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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 (20001 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 (4705 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 (9426 genes with cutoff value 2 normalized read counts). The total number of genes excluded due to the application of gene filters was 4845. The total (unified) number of genes excluded due to the application of all filters was 31528. The resulting gene counts table was subjected to differential expression analysis for the contrasts wt versus 3308, wt versus 3312, wt versus 3343, 3308 versus 3343, 3312 versus 3343, 3308 versus 3312 using the Bioconductor package DESeq. The final numbers of differentially expressed genes were (per contrast): for the contrast wt versus 3308, 1017 (216) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 311 (78) were up-regulated, 631 (138) were down-regulated and 75 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log2 scale, for the contrast wt versus 3312, 404 (57) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 168 (30) were up-regulated, 200 (27) were down-regulated and 36 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log2 scale, for the contrast wt versus 3343, 656 (119) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 255 (60) were up-regulated, 344 (59) were down-regulated and 57 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log2 scale, for the contrast 3308 versus 3343, 234 (8) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 197 (7) were up-regulated, 34 (1) were down-regulated and 3 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log2 scale, for the contrast 3312 versus 3343, 68 (1) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 29 (1) were up-regulated, 39 (0) were down-regulated and 0 (0) were not differentially expressed according to an absolute fold change cutoff value of 1 in log2 scale, for the contrast 3308 versus 3312, 90 (12) statistically significant genes were found with a p-value (FDR or adjusted p-value) threshold of 0.05 and of these, 78 (12) were up-regulated, 11 (0) were down-regulated and 1 (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, 3312, 3343, 3308
Samples included: IT3R40-wt1, IT3R41-wt2, IT3R42-wt5, IT3R43-wt15, IT3R44-wt16, IT3R45-wt17, IT3R35-3312-1, IT3R36-3312-3, IT3R37-3343-2, IT3R38-3343-3, IT3R39-3343-4, IT3R46-3308-1, IT3R47-3308-2, IT3R48-3308-4
Samples excluded:
none
Requested contrasts: wt_vs_3308, wt_vs_3312, wt_vs_3343, 3308_vs_3343, 3312_vs_3343, 3308_vs_3312
Library sizes:
- IT3R40-wt1: 4335736
- IT3R41-wt2: 3322994
- IT3R42-wt5: 1354321
- IT3R43-wt15: 2854898
- IT3R44-wt16: 492301
- IT3R45-wt17: 2092992
- IT3R35-3312-1: 3987742
- IT3R36-3312-3: 3608258
- IT3R37-3343-2: 3600045
- IT3R38-3343-3: 3923314
- IT3R39-3343-4: 1936215
- IT3R46-3308-1: 3390266
- IT3R47-3308-2: 1258598
- IT3R48-3308-4: 3344475
Annotation: download
Organism: mouse ( Mus musculus), genome version alias mm10
Annotation source: Ensembl genomes
Count type: utr
Exon filters:
none applied
Gene filters:
length, avg.reads, expression, biotype - avg.reads
- average.per.bp: 100
- quantile: 0.25
- expression
- median: TRUE
- mean: FALSE
- quantile: NA
- known: NA
- custom: NA
- biotype
- pseudogene: FALSE
- snRNA: FALSE
- protein_coding: FALSE
- antisense: FALSE
- miRNA: FALSE
- snoRNA: FALSE
- lincRNA: FALSE
- processed_transcript: FALSE
- misc_RNA: FALSE
- rRNA: TRUE
- sense_intronic: FALSE
- sense_overlapping: FALSE
- polymorphic_pseudogene: FALSE
- IG_C_gene: FALSE
- IG_J_gene: FALSE
- IG_D_gene: FALSE
- IG_LV_gene: FALSE
- IG_V_gene: FALSE
- IG_V_pseudogene: TRUE
- TR_V_gene: FALSE
- TR_V_pseudogene: TRUE
- three_prime_overlapping_ncrna: FALSE
Filter application: after normalization
Normalization algorithm: DESeq
Normalization arguments:
locfunc - [[list(locfunc = function (x, na.rm = FALSE)
standardGeneric("median"))locfunc
Statistical algorithm(s): DESeq
Statistical arguments for DESeq: method, sharingMode, fitType - method: blind
- sharingMode: fit-only
- fitType: local
Meta-analysis method: no meta-analysis, reported p-values from the first supplied statistical algorithm
Multiple testing correction: Benjamini-Hochberg FDR
p-value threshold: 0.05
Logarithmic tranformation offset: 1
Analysis preset: not available
Quality control plots: multidimensional scaling, biotype detection, biotype counts, sample and biotype saturation, filtered biotypes, correlation heatmap and correlogram, pairwise scatterplots between samples, boxplots, GC-content bias, transcript length bias, mean-difference plot, mean-variance plot, DEG biotype detection, volcano plot, DEG heatmap
Figure format: png, pdf
Output directory: /data/images/proton/run327/www//metaseqr1
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: 27 minutes 44 seconds
Filtered genes
Number of filtered genes: 31528 which is the union of
- Filtered because of zero reads: 20001
-
Filtered because of exon filters: 0
-
Filtered because of gene filters: 11527
which is the union of
- length: 4705 genes with filter cutoff value 500
- avg.reads: 0 genes with filter cutoff value 0
- expression: 9426 genes further decomposed to (filter name, filtered genes, filter cutoff):
- median: 9426 genes with filter cutoff value 2
- biotype: 139 genes with filter cutoff value rRNA, IG_V_pseudogene, TR_V_pseudogene
Differentially expressed genes
Number of differentially expressed genes per contrast:
- wt_vs_3308: 1017 (216) statistically significant genes of which 311 (78) up regulated, 631 (138) down regulated and 75 (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_3312: 404 (57) statistically significant genes of which 168 (30) up regulated, 200 (27) down regulated and 36 (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_3343: 656 (119) statistically significant genes of which 255 (60) up regulated, 344 (59) down regulated and 57 (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.
- 3308_vs_3343: 234 (8) statistically significant genes of which 197 (7) up regulated, 34 (1) down regulated and 3 (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.
- 3312_vs_3343: 68 (1) statistically significant genes of which 29 (1) up regulated, 39 (0) down regulated and 0 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log2 scale.
- 3308_vs_3312: 90 (12) statistically significant genes of which 78 (12) up regulated, 11 (0) down regulated and 1 (0) not differentially expressed according to a p-value (FDR or adjusted p-value) threshold of 0.05 and an absolute fold change cutoff value of 1 in log2 scale.
Run log[ 2017-01-11 13:49:56 ] FATAL Condition names in sample list and contrast list do not match! Check if the contrasts follow the appropriate format (e.g. "_vs_" separating contrasting conditions... [ 2017-01-11 13:50:22 ] INFO 2017-01-11 13:50:22: Data processing started... [ 2017-01-11 13:50:22 ] INFO Read counts file: imported sam/bam/bed files [ 2017-01-11 13:50:22 ] INFO Conditions: wt, 3308 [ 2017-01-11 13:50:22 ] INFO Samples to include: 007, 009, 010, 011, 012, 013, 014, 015, 016, 019, 020, 021, 022, 025, IT3R46-3308-1, IT3R47-3308-2, IT3R48-3308-4 [ 2017-01-11 13:50:22 ] INFO Samples to exclude: none [ 2017-01-11 13:50:22 ] INFO Requested contrasts: wt_vs_3308 [ 2017-01-11 13:50:22 ] INFO Annotation: download [ 2017-01-11 13:50:22 ] INFO Organism: mm10 [ 2017-01-11 13:50:22 ] INFO Reference source: ensembl [ 2017-01-11 13:50:22 ] INFO Count type: utr [ 2017-01-11 13:50:22 ] INFO Exon filters: none applied [ 2017-01-11 13:50:22 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-01-11 13:50:22 ] INFO length: [ 2017-01-11 13:50:22 ] INFO length: 500 [ 2017-01-11 13:50:22 ] INFO avg.reads: [ 2017-01-11 13:50:22 ] INFO average.per.bp: 100 [ 2017-01-11 13:50:22 ] INFO quantile: 0.25 [ 2017-01-11 13:50:22 ] INFO expression: [ 2017-01-11 13:50:22 ] INFO median: TRUE [ 2017-01-11 13:50:22 ] INFO mean: FALSE [ 2017-01-11 13:50:22 ] INFO quantile: NA [ 2017-01-11 13:50:22 ] INFO known: NA [ 2017-01-11 13:50:22 ] INFO custom: NA [ 2017-01-11 13:50:22 ] INFO biotype: [ 2017-01-11 13:50:22 ] INFO pseudogene: FALSE [ 2017-01-11 13:50:22 ] INFO snRNA: FALSE [ 2017-01-11 13:50:22 ] INFO protein_coding: FALSE [ 2017-01-11 13:50:22 ] INFO antisense: FALSE [ 2017-01-11 13:50:22 ] INFO miRNA: FALSE [ 2017-01-11 13:50:22 ] INFO snoRNA: FALSE [ 2017-01-11 13:50:22 ] INFO lincRNA: FALSE [ 2017-01-11 13:50:22 ] INFO processed_transcript: FALSE [ 2017-01-11 13:50:22 ] INFO misc_RNA: FALSE [ 2017-01-11 13:50:22 ] INFO rRNA: TRUE [ 2017-01-11 13:50:22 ] INFO sense_intronic: FALSE [ 2017-01-11 13:50:22 ] INFO sense_overlapping: FALSE [ 2017-01-11 13:50:22 ] INFO polymorphic_pseudogene: FALSE [ 2017-01-11 13:50:22 ] INFO IG_C_gene: FALSE [ 2017-01-11 13:50:22 ] INFO IG_J_gene: FALSE [ 2017-01-11 13:50:22 ] INFO IG_D_gene: FALSE [ 2017-01-11 13:50:22 ] INFO IG_LV_gene: FALSE [ 2017-01-11 13:50:22 ] INFO IG_V_gene: FALSE [ 2017-01-11 13:50:22 ] INFO IG_V_pseudogene: TRUE [ 2017-01-11 13:50:22 ] INFO TR_V_gene: FALSE [ 2017-01-11 13:50:22 ] INFO TR_V_pseudogene: TRUE [ 2017-01-11 13:50:22 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-01-11 13:50:22 ] INFO Filter application: postnorm [ 2017-01-11 13:50:22 ] INFO Normalization algorithm: deseq [ 2017-01-11 13:50:22 ] INFO Normalization arguments: [ 2017-01-11 13:50:22 ] INFO locfunc: [ 2017-01-11 13:50:22 ] INFO [[ [ 2017-01-11 13:50:22 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-01-11 13:50:22 ] INFO locfunc [ 2017-01-11 13:50:22 ] INFO Statistical algorithm: deseq [ 2017-01-11 13:50:22 ] INFO Statistical arguments: [ 2017-01-11 13:50:22 ] INFO deseq: blind, fit-only, local [ 2017-01-11 13:50:22 ] INFO