 25635100 | ENSMUSG00000059479 | 0.5666 | + | B3gnt8 | protein_coding | 9.75e-08 | 2.86e-05 | 4.772590 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 5.04e+00 | 4.39e+00 | 4.81e+00 | 4.02e-03 | 2.51e-03 | 3.39e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 90891241 | 90893115 | ENSMUSG00000029380 | 0.4464 | + | Cxcl1 | protein_coding | 1.05e-07 | 3.01e-05 | -1.913305 | 1.24e+01 | 8.01e+00 | 1.17e+01 | 2.86e+00 | 1.39e-01 | 1.80e+00 | 9.63e+00 | 9.59e+00 | 9.62e+00 | 4.30e-01 | 4.17e-01 | 4.26e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 180456245 | 180474867 | ENSMUSG00000038963 | 0.5335 | + | Slco4a1 | protein_coding | 1.07e-07 | 3.01e-05 | -3.700440 | 5.93e+00 | 2.00e+00 | 6.02e+00 | 1.92e-02 | 9.60e-04 | 2.05e-02 | 1.00e+00 | 1.58e+00 | 2.32e+00 | 3.20e-04 | 6.40e-04 | 1.28e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 83766321 | 83774316 | ENSMUSG00000027996 | 0.4816 | + | Sfrp2 | protein_coding | 1.22e-07 | 3.38e-05 | 2.718655 | 9.47e+00 | 8.37e+00 | 9.31e+00 | 1.53e-01 | 7.10e-02 | 1.37e-01 | 1.17e+01 | 1.23e+01 | 1.14e+01 | 7.16e-01 | 1.06e+00 | 5.96e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for Tg197_C_vs_C_221_222.Download the whole result list for Tg197_C_vs_C_221_222.Download the raw read counts table for the experiment.Download the normalized read counts table for the experiment.
References
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