Meta-analysis method: none [ 2017-01-11 13:50:22 ] INFO Multiple testing correction: BH [ 2017-01-11 13:50:22 ] INFO p-value threshold: 0.05 [ 2017-01-11 13:50:22 ] INFO Logarithmic transformation offset: 1 [ 2017-01-11 13:50:22 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-01-11 13:50:22 ] INFO Figure format: png, pdf [ 2017-01-11 13:50:22 ] INFO Output directory: /data/images/proton/run327/www//metaseqr1 [ 2017-01-11 13:50:22 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-01-11 13:50:22 ] INFO Output scale(s): log2, rpgm [ 2017-01-11 13:50:22 ] INFO Output values: normalized [ 2017-01-11 13:50:22 ] INFO Downloading gene annotation for mm10... [ 2017-01-11 13:50:49 ] INFO 2017-01-11 13:50:49: Data processing started... [ 2017-01-11 13:50:49 ] INFO Read counts file: imported sam/bam/bed files [ 2017-01-11 13:50:49 ] INFO Conditions: wt, 3312, 3343, 3308 [ 2017-01-11 13:50:49 ] INFO Samples to include: 007, 009, 010, 011, 012, 013, 014, 015, 016, 019, 020, 021, 022, 025, IT3R35-3312-1, IT3R36-3312-3, IT3R37-3343-2, IT3R38-3343-3, IT3R39-3343-4, IT3R46-3308-1, IT3R47-3308-2, IT3R48-3308-4 [ 2017-01-11 13:50:49 ] INFO Samples to exclude: none [ 2017-01-11 13:50:49 ] INFO Requested contrasts: wt_vs_3308 [ 2017-01-11 13:50:49 ] INFO Annotation: download [ 2017-01-11 13:50:49 ] INFO Organism: mm10 [ 2017-01-11 13:50:49 ] INFO Reference source: ensembl [ 2017-01-11 13:50:49 ] INFO Count type: utr [ 2017-01-11 13:50:49 ] INFO Exon filters: none applied [ 2017-01-11 13:50:49 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-01-11 13:50:49 ] INFO length: [ 2017-01-11 13:50:49 ] INFO length: 500 [ 2017-01-11 13:50:49 ] INFO avg.reads: [ 2017-01-11 13:50:49 ] INFO average.per.bp: 100 [ 2017-01-11 13:50:49 ] INFO quantile: 0.25 [ 2017-01-11 13:50:49 ] INFO expression: [ 2017-01-11 13:50:49 ] INFO median: TRUE [ 2017-01-11 13:50:49 ] INFO mean: FALSE [ 2017-01-11 13:50:49 ] INFO quantile: NA [ 2017-01-11 13:50:49 ] INFO known: NA [ 2017-01-11 13:50:49 ] INFO custom: NA [ 2017-01-11 13:50:49 ] INFO biotype: [ 2017-01-11 13:50:49 ] INFO pseudogene: FALSE [ 2017-01-11 13:50:49 ] INFO snRNA: FALSE [ 2017-01-11 13:50:49 ] INFO protein_coding: FALSE [ 2017-01-11 13:50:49 ] INFO antisense: FALSE [ 2017-01-11 13:50:49 ] INFO miRNA: FALSE [ 2017-01-11 13:50:49 ] INFO snoRNA: FALSE [ 2017-01-11 13:50:49 ] INFO lincRNA: FALSE [ 2017-01-11 13:50:49 ] INFO processed_transcript: FALSE [ 2017-01-11 13:50:49 ] INFO misc_RNA: FALSE [ 2017-01-11 13:50:49 ] INFO rRNA: TRUE [ 2017-01-11 13:50:49 ] INFO sense_intronic: FALSE [ 2017-01-11 13:50:49 ] INFO sense_overlapping: FALSE [ 2017-01-11 13:50:49 ] INFO polymorphic_pseudogene: FALSE [ 2017-01-11 13:50:49 ] INFO IG_C_gene: FALSE [ 2017-01-11 13:50:49 ] INFO IG_J_gene: FALSE [ 2017-01-11 13:50:49 ] INFO IG_D_gene: FALSE [ 2017-01-11 13:50:49 ] INFO IG_LV_gene: FALSE [ 2017-01-11 13:50:49 ] INFO IG_V_gene: FALSE [ 2017-01-11 13:50:49 ] INFO IG_V_pseudogene: TRUE [ 2017-01-11 13:50:49 ] INFO TR_V_gene: FALSE [ 2017-01-11 13:50:49 ] INFO TR_V_pseudogene: TRUE [ 2017-01-11 13:50:49 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-01-11 13:50:49 ] INFO Filter application: postnorm [ 2017-01-11 13:50:49 ] INFO Normalization algorithm: deseq [ 2017-01-11 13:50:49 ] INFO Normalization arguments: [ 2017-01-11 13:50:49 ] INFO locfunc: [ 2017-01-11 13:50:49 ] INFO [[ [ 2017-01-11 13:50:49 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-01-11 13:50:49 ] INFO locfunc [ 2017-01-11 13:50:49 ] INFO Statistical algorithm: deseq [ 2017-01-11 13:50:49 ] INFO Statistical arguments: [ 2017-01-11 13:50:49 ] INFO deseq: blind, fit-only, local [ 2017-01-11 13:50:49 ] INFO Meta-analysis method: none [ 2017-01-11 13:50:49 ] INFO Multiple testing correction: BH [ 2017-01-11 13:50:49 ] INFO p-value threshold: 0.05 [ 2017-01-11 13:50:49 ] INFO Logarithmic transformation offset: 1 [ 2017-01-11 13:50:49 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-01-11 13:50:49 ] INFO Figure format: png, pdf [ 2017-01-11 13:50:49 ] INFO Output directory: /data/images/proton/run327/www//metaseqr1 [ 2017-01-11 13:50:49 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-01-11 13:50:49 ] INFO Output scale(s): log2, rpgm [ 2017-01-11 13:50:49 ] INFO Output values: normalized [ 2017-01-11 13:50:49 ] INFO Downloading gene annotation for mm10... [ 2017-01-11 13:50:57 ] FATAL Raw reads input file does not exist! Please check! [ 2017-01-11 13:51:10 ] FATAL Raw reads input file does not exist! Please check! [ 2017-01-11 13:51:58 ] FATAL Raw reads input file does not exist! Please check! [ 2017-01-11 13:52:14 ] INFO 2017-01-11 13:52:14: Data processing started... [ 2017-01-11 13:52:14 ] INFO Read counts file: imported sam/bam/bed files [ 2017-01-11 13:52:14 ] INFO Conditions: wt, 3312, 3343, 3308 [ 2017-01-11 13:52:14 ] INFO Samples to include: 007, 009, 010, 011, 012, 013, 014, 015, 016, 019, 020, 021, 022, 025, IT3R35-3312-1, IT3R36-3312-3, IT3R37-3343-2, IT3R38-3343-3, IT3R39-3343-4, IT3R46-3308-1, IT3R47-3308-2, IT3R48-3308-4 [ 2017-01-11 13:52:14 ] INFO Samples to exclude: none [ 2017-01-11 13:52:14 ] INFO Requested contrasts: wt_vs_3308 [ 2017-01-11 13:52:14 ] INFO Annotation: download [ 2017-01-11 13:52:14 ] INFO Organism: mm10 [ 2017-01-11 13:52:14 ] INFO Reference source: ensembl [ 2017-01-11 13:52:14 ] INFO Count type: utr [ 2017-01-11 13:52:14 ] INFO Exon filters: none applied [ 2017-01-11 13:52:14 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-01-11 13:52:14 ] INFO length: [ 2017-01-11 13:52:14 ] INFO length: 500 [ 2017-01-11 13:52:14 ] INFO avg.reads: [ 2017-01-11 13:52:14 ] INFO average.per.bp: 100 [ 2017-01-11 13:52:14 ] INFO quantile: 0.25 [ 2017-01-11 13:52:14 ] INFO expression: [ 2017-01-11 13:52:14 ] INFO median: TRUE [ 2017-01-11 13:52:14 ] INFO mean: FALSE [ 2017-01-11 13:52:14 ] INFO quantile: NA [ 2017-01-11 13:52:14 ] INFO known: NA [ 2017-01-11 13:52:14 ] INFO custom: NA [ 2017-01-11 13:52:14 ] INFO biotype: [ 2017-01-11 13:52:14 ] INFO pseudogene: FALSE [ 2017-01-11 13:52:14 ] INFO snRNA: FALSE [ 2017-01-11 13:52:14 ] INFO protein_coding: FALSE [ 2017-01-11 13:52:14 ] INFO antisense: FALSE [ 2017-01-11 13:52:14 ] INFO miRNA: FALSE [ 2017-01-11 13:52:14 ] INFO snoRNA: FALSE [ 2017-01-11 13:52:14 ] INFO lincRNA: FALSE [ 2017-01-11 13:52:14 ] INFO processed_transcript: FALSE [ 2017-01-11 13:52:14 ] INFO misc_RNA: FALSE [ 2017-01-11 13:52:14 ] INFO rRNA: TRUE [ 2017-01-11 13:52:14 ] INFO sense_intronic: FALSE [ 2017-01-11 13:52:14 ] INFO sense_overlapping: FALSE [ 2017-01-11 13:52:14 ] INFO polymorphic_pseudogene: FALSE [ 2017-01-11 13:52:14 ] INFO IG_C_gene: FALSE [ 2017-01-11 13:52:14 ] INFO IG_J_gene: FALSE [ 2017-01-11 13:52:14 ] INFO IG_D_gene: FALSE [ 2017-01-11 13:52:14 ] INFO IG_LV_gene: FALSE [ 2017-01-11 13:52:14 ] INFO IG_V_gene: FALSE [ 2017-01-11 13:52:14 ] INFO IG_V_pseudogene: TRUE [ 2017-01-11 13:52:14 ] INFO TR_V_gene: FALSE [ 2017-01-11 13:52:14 ] INFO TR_V_pseudogene: TRUE [ 2017-01-11 13:52:14 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-01-11 13:52:14 ] INFO Filter application: postnorm [ 2017-01-11 13:52:14 ] INFO Normalization algorithm: deseq [ 2017-01-11 13:52:14 ] INFO Normalization arguments: [ 2017-01-11 13:52:14 ] INFO locfunc: [ 2017-01-11 13:52:14 ] INFO [[ [ 2017-01-11 13:52:14 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-01-11 13:52:14 ] INFO locfunc [ 2017-01-11 13:52:14 ] INFO Statistical algorithm: deseq [ 2017-01-11 13:52:14 ] INFO Statistical arguments: [ 2017-01-11 13:52:14 ] INFO deseq: blind, fit-only, local [ 2017-01-11 13:52:14 ] INFO Meta-analysis method: none [ 2017-01-11 13:52:14 ] INFO Multiple testing correction: BH [ 2017-01-11 13:52:14 ] INFO p-value threshold: 0.05 [ 2017-01-11 13:52:14 ] INFO Logarithmic transformation offset: 1 [ 2017-01-11 13:52:14 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-01-11 13:52:14 ] INFO Figure format: png, pdf [ 2017-01-11 13:52:14 ] INFO Output directory: /data/images/proton/run327/www//metaseqr1 [ 2017-01-11 13:52:14 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-01-11 13:52:14 ] INFO Output scale(s): log2, rpgm [ 2017-01-11 13:52:14 ] INFO Output values: normalized [ 2017-01-11 13:52:14 ] INFO Downloading gene annotation for mm10... [ 2017-01-11 13:52:32 ] FATAL Raw reads input file does not exist! Please check! [ 2017-01-11 13:53:41 ] FATAL Raw reads input file does not exist! Please check! [ 2017-01-11 13:54:25 ] FATAL Raw reads input file does not exist! Please check! [ 2017-01-11 13:55:23 ] FATAL Raw reads input file wt does not exist! Please check! [ 2017-01-11 13:57:40 ] INFO 2017-01-11 13:57:40: Data processing started... [ 2017-01-11 13:57:40 ] INFO Read counts file: imported sam/bam/bed files [ 2017-01-11 13:57:40 ] INFO Conditions: wt, 3312, 3343, 3308 [ 2017-01-11 13:57:40 ] INFO Samples to include: 007, 009, 010, 011, 012, 013, 014, 015, 016, 019, 020, 021, 022, 025, IT3R40-wt1, IT3R41-wt2, IT3R42-wt5, IT3R43-wt15, IT3R44-wt16, IT3R45-wt17, IT3R35-3312-1, IT3R36-3312-3, IT3R37-3343-2, IT3R38-3343-3, IT3R39-3343-4, IT3R46-3308-1, IT3R47-3308-2, IT3R48-3308-4 [ 2017-01-11 13:57:40 ] INFO Samples to exclude: none [ 2017-01-11 13:57:40 ] INFO Requested contrasts: wt_vs_3308 [ 2017-01-11 13:57:40 ] INFO Annotation: download [ 2017-01-11 13:57:40 ] INFO Organism: mm10 [ 2017-01-11 13:57:40 ] INFO Reference source: ensembl [ 2017-01-11 13:57:40 ] INFO Count type: utr [ 2017-01-11 13:57:40 ] INFO Exon filters: none applied [ 2017-01-11 13:57:40 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-01-11 13:57:40 ] INFO length: [ 2017-01-11 13:57:40 ] INFO length: 500 [ 2017-01-11 13:57:40 ] INFO avg.reads: [ 2017-01-11 13:57:40 ] INFO average.per.bp: 100 [ 2017-01-11 13:57:40 ] INFO quantile: 0.25 [ 2017-01-11 13:57:40 ] INFO expression: [ 2017-01-11 13:57:40 ] INFO median: TRUE [ 2017-01-11 13:57:40 ] INFO mean: FALSE [ 2017-01-11 13:57:40 ] INFO quantile: NA [ 2017-01-11 13:57:40 ] INFO known: NA [ 2017-01-11 13:57:40 ] INFO custom: NA [ 2017-01-11 13:57:40 ] INFO biotype: [ 2017-01-11 13:57:40 ] INFO pseudogene: FALSE [ 2017-01-11 13:57:40 ] INFO snRNA: FALSE [ 2017-01-11 13:57:40 ] INFO protein_coding: FALSE [ 2017-01-11 13:57:40 ] INFO antisense: FALSE [ 2017-01-11 13:57:40 ] INFO miRNA: FALSE [ 2017-01-11 13:57:40 ] INFO snoRNA: FALSE [ 2017-01-11 13:57:40 ] INFO lincRNA: FALSE [ 2017-01-11 13:57:40 ] INFO processed_transcript: FALSE [ 2017-01-11 13:57:40 ] INFO misc_RNA: FALSE [ 2017-01-11 13:57:40 ] INFO rRNA: TRUE [ 2017-01-11 13:57:40 ] INFO sense_intronic: FALSE [ 2017-01-11 13:57:40 ] INFO sense_overlapping: FALSE [ 2017-01-11 13:57:40 ] INFO polymorphic_pseudogene: FALSE [ 2017-01-11 13:57:40 ] INFO IG_C_gene: FALSE [ 2017-01-11 13:57:40 ] INFO IG_J_gene: FALSE [ 2017-01-11 13:57:40 ] INFO IG_D_gene: FALSE [ 2017-01-11 13:57:40 ] INFO IG_LV_gene: FALSE [ 2017-01-11 13:57:40 ] INFO IG_V_gene: FALSE [ 2017-01-11 13:57:40 ] INFO IG_V_pseudogene: TRUE [ 2017-01-11 13:57:40 ] INFO TR_V_gene: FALSE [ 2017-01-11 13:57:40 ] INFO TR_V_pseudogene: TRUE [ 2017-01-11 13:57:40 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-01-11 13:57:40 ] INFO Filter application: postnorm [ 2017-01-11 13:57:40 ] INFO Normalization algorithm: deseq [ 2017-01-11 13:57:40 ] INFO Normalization arguments: [ 2017-01-11 13:57:40 ] INFO locfunc: [ 2017-01-11 13:57:40 ] INFO [[ [ 2017-01-11 13:57:40 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-01-11 13:57:40 ] INFO locfunc [ 2017-01-11 13:57:40 ] INFO Statistical algorithm: deseq [ 2017-01-11 13:57:40 ] INFO Statistical arguments: [ 2017-01-11 13:57:40 ] INFO deseq: blind, fit-only, local [ 2017-01-11 13:57:40 ] INFO Meta-analysis method: none [ 2017-01-11 13:57:40 ] INFO Multiple testing correction: BH [ 2017-01-11 13:57:40 ] INFO p-value threshold: 0.05 [ 2017-01-11 13:57:40 ] INFO Logarithmic transformation offset: 1 [ 2017-01-11 13:57:40 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-01-11 13:57:40 ] INFO Figure format: png, pdf [ 2017-01-11 13:57:40 ] INFO Output directory: /data/images/proton/run327/www//metaseqr1 [ 2017-01-11 13:57:40 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-01-11 13:57:40 ] INFO Output scale(s): log2, rpgm [ 2017-01-11 13:57:40 ] INFO Output values: normalized [ 2017-01-11 13:57:40 ] INFO Downloading gene annotation for mm10... [ 2017-01-11 13:57:48 ] INFO Downloading transcript annotation for mm10... [ 2017-01-11 14:00:06 ] INFO Converting annotation to GenomicRanges object... [ 2017-01-11 14:00:06 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2017-01-11 14:02:54 ] INFO Flanking merged transcript 3' UTRs per 500bp... [ 2017-01-11 14:02:58 ] INFO Reading bam file 007.bam for sample with name 007. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 009.bam for sample with name 009. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 010.bam for sample with name 010. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 011.bam for sample with name 011. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 012.bam for sample with name 012. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 013.bam for sample with name 013. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 014.bam for sample with name 014. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 015.bam for sample with name 015. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 016.bam for sample with name 016. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 019.bam for sample with name 019. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 020.bam for sample with name 020. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 021.bam for sample with name 021. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 022.bam for sample with name 022. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file 025.bam for sample with name 025. This might take some time... [ 2017-01-11 14:02:59 ] INFO Reading bam file IT3R40-wt1.bam for sample with name IT3R40-wt1. This might take some time... [ 2017-01-11 14:02:59 ] INFO Reading bam file IT3R41-wt2.bam for sample with name IT3R41-wt2. This might take some time... [ 2017-01-11 14:02:59 ] INFO Reading bam file IT3R42-wt5.bam for sample with name IT3R42-wt5. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file IT3R43-wt15.bam for sample with name IT3R43-wt15. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file IT3R44-wt16.bam for sample with name IT3R44-wt16. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Reading bam file IT3R45-wt17.bam for sample with name IT3R45-wt17. This might take some time... [ 2017-01-11 14:02:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:02:59 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:02:59 ] INFO ...for single-end reads... [ 2017-01-11 14:02:59 ] INFO ...ignoring strandedness... [ 2017-01-11 14:02:59 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:02:59 ] INFO ...for single-end reads... [ 2017-01-11 14:02:59 ] INFO ...ignoring strandedness... [ 2017-01-11 14:02:59 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:02:59 ] INFO ...for single-end reads... [ 2017-01-11 14:02:59 ] INFO ...ignoring strandedness... [ 2017-01-11 14:02:59 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:02:59 ] INFO ...for single-end reads... [ 2017-01-11 14:02:59 ] INFO ...ignoring strandedness... [ 2017-01-11 14:02:59 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:02:59 ] INFO ...for single-end reads... [ 2017-01-11 14:02:59 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:00 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:00 ] INFO ...for single-end reads... [ 2017-01-11 14:03:00 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:00 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:00 ] INFO ...for single-end reads... [ 2017-01-11 14:03:00 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:00 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:00 ] INFO ...for single-end reads... [ 2017-01-11 14:03:00 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:00 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:00 ] INFO ...for single-end reads... [ 2017-01-11 14:03:00 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:01 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:01 ] INFO ...for single-end reads... [ 2017-01-11 14:03:01 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:01 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:01 ] INFO ...for single-end reads... [ 2017-01-11 14:03:01 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:01 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:01 ] INFO ...for single-end reads... [ 2017-01-11 14:03:01 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:01 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:01 ] INFO ...for single-end reads... [ 2017-01-11 14:03:01 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:02 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:02 ] INFO ...for single-end reads... [ 2017-01-11 14:03:02 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:02 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:02 ] INFO ...for single-end reads... [ 2017-01-11 14:03:02 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:02 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:02 ] INFO ...for single-end reads... [ 2017-01-11 14:03:02 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:03 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:03 ] INFO ...for single-end reads... [ 2017-01-11 14:03:03 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:04 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:04 ] INFO ...for single-end reads... [ 2017-01-11 14:03:04 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:04 ] INFO Reading bam file IT3R36-3312-3.bam for sample with name IT3R36-3312-3. This might take some time... [ 2017-01-11 14:03:04 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:03:05 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:05 ] INFO ...for single-end reads... [ 2017-01-11 14:03:05 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:06 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:06 ] INFO ...for single-end reads... [ 2017-01-11 14:03:06 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:07 ] INFO Reading bam file IT3R38-3343-3.bam for sample with name IT3R38-3343-3. This might take some time... [ 2017-01-11 14:03:07 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:03:09 ] INFO Reading bam file IT3R46-3308-1.bam for sample with name IT3R46-3308-1. This might take some time... [ 2017-01-11 14:03:09 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:03:10 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:10 ] INFO ...for single-end reads... [ 2017-01-11 14:03:10 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:12 ] INFO Reading bam file IT3R37-3343-2.bam for sample with name IT3R37-3343-2. This might take some time... [ 2017-01-11 14:03:12 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:03:14 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:14 ] INFO ...for single-end reads... [ 2017-01-11 14:03:14 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:14 ] INFO Reading bam file IT3R35-3312-1.bam for sample with name IT3R35-3312-1. This might take some time... [ 2017-01-11 14:03:14 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:03:14 ] INFO Reading bam file IT3R48-3308-4.bam for sample with name IT3R48-3308-4. This might take some time... [ 2017-01-11 14:03:14 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:03:15 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:15 ] INFO ...for single-end reads... [ 2017-01-11 14:03:15 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:17 ] INFO Reading bam file IT3R39-3343-4.bam for sample with name IT3R39-3343-4. This might take some time... [ 2017-01-11 14:03:17 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:03:18 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:18 ] INFO ...for single-end reads... [ 2017-01-11 14:03:18 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:20 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:20 ] INFO ...for single-end reads... [ 2017-01-11 14:03:20 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:20 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:20 ] INFO ...for single-end reads... [ 2017-01-11 14:03:20 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:20 ] INFO Reading bam file IT3R47-3308-2.bam for sample with name IT3R47-3308-2. This might take some time... [ 2017-01-11 14:03:20 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:03:21 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:21 ] INFO ...for single-end reads... [ 2017-01-11 14:03:21 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:23 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:03:23 ] INFO ...for single-end reads... [ 2017-01-11 14:03:23 ] INFO ...ignoring strandedness... [ 2017-01-11 14:03:54 ] INFO Exporting raw read counts table to /data/images/proton/run327/www//metaseqr1/lists/raw_counts_table.txt.gz [ 2017-01-11 14:03:58 ] INFO Checking chromosomes in transcript counts and gene annotation... [ 2017-01-11 14:03:58 ] INFO Processing transcripts... [ 2017-01-11 14:03:58 ] INFO Separating transcripts (UTR regions) per gene for 007... [ 2017-01-11 14:04:15 ] INFO Separating transcripts (UTR regions) per gene for 009... [ 2017-01-11 14:04:36 ] INFO Separating transcripts (UTR regions) per gene for 010... [ 2017-01-11 14:04:56 ] INFO Separating transcripts (UTR regions) per gene for 011... [ 2017-01-11 14:05:18 ] INFO Separating transcripts (UTR regions) per gene for 012... [ 2017-01-11 14:05:39 ] INFO Separating transcripts (UTR regions) per gene for 013... [ 2017-01-11 14:06:01 ] INFO Separating transcripts (UTR regions) per gene for 014... [ 2017-01-11 14:06:24 ] INFO Separating transcripts (UTR regions) per gene for 015... [ 2017-01-11 14:06:46 ] INFO Separating transcripts (UTR regions) per gene for 016... [ 2017-01-11 14:07:11 ] INFO Separating transcripts (UTR regions) per gene for 019... [ 2017-01-11 14:07:31 ] INFO Separating transcripts (UTR regions) per gene for 020... [ 2017-01-11 14:07:53 ] INFO Separating transcripts (UTR regions) per gene for 021... [ 2017-01-11 14:08:19 ] INFO Separating transcripts (UTR regions) per gene for 022... [ 2017-01-11 14:08:42 ] INFO Separating transcripts (UTR regions) per gene for 025... [ 2017-01-11 14:09:04 ] INFO Separating transcripts (UTR regions) per gene for IT3R40-wt1... [ 2017-01-11 14:09:32 ] INFO Separating transcripts (UTR regions) per gene for IT3R41-wt2... [ 2017-01-11 14:09:58 ] INFO Separating transcripts (UTR regions) per gene for IT3R42-wt5... [ 2017-01-11 14:10:19 ] INFO Separating transcripts (UTR regions) per gene for IT3R43-wt15... [ 2017-01-11 14:10:44 ] INFO Separating transcripts (UTR regions) per gene for IT3R44-wt16... [ 2017-01-11 14:11:06 ] INFO Separating transcripts (UTR regions) per gene for IT3R45-wt17... [ 2017-01-11 14:11:25 ] INFO Separating transcripts (UTR regions) per gene for IT3R35-3312-1... [ 2017-01-11 14:11:46 ] INFO Separating transcripts (UTR regions) per gene for IT3R36-3312-3... [ 2017-01-11 14:12:09 ] INFO Separating transcripts (UTR regions) per gene for IT3R37-3343-2... [ 2017-01-11 14:12:33 ] INFO Separating transcripts (UTR regions) per gene for IT3R38-3343-3... [ 2017-01-11 14:12:59 ] INFO Separating transcripts (UTR regions) per gene for IT3R39-3343-4... [ 2017-01-11 14:13:20 ] INFO Separating transcripts (UTR regions) per gene for IT3R46-3308-1... [ 2017-01-11 14:13:41 ] INFO Separating transcripts (UTR regions) per gene for IT3R47-3308-2... [ 2017-01-11 14:14:01 ] INFO Separating transcripts (UTR regions) per gene for IT3R48-3308-4... [ 2017-01-11 14:14:23 ] INFO Saving gene model to /data/images/proton/run327/www//metaseqr1/data/gene_model.RData [ 2017-01-11 14:14:30 ] INFO Summarizing count data... [ 2017-01-11 14:15:10 ] INFO Removing genes with zero counts in all samples... [ 2017-01-11 14:15:10 ] INFO Normalizing with: deseq [ 2017-01-11 14:15:11 ] INFO Applying gene filter length... [ 2017-01-11 14:15:11 ] INFO Threshold below which ignored: 500 [ 2017-01-11 14:15:11 ] INFO Applying gene filter avg.reads... [ 2017-01-11 14:15:12 ] INFO Threshold below which ignored: 0 [ 2017-01-11 14:15:12 ] INFO Applying gene filter expression... [ 2017-01-11 14:15:13 ] INFO Threshold below which ignored: 0 [ 2017-01-11 14:15:13 ] INFO Applying gene filter biotype... [ 2017-01-11 14:15:13 ] INFO Biotypes ignored: rRNA, IG_V_pseudogene, TR_V_pseudogene [ 2017-01-11 14:15:13 ] INFO 23127 genes filtered out [ 2017-01-11 14:15:13 ] INFO 26421 genes remain after filtering [ 2017-01-11 14:15:13 ] INFO Running statistical tests with: deseq [ 2017-01-11 14:15:13 ] INFO Contrast: wt_vs_3308 [ 2017-01-11 14:15:34 ] INFO Contrast wt_vs_3308: found 336 genes [ 2017-01-11 14:15:34 ] INFO Exporting and compressing normalized read counts table to /data/images/proton/run327/www//metaseqr1/lists/normalized_counts_table.txt [ 2017-01-11 14:15:36 ] INFO Building output files... [ 2017-01-11 14:15:37 ] INFO Contrast: wt_vs_3308 [ 2017-01-11 14:15:37 ] INFO Adding non-filtered data... [ 2017-01-11 14:15:37 ] INFO binding annotation... [ 2017-01-11 14:15:38 ] INFO binding p-values... [ 2017-01-11 14:15:39 ] INFO binding FDRs... [ 2017-01-11 14:15:39 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:15:39 ] INFO binding all normalized counts for wt... [ 2017-01-11 14:15:45 ] INFO binding all normalized counts for 3308... [ 2017-01-11 14:15:46 ] INFO binding filtering flags... [ 2017-01-11 14:15:47 ] INFO Writing output... [ 2017-01-11 14:15:47 ] INFO Adding filtered data... [ 2017-01-11 14:15:47 ] INFO binding annotation... [ 2017-01-11 14:15:47 ] INFO binding p-values... [ 2017-01-11 14:15:47 ] INFO binding FDRs... [ 2017-01-11 14:15:48 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:15:48 ] INFO binding all normalized counts for wt... [ 2017-01-11 14:15:48 ] INFO binding all normalized counts for 3308... [ 2017-01-11 14:15:48 ] INFO binding filtering flags... [ 2017-01-11 14:15:49 ] INFO Writing output... [ 2017-01-11 14:15:52 ] INFO Creating quality control graphs... [ 2017-01-11 14:15:52 ] INFO Plotting in png format... [ 2017-01-11 14:15:52 ] INFO Plotting mds... [ 2017-01-11 14:15:54 ] INFO Plotting biodetection... [ 2017-01-11 14:15:57 ] INFO Plotting countsbio... [ 2017-01-11 14:16:02 ] INFO Plotting saturation... [ 2017-01-11 14:16:25 ] INFO Plotting readnoise... [ 2017-01-11 14:16:42 ] INFO Plotting correl... [ 2017-01-11 14:16:43 ] INFO Plotting pairwise... [ 2017-01-11 14:27:18 ] INFO 2017-01-11 14:27:18: Data processing started... [ 2017-01-11 14:27:18 ] INFO Read counts file: imported sam/bam/bed files [ 2017-01-11 14:27:18 ] INFO Conditions: wt, 3312, 3343, 3308 [ 2017-01-11 14:27:18 ] INFO Samples to include: IT3R40-wt1, IT3R41-wt2, IT3R42-wt5, IT3R43-wt15, IT3R44-wt16, IT3R45-wt17, IT3R35-3312-1, IT3R36-3312-3, IT3R37-3343-2, IT3R38-3343-3, IT3R39-3343-4, IT3R46-3308-1, IT3R47-3308-2, IT3R48-3308-4 [ 2017-01-11 14:27:18 ] INFO Samples to exclude: none [ 2017-01-11 14:27:18 ] INFO Requested contrasts: wt_vs_3308, wt_vs_3312, wt_vs_3343, 3308_vs_3343, 3312_vs_3343, 3308_vs_3312 [ 2017-01-11 14:27:18 ] INFO Annotation: download [ 2017-01-11 14:27:18 ] INFO Organism: mm10 [ 2017-01-11 14:27:18 ] INFO Reference source: ensembl [ 2017-01-11 14:27:18 ] INFO Count type: utr [ 2017-01-11 14:27:18 ] INFO Exon filters: none applied [ 2017-01-11 14:27:18 ] INFO Gene filters: length, avg.reads, expression, biotype [ 2017-01-11 14:27:18 ] INFO length: [ 2017-01-11 14:27:18 ] INFO length: 500 [ 2017-01-11 14:27:18 ] INFO avg.reads: [ 2017-01-11 14:27:18 ] INFO average.per.bp: 100 [ 2017-01-11 14:27:18 ] INFO quantile: 0.25 [ 2017-01-11 14:27:18 ] INFO expression: [ 2017-01-11 14:27:18 ] INFO median: TRUE [ 2017-01-11 14:27:18 ] INFO mean: FALSE [ 2017-01-11 14:27:18 ] INFO quantile: NA [ 2017-01-11 14:27:18 ] INFO known: NA [ 2017-01-11 14:27:18 ] INFO custom: NA [ 2017-01-11 14:27:18 ] INFO biotype: [ 2017-01-11 14:27:18 ] INFO pseudogene: FALSE [ 2017-01-11 14:27:18 ] INFO snRNA: FALSE [ 2017-01-11 14:27:18 ] INFO protein_coding: FALSE [ 2017-01-11 14:27:18 ] INFO antisense: FALSE [ 2017-01-11 14:27:18 ] INFO miRNA: FALSE [ 2017-01-11 14:27:18 ] INFO snoRNA: FALSE [ 2017-01-11 14:27:18 ] INFO lincRNA: FALSE [ 2017-01-11 14:27:18 ] INFO processed_transcript: FALSE [ 2017-01-11 14:27:18 ] INFO misc_RNA: FALSE [ 2017-01-11 14:27:18 ] INFO rRNA: TRUE [ 2017-01-11 14:27:18 ] INFO sense_intronic: FALSE [ 2017-01-11 14:27:18 ] INFO sense_overlapping: FALSE [ 2017-01-11 14:27:18 ] INFO polymorphic_pseudogene: FALSE [ 2017-01-11 14:27:18 ] INFO IG_C_gene: FALSE [ 2017-01-11 14:27:18 ] INFO IG_J_gene: FALSE [ 2017-01-11 14:27:18 ] INFO IG_D_gene: FALSE [ 2017-01-11 14:27:18 ] INFO IG_LV_gene: FALSE [ 2017-01-11 14:27:18 ] INFO IG_V_gene: FALSE [ 2017-01-11 14:27:18 ] INFO IG_V_pseudogene: TRUE [ 2017-01-11 14:27:18 ] INFO TR_V_gene: FALSE [ 2017-01-11 14:27:18 ] INFO TR_V_pseudogene: TRUE [ 2017-01-11 14:27:18 ] INFO three_prime_overlapping_ncrna: FALSE [ 2017-01-11 14:27:18 ] INFO Filter application: postnorm [ 2017-01-11 14:27:18 ] INFO Normalization algorithm: deseq [ 2017-01-11 14:27:18 ] INFO Normalization arguments: [ 2017-01-11 14:27:18 ] INFO locfunc: [ 2017-01-11 14:27:18 ] INFO [[ [ 2017-01-11 14:27:18 ] INFO list(locfunc = function (x, na.rm = FALSE) standardGeneric("median")) [ 2017-01-11 14:27:18 ] INFO locfunc [ 2017-01-11 14:27:18 ] INFO Statistical algorithm: deseq [ 2017-01-11 14:27:18 ] INFO Statistical arguments: [ 2017-01-11 14:27:18 ] INFO deseq: blind, fit-only, local [ 2017-01-11 14:27:18 ] INFO Meta-analysis method: none [ 2017-01-11 14:27:18 ] INFO Multiple testing correction: BH [ 2017-01-11 14:27:18 ] INFO p-value threshold: 0.05 [ 2017-01-11 14:27:18 ] INFO Logarithmic transformation offset: 1 [ 2017-01-11 14:27:18 ] INFO Quality control plots: mds, biodetection, countsbio, saturation, readnoise, filtered, correl, pairwise, boxplot, gcbias, lengthbias, meandiff, meanvar, biodist, volcano, deheatmap [ 2017-01-11 14:27:18 ] INFO Figure format: png, pdf [ 2017-01-11 14:27:18 ] INFO Output directory: /data/images/proton/run327/www//metaseqr1 [ 2017-01-11 14:27:18 ] INFO Output data: annotation, p.value, adj.p.value, fold.change, counts, flags [ 2017-01-11 14:27:18 ] INFO Output scale(s): log2, rpgm [ 2017-01-11 14:27:18 ] INFO Output values: normalized [ 2017-01-11 14:27:18 ] INFO Downloading gene annotation for mm10... [ 2017-01-11 14:27:25 ] INFO Downloading transcript annotation for mm10... [ 2017-01-11 14:30:09 ] INFO Converting annotation to GenomicRanges object... [ 2017-01-11 14:30:09 ] INFO Merging transcript 3' UTRs to create unique gene/transcript models... [ 2017-01-11 14:32:56 ] INFO Flanking merged transcript 3' UTRs per 500bp... [ 2017-01-11 14:32:59 ] INFO Reading bam file IT3R40-wt1.bam for sample with name IT3R40-wt1. This might take some time... [ 2017-01-11 14:32:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:32:59 ] INFO Reading bam file IT3R41-wt2.bam for sample with name IT3R41-wt2. This might take some time... [ 2017-01-11 14:32:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:32:59 ] INFO Reading bam file IT3R42-wt5.bam for sample with name IT3R42-wt5. This might take some time... [ 2017-01-11 14:32:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:32:59 ] INFO Reading bam file IT3R43-wt15.bam for sample with name IT3R43-wt15. This might take some time... [ 2017-01-11 14:32:59 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:33:00 ] INFO Reading bam file IT3R44-wt16.bam for sample with name IT3R44-wt16. This might take some time... [ 2017-01-11 14:33:00 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:33:00 ] INFO Reading bam file IT3R45-wt17.bam for sample with name IT3R45-wt17. This might take some time... [ 2017-01-11 14:33:00 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:33:00 ] INFO Reading bam file IT3R35-3312-1.bam for sample with name IT3R35-3312-1. This might take some time... [ 2017-01-11 14:33:00 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:33:00 ] INFO Reading bam file IT3R36-3312-3.bam for sample with name IT3R36-3312-3. This might take some time... [ 2017-01-11 14:33:00 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:33:00 ] INFO Reading bam file IT3R37-3343-2.bam for sample with name IT3R37-3343-2. This might take some time... [ 2017-01-11 14:33:00 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:33:00 ] INFO Reading bam file IT3R38-3343-3.bam for sample with name IT3R38-3343-3. This might take some time... [ 2017-01-11 14:33:00 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:33:00 ] INFO Reading bam file IT3R39-3343-4.bam for sample with name IT3R39-3343-4. This might take some time... [ 2017-01-11 14:33:00 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:33:00 ] INFO Reading bam file IT3R46-3308-1.bam for sample with name IT3R46-3308-1. This might take some time... [ 2017-01-11 14:33:00 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:33:00 ] INFO Reading bam file IT3R47-3308-2.bam for sample with name IT3R47-3308-2. This might take some time... [ 2017-01-11 14:33:00 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:33:00 ] INFO Reading bam file IT3R48-3308-4.bam for sample with name IT3R48-3308-4. This might take some time... [ 2017-01-11 14:33:00 ] WARN Information regarding strandedness of the reads is not correctly provided! Assuming unstranded... [ 2017-01-11 14:33:00 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:00 ] INFO ...for single-end reads... [ 2017-01-11 14:33:00 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:02 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:02 ] INFO ...for single-end reads... [ 2017-01-11 14:33:02 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:02 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:02 ] INFO ...for single-end reads... [ 2017-01-11 14:33:02 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:03 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:03 ] INFO ...for single-end reads... [ 2017-01-11 14:33:03 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:03 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:03 ] INFO ...for single-end reads... [ 2017-01-11 14:33:03 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:04 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:04 ] INFO ...for single-end reads... [ 2017-01-11 14:33:04 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:05 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:05 ] INFO ...for single-end reads... [ 2017-01-11 14:33:05 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:06 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:06 ] INFO ...for single-end reads... [ 2017-01-11 14:33:06 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:06 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:06 ] INFO ...for single-end reads... [ 2017-01-11 14:33:06 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:06 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:06 ] INFO ...for single-end reads... [ 2017-01-11 14:33:06 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:06 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:06 ] INFO ...for single-end reads... [ 2017-01-11 14:33:06 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:07 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:07 ] INFO ...for single-end reads... [ 2017-01-11 14:33:07 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:07 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:07 ] INFO ...for single-end reads... [ 2017-01-11 14:33:07 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:07 ] INFO Counting reads overlapping with given annotation... [ 2017-01-11 14:33:07 ] INFO ...for single-end reads... [ 2017-01-11 14:33:07 ] INFO ...ignoring strandedness... [ 2017-01-11 14:33:34 ] INFO Exporting raw read counts table to /data/images/proton/run327/www//metaseqr1/lists/raw_counts_table.txt.gz [ 2017-01-11 14:33:36 ] INFO Checking chromosomes in transcript counts and gene annotation... [ 2017-01-11 14:33:36 ] INFO Processing transcripts... [ 2017-01-11 14:33:36 ] INFO Separating transcripts (UTR regions) per gene for IT3R40-wt1... [ 2017-01-11 14:33:51 ] INFO Separating transcripts (UTR regions) per gene for IT3R41-wt2... [ 2017-01-11 14:34:11 ] INFO Separating transcripts (UTR regions) per gene for IT3R42-wt5... [ 2017-01-11 14:34:29 ] INFO Separating transcripts (UTR regions) per gene for IT3R43-wt15... [ 2017-01-11 14:34:47 ] INFO Separating transcripts (UTR regions) per gene for IT3R44-wt16... [ 2017-01-11 14:35:05 ] INFO Separating transcripts (UTR regions) per gene for IT3R45-wt17... [ 2017-01-11 14:35:26 ] INFO Separating transcripts (UTR regions) per gene for IT3R35-3312-1... [ 2017-01-11 14:35:48 ] INFO Separating transcripts (UTR regions) per gene for IT3R36-3312-3... [ 2017-01-11 14:36:06 ] INFO Separating transcripts (UTR regions) per gene for IT3R37-3343-2... [ 2017-01-11 14:36:24 ] INFO Separating transcripts (UTR regions) per gene for IT3R38-3343-3... [ 2017-01-11 14:36:42 ] INFO Separating transcripts (UTR regions) per gene for IT3R39-3343-4... [ 2017-01-11 14:37:02 ] INFO Separating transcripts (UTR regions) per gene for IT3R46-3308-1... [ 2017-01-11 14:37:20 ] INFO Separating transcripts (UTR regions) per gene for IT3R47-3308-2... [ 2017-01-11 14:37:41 ] INFO Separating transcripts (UTR regions) per gene for IT3R48-3308-4... [ 2017-01-11 14:37:59 ] INFO Saving gene model to /data/images/proton/run327/www//metaseqr1/data/gene_model.RData [ 2017-01-11 14:38:03 ] INFO Summarizing count data... [ 2017-01-11 14:38:43 ] INFO Removing genes with zero counts in all samples... [ 2017-01-11 14:38:43 ] INFO Normalizing with: deseq [ 2017-01-11 14:38:43 ] INFO Applying gene filter length... [ 2017-01-11 14:38:43 ] INFO Threshold below which ignored: 500 [ 2017-01-11 14:38:43 ] INFO Applying gene filter avg.reads... [ 2017-01-11 14:38:43 ] INFO Threshold below which ignored: 0 [ 2017-01-11 14:38:43 ] INFO Applying gene filter expression... [ 2017-01-11 14:38:43 ] INFO Threshold below which ignored: 2 [ 2017-01-11 14:38:43 ] INFO Applying gene filter biotype... [ 2017-01-11 14:38:43 ] INFO Biotypes ignored: rRNA, IG_V_pseudogene, TR_V_pseudogene [ 2017-01-11 14:38:43 ] INFO 31528 genes filtered out [ 2017-01-11 14:38:43 ] INFO 18020 genes remain after filtering [ 2017-01-11 14:38:43 ] INFO Running statistical tests with: deseq [ 2017-01-11 14:38:44 ] INFO Contrast: wt_vs_3308 [ 2017-01-11 14:38:57 ] INFO Contrast: wt_vs_3312 [ 2017-01-11 14:39:11 ] INFO Contrast: wt_vs_3343 [ 2017-01-11 14:39:25 ] INFO Contrast: 3308_vs_3343 [ 2017-01-11 14:39:37 ] INFO Contrast: 3312_vs_3343 [ 2017-01-11 14:39:48 ] INFO Contrast: 3308_vs_3312 [ 2017-01-11 14:39:59 ] INFO Contrast wt_vs_3308: found 1017 genes [ 2017-01-11 14:39:59 ] INFO Contrast wt_vs_3312: found 404 genes [ 2017-01-11 14:39:59 ] INFO Contrast wt_vs_3343: found 656 genes [ 2017-01-11 14:39:59 ] INFO Contrast 3308_vs_3343: found 234 genes [ 2017-01-11 14:39:59 ] INFO Contrast 3312_vs_3343: found 68 genes [ 2017-01-11 14:39:59 ] INFO Contrast 3308_vs_3312: found 90 genes [ 2017-01-11 14:39:59 ] INFO Exporting and compressing normalized read counts table to /data/images/proton/run327/www//metaseqr1/lists/normalized_counts_table.txt [ 2017-01-11 14:40:00 ] INFO Building output files... [ 2017-01-11 14:40:02 ] INFO Contrast: wt_vs_3308 [ 2017-01-11 14:40:02 ] INFO Adding non-filtered data... [ 2017-01-11 14:40:02 ] INFO binding annotation... [ 2017-01-11 14:40:03 ] INFO binding p-values... [ 2017-01-11 14:40:03 ] INFO binding FDRs... [ 2017-01-11 14:40:04 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:40:04 ] INFO binding all normalized counts for wt... [ 2017-01-11 14:40:05 ] INFO binding all normalized counts for 3308... [ 2017-01-11 14:40:06 ] INFO binding filtering flags... [ 2017-01-11 14:40:06 ] INFO Writing output... [ 2017-01-11 14:40:06 ] INFO Adding filtered data... [ 2017-01-11 14:40:06 ] INFO binding annotation... [ 2017-01-11 14:40:06 ] INFO binding p-values... [ 2017-01-11 14:40:06 ] INFO binding FDRs... [ 2017-01-11 14:40:07 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:40:07 ] INFO binding all normalized counts for wt... [ 2017-01-11 14:40:07 ] INFO binding all normalized counts for 3308... [ 2017-01-11 14:40:07 ] INFO binding filtering flags... [ 2017-01-11 14:40:08 ] INFO Writing output... [ 2017-01-11 14:40:10 ] INFO Contrast: wt_vs_3312 [ 2017-01-11 14:40:10 ] INFO Adding non-filtered data... [ 2017-01-11 14:40:10 ] INFO binding annotation... [ 2017-01-11 14:40:13 ] INFO binding p-values... [ 2017-01-11 14:40:13 ] INFO binding FDRs... [ 2017-01-11 14:40:13 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:40:13 ] INFO binding all normalized counts for wt... [ 2017-01-11 14:40:14 ] INFO binding all normalized counts for 3312... [ 2017-01-11 14:40:15 ] INFO binding filtering flags... [ 2017-01-11 14:40:16 ] INFO Writing output... [ 2017-01-11 14:40:16 ] INFO Adding filtered data... [ 2017-01-11 14:40:16 ] INFO binding annotation... [ 2017-01-11 14:40:16 ] INFO binding p-values... [ 2017-01-11 14:40:16 ] INFO binding FDRs... [ 2017-01-11 14:40:16 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:40:16 ] INFO binding all normalized counts for wt... [ 2017-01-11 14:40:16 ] INFO binding all normalized counts for 3312... [ 2017-01-11 14:40:16 ] INFO binding filtering flags... [ 2017-01-11 14:40:17 ] INFO Writing output... [ 2017-01-11 14:40:19 ] INFO Contrast: wt_vs_3343 [ 2017-01-11 14:40:19 ] INFO Adding non-filtered data... [ 2017-01-11 14:40:19 ] INFO binding annotation... [ 2017-01-11 14:40:20 ] INFO binding p-values... [ 2017-01-11 14:40:20 ] INFO binding FDRs... [ 2017-01-11 14:40:20 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:40:20 ] INFO binding all normalized counts for wt... [ 2017-01-11 14:40:21 ] INFO binding all normalized counts for 3343... [ 2017-01-11 14:40:22 ] INFO binding filtering flags... [ 2017-01-11 14:40:23 ] INFO Writing output... [ 2017-01-11 14:40:23 ] INFO Adding filtered data... [ 2017-01-11 14:40:23 ] INFO binding annotation... [ 2017-01-11 14:40:23 ] INFO binding p-values... [ 2017-01-11 14:40:23 ] INFO binding FDRs... [ 2017-01-11 14:40:23 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:40:23 ] INFO binding all normalized counts for wt... [ 2017-01-11 14:40:23 ] INFO binding all normalized counts for 3343... [ 2017-01-11 14:40:23 ] INFO binding filtering flags... [ 2017-01-11 14:40:24 ] INFO Writing output... [ 2017-01-11 14:40:26 ] INFO Contrast: 3308_vs_3343 [ 2017-01-11 14:40:26 ] INFO Adding non-filtered data... [ 2017-01-11 14:40:26 ] INFO binding annotation... [ 2017-01-11 14:40:27 ] INFO binding p-values... [ 2017-01-11 14:40:27 ] INFO binding FDRs... [ 2017-01-11 14:40:27 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:40:28 ] INFO binding all normalized counts for 3308... [ 2017-01-11 14:40:28 ] INFO binding all normalized counts for 3343... [ 2017-01-11 14:40:29 ] INFO binding filtering flags... [ 2017-01-11 14:40:29 ] INFO Writing output... [ 2017-01-11 14:40:29 ] INFO Adding filtered data... [ 2017-01-11 14:40:29 ] INFO binding annotation... [ 2017-01-11 14:40:29 ] INFO binding p-values... [ 2017-01-11 14:40:29 ] INFO binding FDRs... [ 2017-01-11 14:40:30 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:40:30 ] INFO binding all normalized counts for 3308... [ 2017-01-11 14:40:30 ] INFO binding all normalized counts for 3343... [ 2017-01-11 14:40:30 ] INFO binding filtering flags... [ 2017-01-11 14:40:31 ] INFO Writing output... [ 2017-01-11 14:40:33 ] INFO Contrast: 3312_vs_3343 [ 2017-01-11 14:40:33 ] INFO Adding non-filtered data... [ 2017-01-11 14:40:33 ] INFO binding annotation... [ 2017-01-11 14:40:33 ] INFO binding p-values... [ 2017-01-11 14:40:33 ] INFO binding FDRs... [ 2017-01-11 14:40:34 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:40:34 ] INFO binding all normalized counts for 3312... [ 2017-01-11 14:40:34 ] INFO binding all normalized counts for 3343... [ 2017-01-11 14:40:35 ] INFO binding filtering flags... [ 2017-01-11 14:40:35 ] INFO Writing output... [ 2017-01-11 14:40:35 ] INFO Adding filtered data... [ 2017-01-11 14:40:35 ] INFO binding annotation... [ 2017-01-11 14:40:35 ] INFO binding p-values... [ 2017-01-11 14:40:35 ] INFO binding FDRs... [ 2017-01-11 14:40:36 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:40:36 ] INFO binding all normalized counts for 3312... [ 2017-01-11 14:40:36 ] INFO binding all normalized counts for 3343... [ 2017-01-11 14:40:36 ] INFO binding filtering flags... [ 2017-01-11 14:40:37 ] INFO Writing output... [ 2017-01-11 14:40:38 ] INFO Contrast: 3308_vs_3312 [ 2017-01-11 14:40:38 ] INFO Adding non-filtered data... [ 2017-01-11 14:40:38 ] INFO binding annotation... [ 2017-01-11 14:40:39 ] INFO binding p-values... [ 2017-01-11 14:40:39 ] INFO binding FDRs... [ 2017-01-11 14:40:40 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:40:40 ] INFO binding all normalized counts for 3308... [ 2017-01-11 14:40:40 ] INFO binding all normalized counts for 3312... [ 2017-01-11 14:40:41 ] INFO binding filtering flags... [ 2017-01-11 14:40:41 ] INFO Writing output... [ 2017-01-11 14:40:41 ] INFO Adding filtered data... [ 2017-01-11 14:40:41 ] INFO binding annotation... [ 2017-01-11 14:40:41 ] INFO binding p-values... [ 2017-01-11 14:40:41 ] INFO binding FDRs... [ 2017-01-11 14:40:42 ] INFO binding log2 normalized fold changes... [ 2017-01-11 14:40:42 ] INFO binding all normalized counts for 3308... [ 2017-01-11 14:40:42 ] INFO binding all normalized counts for 3312... [ 2017-01-11 14:40:42 ] INFO binding filtering flags... [ 2017-01-11 14:40:43 ] INFO Writing output... [ 2017-01-11 14:40:44 ] INFO Creating quality control graphs... [ 2017-01-11 14:40:44 ] INFO Plotting in png format... [ 2017-01-11 14:40:44 ] INFO Plotting mds... [ 2017-01-11 14:40:45 ] INFO Plotting biodetection... [ 2017-01-11 14:40:46 ] INFO Plotting countsbio... [ 2017-01-11 14:40:49 ] INFO Plotting saturation... [ 2017-01-11 14:41:00 ] INFO Plotting readnoise... [ 2017-01-11 14:41:05 ] INFO Plotting correl... [ 2017-01-11 14:41:05 ] INFO Plotting pairwise... [ 2017-01-11 14:42:19 ] INFO Plotting boxplot... [ 2017-01-11 14:42:19 ] INFO Plotting gcbias... [ 2017-01-11 14:42:21 ] INFO Plotting lengthbias... [ 2017-01-11 14:42:22 ] INFO Plotting meandiff... [ 2017-01-11 14:42:25 ] INFO Plotting meanvar... [ 2017-01-11 14:42:53 ] INFO Plotting boxplot... [ 2017-01-11 14:42:54 ] INFO Plotting gcbias... [ 2017-01-11 14:42:55 ] INFO Plotting lengthbias... [ 2017-01-11 14:42:56 ] INFO Plotting meandiff... [ 2017-01-11 14:43:00 ] INFO Plotting meanvar... [ 2017-01-11 14:43:29 ] INFO Plotting biodist... [ 2017-01-11 14:43:29 ] INFO Contrast: wt_vs_3308 [ 2017-01-11 14:43:29 ] INFO Contrast: wt_vs_3312 [ 2017-01-11 14:43:29 ] INFO Contrast: wt_vs_3343 [ 2017-01-11 14:43:30 ] INFO Contrast: 3308_vs_3343 [ 2017-01-11 14:43:30 ] INFO Contrast: 3312_vs_3343 [ 2017-01-11 14:43:30 ] INFO Contrast: 3308_vs_3312 [ 2017-01-11 14:43:31 ] INFO Plotting volcano... [ 2017-01-11 14:43:31 ] INFO Contrast: wt_vs_3308 [ 2017-01-11 14:43:31 ] INFO Contrast: wt_vs_3312 [ 2017-01-11 14:43:32 ] INFO Contrast: wt_vs_3343 [ 2017-01-11 14:43:32 ] INFO Contrast: 3308_vs_3343 [ 2017-01-11 14:43:33 ] INFO Contrast: 3312_vs_3343 [ 2017-01-11 14:43:33 ] INFO Contrast: 3308_vs_3312 [ 2017-01-11 14:43:34 ] INFO Plotting deheatmap... [ 2017-01-11 14:43:34 ] INFO Contrast: wt_vs_3308 [ 2017-01-11 14:44:27 ] INFO Contrast: wt_vs_3312 [ 2017-01-11 14:45:14 ] INFO Contrast: wt_vs_3343 [ 2017-01-11 14:46:02 ] INFO Contrast: 3308_vs_3343 [ 2017-01-11 14:46:47 ] INFO Contrast: 3312_vs_3343 [ 2017-01-11 14:47:30 ] INFO Contrast: 3308_vs_3312 [ 2017-01-11 14:48:13 ] INFO Plotting filtered... [ 2017-01-11 14:48:13 ] INFO Plotting in pdf format... [ 2017-01-11 14:48:13 ] INFO Plotting mds... [ 2017-01-11 14:48:13 ] INFO Plotting biodetection... [ 2017-01-11 14:48:14 ] INFO Plotting countsbio... [ 2017-01-11 14:48:16 ] INFO Plotting saturation... [ 2017-01-11 14:48:25 ] INFO Plotting readnoise... [ 2017-01-11 14:48:30 ] INFO Plotting correl... [ 2017-01-11 14:48:30 ] INFO Plotting pairwise... [ 2017-01-11 14:49:08 ] INFO Plotting boxplot... [ 2017-01-11 14:49:09 ] INFO Plotting gcbias... [ 2017-01-11 14:49:11 ] INFO Plotting lengthbias... [ 2017-01-11 14:49:12 ] INFO Plotting meandiff... [ 2017-01-11 14:49:17 ] INFO Plotting meanvar... [ 2017-01-11 14:49:46 ] INFO Plotting boxplot... [ 2017-01-11 14:49:46 ] INFO Plotting gcbias... [ 2017-01-11 14:49:48 ] INFO Plotting lengthbias... [ 2017-01-11 14:49:50 ] INFO Plotting meandiff... [ 2017-01-11 14:49:54 ] INFO Plotting meanvar... [ 2017-01-11 14:50:26 ] INFO Plotting biodist... [ 2017-01-11 14:50:26 ] INFO Contrast: wt_vs_3308 [ 2017-01-11 14:50:26 ] INFO Contrast: wt_vs_3312 [ 2017-01-11 14:50:27 ] INFO Contrast: wt_vs_3343 [ 2017-01-11 14:50:27 ] INFO Contrast: 3308_vs_3343 [ 2017-01-11 14:50:27 ] INFO Contrast: 3312_vs_3343 [ 2017-01-11 14:50:27 ] INFO Contrast: 3308_vs_3312 [ 2017-01-11 14:50:27 ] INFO Plotting volcano... [ 2017-01-11 14:50:27 ] INFO Contrast: wt_vs_3308 [ 2017-01-11 14:50:28 ] INFO Contrast: wt_vs_3312 [ 2017-01-11 14:50:28 ] INFO Contrast: wt_vs_3343 [ 2017-01-11 14:50:28 ] INFO Contrast: 3308_vs_3343 [ 2017-01-11 14:50:29 ] INFO Contrast: 3312_vs_3343 [ 2017-01-11 14:50:29 ] INFO Contrast: 3308_vs_3312 [ 2017-01-11 14:50:29 ] INFO Plotting deheatmap... [ 2017-01-11 14:50:29 ] INFO Contrast: wt_vs_3308 [ 2017-01-11 14:51:18 ] INFO Contrast: wt_vs_3312 [ 2017-01-11 14:52:04 ] INFO Contrast: wt_vs_3343 [ 2017-01-11 14:52:52 ] INFO Contrast: 3308_vs_3343 [ 2017-01-11 14:53:35 ] INFO Contrast: 3312_vs_3343 [ 2017-01-11 14:54:17 ] INFO Contrast: 3308_vs_3312 [ 2017-01-11 14:54:59 ] INFO Plotting filtered... [ 2017-01-11 14:54:59 ] INFO Creating HTML report... [ 2017-01-11 14:54:59 ] 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
Mean-difference
Mean-variance
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_3308The 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_3308. 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_3308 | log2_normalized_counts_IT3R40-wt1 | log2_normalized_counts_IT3R41-wt2 | log2_normalized_counts_IT3R42-wt5 | log2_normalized_counts_IT3R43-wt15 | log2_normalized_counts_IT3R44-wt16 | log2_normalized_counts_IT3R45-wt17 | rpgm_normalized_counts_IT3R40-wt1 | rpgm_normalized_counts_IT3R41-wt2 | rpgm_normalized_counts_IT3R42-wt5 | rpgm_normalized_counts_IT3R43-wt15 | rpgm_normalized_counts_IT3R44-wt16 | rpgm_normalized_counts_IT3R45-wt17 | log2_normalized_counts_IT3R46-3308-1 | log2_normalized_counts_IT3R47-3308-2 | log2_normalized_counts_IT3R48-3308-4 | rpgm_normalized_counts_IT3R46-3308-1 | rpgm_normalized_counts_IT3R47-3308-2 | rpgm_normalized_counts_IT3R48-3308-4 | LN | AR | MD | MN | QN | KN | CM | BT |
|---|
| chr12 | 104146382 | 104153870 | ENSMUSG00000066361 | 0.4806 | - | Serpina3c | protein_coding | 2.83e-23 | 5.11e-19 | -6.558668 | 1.11e+01 | 1.03e+01 | 1.08e+01 | 1.05e+01 | 1.04e+01 | 1.18e+01 | 1.06e+00 | 5.98e-01 | 8.57e-01 | 6.77e-01 | 6.25e-01 | 1.73e+00 | 4.46e+00 | 4.70e+00 | 3.81e+00 | 9.98e-03 | 1.19e-02 | 6.18e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 26307169 | 26315088 | ENSMUSG00000074254 | 0.4619 | + | Cyp2a4 | protein_coding | 1.24e-21 | 1.11e-17 | -6.583680 | 1.17e+01 | 1.29e+01 | 1.31e+01 | 1.18e+01 | 7.55e+00 | 1.04e+01 | 2.33e+00 | 5.11e+00 | 6.02e+00 | 2.44e+00 | 1.28e-01 | 9.49e-01 | 5.93e+00 | 5.21e+00 | 4.95e+00 | 4.12e-02 | 2.47e-02 | 2.06e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 142575529 | 142578143 | ENSMUSG00000000031 | 0.5583 | - | H19 | lincRNA | 5.81e-21 | 3.49e-17 | -6.550105 | 7.97e+00 | 8.93e+00 | 8.78e+00 | 9.83e+00 | 6.79e+00 | 5.67e+00 | 8.82e-02 | 1.73e-01 | 1.55e-01 | 3.22e-01 | 3.90e-02 | 1.77e-02 | 1.00e+00 | 3.17e+00 | 0.00e+00 | 3.54e-04 | 2.83e-03 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 90490737 | 90508907 | ENSMUSG00000054932 | 0.4053 | + | Afp | protein_coding | 1.12e-20 | 5.03e-17 | -6.464497 | 9.35e+00 | 9.78e+00 | 9.62e+00 | 9.53e+00 | 6.60e+00 | 9.11e+00 | 1.30e-01 | 1.75e-01 | 1.56e-01 | 1.47e-01 | 1.92e-02 | 1.10e-01 | 2.81e+00 | 0.00e+00 | 3.70e+00 | 1.20e-03 | 0.00e+00 | 2.39e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 31125306 | 31129646 | ENSMUSG00000024029 | 0.5139 | - | Tff3 | protein_coding | 2.00e-19 | 6.80e-16 | -5.847057 | 9.36e+00 | 7.91e+00 | 9.39e+00 | 9.89e+00 | 9.32e+00 | 9.05e+00 | 4.57e-01 | 1.67e-01 | 4.68e-01 | 6.62e-01 | 4.47e-01 | 3.69e-01 | 3.58e+00 | 4.17e+00 | 1.00e+00 | 7.69e-03 | 1.19e-02 | 6.99e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 7197782 | 7202546 | ENSMUSG00000020429 | 0.4886 | + | Igfbp1 | protein_coding | 2.27e-19 | 6.80e-16 | -5.702771 | 8.74e+00 | 1.11e+01 | 9.56e+00 | 1.23e+01 | 7.31e+00 | 1.13e+01 | 2.39e-01 | 1.25e+00 | 4.22e-01 | 2.85e+00 | 8.86e-02 | 1.40e+00 | 4.95e+00 | 4.91e+00 | 5.52e+00 | 1.68e-02 | 1.63e-02 | 2.52e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 149368476 | 149430682 | ENSMUSG00000107314 | 0.4719 | + | Gm20488 | processed_transcript | 5.39e-17 | 1.39e-13 | -7.035257 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 4.86e+00 | 1.06e+01 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 7.97e-04 | 2.23e-02 | 1.23e+00 | 1.58e+00 | 0.00e+00 | 1.00e+00 | 1.59e-03 | 0.00e+00 | 7.97e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 149411749 | 149431723 | ENSMUSG00000029659 | 0.4657 | + | Medag | protein_coding | 1.66e-16 | 3.75e-13 | -7.038919 | 0.00e+00 | 1.00e+00 | 1.58e+00 | 1.58e+00 | 4.86e+00 | 1.06e+01 | 0.00e+00 | 2.31e-04 | 4.63e-04 | 4.63e-04 | 6.48e-03 | 3.56e-01 | 1.58e+00 | 0.00e+00 | 1.00e+00 | 4.63e-04 | 0.00e+00 | 2.31e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr14 | 55575617 | 55576952 | ENSMUSG00000022215 | 0.5808 | + | Fitm1 | protein_coding | 4.11e-16 | 8.22e-13 | 3.975909 | 4.91e+00 | 4.00e+00 | 5.00e+00 | 5.55e+00 | 5.81e+00 | 5.73e+00 | 2.27e-02 | 1.17e-02 | 2.42e-02 | 3.60e-02 | 4.30e-02 | 4.07e-02 | 9.46e+00 | 9.55e+00 | 8.60e+00 | 5.50e-01 | 5.85e-01 | 3.03e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 32384633 | 32388252 | ENSMUSG00000026822 | 0.5470 | - | Lcn2 | protein_coding | 2.07e-15 | 3.72e-12 | -5.873005 | 6.55e+00 | 9.46e+00 | 8.81e+00 | 7.97e+00 | 4.46e+00 | 6.88e+00 | 1.77e-02 | 1.34e-01 | 8.56e-02 | 4.76e-02 | 4.00e-03 | 2.23e-02 | 3.32e+00 | 0.00e+00 | 1.58e+00 | 1.71e-03 | 0.00e+00 | 3.81e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 128908919 | 128912816 | ENSMUSG00000025351 | 0.5818 | + | Cd63 | protein_coding | 6.00e-15 | 9.84e-12 | -4.633703 | 1.10e+01 | 1.19e+01 | 1.12e+01 | 1.21e+01 | 7.38e+00 | 1.13e+01 | 1.56e+00 | 2.96e+00 | 1.72e+00 | 3.26e+00 | 1.24e-01 | 1.86e+00 | 7.04e+00 | 6.41e+00 | 6.51e+00 | 9.85e-02 | 6.32e-02 | 6.77e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 52272426 | 52613950 | ENSMUSG00000055653 | 0.3967 | - | Gpc3 | protein_coding | 1.93e-14 | 2.90e-11 | -5.755841 | 6.44e+00 | 8.55e+00 | 8.32e+00 | 7.48e+00 | 8.62e+00 | 7.31e+00 | 2.60e-02 | 1.13e-01 | 9.64e-02 | 5.38e-02 | 1.19e-01 | 4.78e-02 | 2.32e+00 | 2.81e+00 | 1.00e+00 | 1.21e-03 | 1.81e-03 | 3.02e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 54286486 | 54341786 | ENSMUSG00000046167 | 0.4529 | + | Gldn | protein_coding | 1.01e-13 | 1.40e-10 | -6.491853 | 3.58e+00 | 7.99e+00 | 7.15e+00 | 7.32e+00 | 0.00e+00 | 7.23e+00 | 2.60e-03 | 6.01e-02 | 3.34e-02 | 3.76e-02 | 0.00e+00 | 3.53e-02 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 2.37e-04 | 0.00e+00 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr19 | 44293676 | 44306864 | ENSMUSG00000025203 | 0.4912 | + | Scd2 | protein_coding | 1.17e-13 | 1.50e-10 | -5.478972 | 7.68e+00 | 7.76e+00 | 8.19e+00 | 7.37e+00 | 8.28e+00 | 7.20e+00 | 4.15e-02 | 4.39e-02 | 5.94e-02 | 3.33e-02 | 6.30e-02 | 2.97e-02 | 2.58e+00 | 2.32e+00 | 2.00e+00 | 1.02e-03 | 8.13e-04 | 6.10e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 68880491 | 68907448 | ENSMUSG00000015568 | 0.4217 | + | Lpl | protein_coding | 1.34e-13 | 1.61e-10 | -4.290702 | 9.89e+00 | 1.05e+01 | 1.02e+01 | 1.17e+01 | 8.11e+00 | 1.00e+01 | 1.07e-01 | 1.58e-01 | 1.33e-01 | 3.71e-01 | 3.09e-02 | 1.17e-01 | 6.44e+00 | 5.95e+00 | 5.91e+00 | 9.65e-03 | 6.84e-03 | 6.62e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 61857321 | 61857876 | ENSMUSG00000081053 | 0.4442 | - | Mup-ps17 | unprocessed_pseudogene | 6.57e-13 | 7.39e-10 | 4.340424 | 2.81e+00 | 1.58e+00 | 0.00e+00 | 1.00e+00 | 3.00e+00 | 3.32e+00 | 4.78e-03 | 1.59e-03 | 0.00e+00 | 7.97e-04 | 5.58e-03 | 7.18e-03 | 5.52e+00 | 5.91e+00 | 7.70e+00 | 3.59e-02 | 4.70e-02 | 1.65e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 164214454 | 164221660 | ENSMUSG00000018211 | 0.4489 | - | Wfdc15b | protein_coding | 1.88e-12 | 1.99e-09 | -5.105304 | 6.70e+00 | 7.10e+00 | 8.11e+00 | 6.94e+00 | 4.86e+00 | 7.81e+00 | 7.38e-02 | 9.75e-02 | 1.98e-01 | 8.75e-02 | 2.01e-02 | 1.61e-01 | 1.00e+00 | 3.17e+00 | 1.00e+00 | 7.17e-04 | 5.73e-03 | 7.17e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 24336853 | 24351494 | ENSMUSG00000026981 | 0.4277 | + | Il1rn | protein_coding | 3.42e-12 | 3.43e-09 | -4.412314 | 8.36e+00 | 8.11e+00 | 8.29e+00 | 9.67e+00 | 4.86e+00 | 9.47e+00 | 5.61e-02 | 4.71e-02 | 5.35e-02 | 1.40e-01 | 4.80e-03 | 1.21e-01 | 3.81e+00 | 3.46e+00 | 5.04e+00 | 2.23e-03 | 1.71e-03 | 5.49e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 46240696 | 46243459 | ENSMUSG00000032080 | 0.5557 | + | Apoa4 | protein_coding | 4.54e-12 | 4.22e-09 | -3.867757 | 1.10e+01 | 1.14e+01 | 1.07e+01 | 1.06e+01 | 1.01e+01 | 1.05e+01 | 1.44e+00 | 1.88e+00 | 1.13e+00 | 1.06e+00 | 7.50e-01 | 1.02e+00 | 7.23e+00 | 6.85e+00 | 6.49e+00 | 1.05e-01 | 8.01e-02 | 6.25e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 115817284 | 115849893 | ENSMUSG00000034127 | 0.4039 | + | Tspan8 | protein_coding | 4.69e-12 | 4.22e-09 | -6.008989 | 6.29e+00 | 7.17e+00 | 7.29e+00 | 6.57e+00 | 3.91e+00 | 7.28e+00 | 4.40e-02 | 8.17e-02 | 8.91e-02 | 5.37e-02 | 8.00e-03 | 8.79e-02 | 1.00e+00 | 0.00e+00 | 1.00e+00 | 5.71e-04 | 0.00e+00 | 5.71e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 93084206 | 93093727 | ENSMUSG00000111013 | 0.4194 | + | RP23-337J18.2 | lincRNA | 1.19e-11 | 9.94e-09 | 5.205114 | 3.17e+00 | 0.00e+00 | 0.00e+00 | 2.32e+00 | 0.00e+00 | 0.00e+00 | 3.19e-03 | 0.00e+00 | 0.00e+00 | 1.59e-03 | 0.00e+00 | 0.00e+00 | 7.18e+00 | 6.99e+00 | 5.91e+00 | 5.74e-02 | 5.02e-02 | 2.35e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 64592542 | 64693054 | ENSMUSG00000037852 | 0.4269 | - | Cpe | protein_coding | 1.21e-11 | 9.94e-09 | -5.512112 | 6.48e+00 | 8.03e+00 | 8.52e+00 | 6.54e+00 | 0.00e+00 | 7.60e+00 | 2.03e-02 | 5.99e-02 | 8.40e-02 | 2.12e-02 | 0.00e+00 | 4.44e-02 | 2.81e+00 | 0.00e+00 | 1.58e+00 | 1.38e-03 | 0.00e+00 | 4.61e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 127526473 | 127541467 | ENSMUSG00000027376 | 0.5336 | - | Prom2 | protein_coding | 1.48e-11 | 1.16e-08 | -6.238405 | 6.19e+00 | 5.67e+00 | 5.83e+00 | 6.79e+00 | 4.46e+00 | 7.12e+00 | 1.04e-02 | 7.24e-03 | 8.11e-03 | 1.59e-02 | 3.04e-03 | 2.00e-02 | 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 | | chr2 | 49619298 | 49774778 | ENSMUSG00000026764 | 0.4546 | + | Kif5c | protein_coding | 3.53e-11 | 2.65e-08 | -6.125844 | 5.09e+00 | 6.32e+00 | 7.11e+00 | 6.55e+00 | 0.00e+00 | 6.17e+00 | 3.34e-03 | 7.98e-03 | 1.38e-02 | 9.40e-03 | 0.00e+00 | 7.18e-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 | | chr11 | 94936224 | 94953042 | ENSMUSG00000001506 | 0.5392 | + | Col1a1 | protein_coding | 5.69e-11 | 4.10e-08 | -4.607626 | 1.58e+00 | 4.17e+00 | 3.17e+00 | 3.32e+00 | 6.51e+00 | 1.01e+01 | 3.11e-04 | 2.64e-03 | 1.24e-03 | 1.40e-03 | 1.40e-02 | 1.69e-01 | 1.00e+00 | 4.17e+00 | 2.32e+00 | 1.55e-04 | 2.64e-03 | 6.21e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 124430759 | 124464794 | ENSMUSG00000008153 | 0.4931 | - | Clstn3 | protein_coding | 8.36e-11 | 5.79e-08 | 2.625377 | 3.17e+00 | 2.81e+00 | 3.17e+00 | 3.58e+00 | 6.79e+00 | 4.81e+00 | 1.13e-03 | 8.45e-04 | 1.13e-03 | 1.55e-03 | 1.55e-02 | 3.80e-03 | 7.52e+00 | 7.67e+00 | 7.29e+00 | 2.58e-02 | 2.84e-02 | 2.18e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 24223517 | 24302790 | ENSMUSG00000020000 | 0.4041 | + | Moxd1 | protein_coding | 9.97e-11 | 6.65e-08 | -5.629357 | 6.57e+00 | 5.49e+00 | 5.21e+00 | 3.32e+00 | 5.13e+00 | 7.44e+00 | 2.56e-02 | 1.20e-02 | 9.81e-03 | 2.45e-03 | 9.27e-03 | 4.72e-02 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 2.73e-04 | 0.00e+00 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 103450898 | 103457223 | ENSMUSG00000021208 | 0.4782 | - | Ifi27l2b | protein_coding | 3.19e-10 | 2.04e-07 | -4.080170 | 7.20e+00 | 7.75e+00 | 8.20e+00 | 7.44e+00 | 6.97e+00 | 7.84e+00 | 1.02e-01 | 1.50e-01 | 2.05e-01 | 1.21e-01 | 8.67e-02 | 1.59e-01 | 3.32e+00 | 4.32e+00 | 2.32e+00 | 6.29e-03 | 1.33e-02 | 2.80e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 106603351 | 106670246 | ENSMUSG00000000303 | 0.4703 | + | Cdh1 | protein_coding | 3.28e-10 | 2.04e-07 | -3.592985 | 1.11e+01 | 1.09e+01 | 1.13e+01 | 1.16e+01 | 7.92e+00 | 1.16e+01 | 5.17e-01 | 4.68e-01 | 6.23e-01 | 7.41e-01 | 5.82e-02 | 7.27e-01 | 7.75e+00 | 6.94e+00 | 7.64e+00 | 5.17e-02 | 2.95e-02 | 4.81e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr13 | 4132615 | 4150654 | ENSMUSG00000021214 | 0.3721 | - | Akr1c18 | protein_coding | 4.61e-10 | 2.77e-07 | -5.412217 | 6.29e+00 | 7.10e+00 | 7.23e+00 | 5.75e+00 | 4.46e+00 | 6.13e+00 | 5.37e-02 | 9.49e-02 | 1.04e-01 | 3.70e-02 | 1.47e-02 | 4.82e-02 | 1.58e+00 | 0.00e+00 | 1.00e+00 | 1.40e-03 | 0.00e+00 | 6.98e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 98422961 | 98446575 | ENSMUSG00000046402 | 0.4941 | + | Rbp1 | protein_coding | 5.53e-10 | 3.21e-07 | -3.794767 | 8.75e+00 | 8.03e+00 | 8.81e+00 | 8.67e+00 | 7.74e+00 | 8.19e+00 | 2.91e-01 | 1.76e-01 | 3.03e-01 | 2.74e-01 | 1.44e-01 | 1.97e-01 | 5.04e+00 | 4.58e+00 | 4.09e+00 | 2.16e-02 | 1.55e-02 | 1.08e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 61670177 | 61674136 | ENSMUSG00000078674 | 0.4104 | - | Mup18 | protein_coding | 5.91e-10 | 3.33e-07 | 2.710471 | 9.20e+00 | 8.29e+00 | 8.06e+00 | 6.69e+00 | 1.18e+01 | 1.11e+01 | 2.32e-01 | 1.24e-01 | 1.05e-01 | 4.04e-02 | 1.45e+00 | 8.90e-01 | 1.26e+01 | 1.33e+01 | 1.28e+01 | 2.42e+00 | 4.13e+00 | 2.74e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 60418046 | 60421952 | ENSMUSG00000078686 | 0.4116 | - | Mup9 | protein_coding | 1.00e-09 | 5.46e-07 | 2.521888 | 9.08e+00 | 8.01e+00 | 8.09e+00 | 7.56e+00 | 1.21e+01 | 1.11e+01 | 1.28e-01 | 6.11e-02 | 6.44e-02 | 4.47e-02 | 1.04e+00 | 5.16e-01 | 1.24e+01 | 1.33e+01 | 1.28e+01 | 1.29e+00 | 2.37e+00 | 1.67e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 127866474 | 127877317 | ENSMUSG00000074639 | 0.4630 | + | BC089597 | protein_coding | 1.03e-09 | 5.47e-07 | -3.661985 | 9.46e+00 | 9.00e+00 | 9.42e+00 | 9.92e+00 | 8.52e+00 | 9.43e+00 | 4.74e-01 | 3.45e-01 | 4.62e-01 | 6.55e-01 | 2.47e-01 | 4.64e-01 | 6.43e+00 | 4.32e+00 | 5.61e+00 | 5.74e-02 | 1.28e-02 | 3.24e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr18 | 34859823 | 34864984 | ENSMUSG00000038418 | 0.5777 | + | Egr1 | protein_coding | 1.87e-09 | 9.53e-07 | -3.277593 | 8.67e+00 | 8.82e+00 | 1.01e+01 | 9.06e+00 | 7.70e+00 | 8.06e+00 | 1.65e-01 | 1.83e-01 | 4.36e-01 | 2.16e-01 | 8.38e-02 | 1.08e-01 | 5.25e+00 | 6.44e+00 | 4.75e+00 | 1.50e-02 | 3.48e-02 | 1.05e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 6885796 | 7052478 | ENSMUSG00000064065 | 0.4093 | - | Ipcef1 | protein_coding | 1.90e-09 | 9.53e-07 | -5.584963 | 6.04e+00 | 5.83e+00 | 6.21e+00 | 4.64e+00 | 0.00e+00 | 6.02e+00 | 5.70e-03 | 4.91e-03 | 6.40e-03 | 2.11e-03 | 0.00e+00 | 5.61e-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 | | chr5 | 100210692 | 100218049 | ENSMUSG00000100157 | 0.4638 | + | 2310034O05Rik | lincRNA | 2.07e-09 | 1.01e-06 | -5.438792 | 6.19e+00 | 6.38e+00 | 6.94e+00 | 3.00e+00 | 5.13e+00 | 4.64e+00 | 2.87e-02 | 3.27e-02 | 4.86e-02 | 2.79e-03 | 1.36e-02 | 9.57e-03 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 3.99e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 61591929 | 61595871 | ENSMUSG00000096688 | 0.4119 | - | Mup17 | protein_coding | 2.44e-09 | 1.16e-06 | 2.051477 | 8.28e+00 | 7.52e+00 | 7.55e+00 | 6.55e+00 | 1.17e+01 | 1.06e+01 | 1.22e-01 | 7.21e-02 | 7.40e-02 | 3.68e-02 | 1.34e+00 | 6.15e-01 | 1.17e+01 | 1.23e+01 | 1.18e+01 | 1.28e+00 | 1.97e+00 | 1.44e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 94172664 | 94173568 | ENSMUSG00000031762 | 0.5569 | + | Mt2 | protein_coding | 2.90e-09 | 1.34e-06 | -3.228219 | 9.42e+00 | 1.03e+01 | 1.05e+01 | 1.16e+01 | 5.39e+00 | 7.72e+00 | 4.90e-01 | 8.79e-01 | 1.02e+00 | 2.17e+00 | 2.94e-02 | 1.51e-01 | 4.25e+00 | 6.58e+00 | 7.89e+00 | 1.29e-02 | 6.81e-02 | 1.70e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 79890853 | 79892656 | ENSMUSG00000061780 | 0.5649 | + | Cfd | protein_coding | 6.06e-09 | 2.69e-06 | 2.249476 | 2.32e+00 | 1.00e+00 | 3.91e+00 | 2.32e+00 | 5.98e+00 | 3.00e+00 | 3.02e-03 | 7.55e-04 | 1.06e-02 | 3.02e-03 | 4.68e-02 | 5.29e-03 | 5.46e+00 | 7.07e+00 | 5.78e+00 | 3.25e-02 | 1.00e-01 | 4.08e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr15 | 74762056 | 74763620 | ENSMUSG00000034634 | 0.5208 | - | Ly6d | protein_coding | 6.13e-09 | 2.69e-06 | -4.031382 | 5.78e+00 | 8.39e+00 | 6.70e+00 | 6.29e+00 | 5.81e+00 | 7.99e+00 | 3.47e-02 | 2.15e-01 | 6.63e-02 | 4.95e-02 | 3.54e-02 | 1.63e-01 | 3.81e+00 | 3.46e+00 | 1.00e+00 | 8.37e-03 | 6.44e-03 | 6.44e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 61783123 | 61801286 | ENSMUSG00000081207 | 0.3985 | + | Gm13775 | processed_transcript | 6.69e-09 | 2.82e-06 | 3.178337 | 4.52e+00 | 3.46e+00 | 3.70e+00 | 2.81e+00 | 5.39e+00 | 4.17e+00 | 1.75e-02 | 7.97e-03 | 9.57e-03 | 4.78e-03 | 3.27e-02 | 1.36e-02 | 7.25e+00 | 7.67e+00 | 7.33e+00 | 1.20e-01 | 1.61e-01 | 1.28e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 25614620 | 25615892 | ENSMUSG00000074261 | 0.5428 | - | Erich4 | protein_coding | 6.74e-09 | 2.82e-06 | -5.448461 | 5.43e+00 | 5.93e+00 | 5.70e+00 | 5.88e+00 | 0.00e+00 | 5.52e+00 | 2.47e-02 | 3.53e-02 | 3.00e-02 | 3.42e-02 | 0.00e+00 | 2.65e-02 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 69682577 | 69696098 | ENSMUSG00000018752 | 0.5154 | - | Tnfsfm13 | protein_coding | 7.13e-09 | 2.85e-06 | -3.622052 | 8.35e+00 | 7.95e+00 | 8.29e+00 | 7.60e+00 | 5.13e+00 | 8.04e+00 | 1.70e-01 | 1.29e-01 | 1.63e-01 | 1.01e-01 | 1.78e-02 | 1.37e-01 | 4.64e+00 | 4.00e+00 | 3.91e+00 | 1.26e-02 | 7.85e-03 | 7.32e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 69682846 | 69685784 | ENSMUSG00000089669 | 0.5162 | - | Tnfsf13 | protein_coding | 7.13e-09 | 2.85e-06 | -3.622052 | 8.35e+00 | 7.95e+00 | 8.29e+00 | 7.60e+00 | 5.13e+00 | 8.04e+00 | 1.98e-01 | 1.50e-01 | 1.90e-01 | 1.17e-01 | 2.07e-02 | 1.59e-01 | 4.64e+00 | 4.00e+00 | 3.91e+00 | 1.46e-02 | 9.13e-03 | 8.52e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr18 | 43728069 | 43737237 | ENSMUSG00000024503 | 0.3967 | - | Spink1 | protein_coding | 8.23e-09 | 3.23e-06 | -5.361944 | 5.52e+00 | 6.27e+00 | 6.88e+00 | 6.13e+00 | 3.00e+00 | 3.32e+00 | 3.35e-02 | 5.65e-02 | 8.70e-02 | 5.13e-02 | 5.20e-03 | 6.69e-03 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 7.43e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 41569775 | 41638158 | ENSMUSG00000061322 | 0.4783 | + | Dnaic1 | protein_coding | 1.19e-08 | 4.48e-06 | -3.405858 | 8.68e+00 | 7.43e+00 | 8.03e+00 | 8.89e+00 | 6.13e+00 | 9.56e+00 | 2.83e-01 | 1.19e-01 | 1.81e-01 | 3.28e-01 | 4.79e-02 | 5.23e-01 | 4.86e+00 | 4.32e+00 | 5.70e+00 | 1.94e-02 | 1.32e-02 | 3.54e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 41638144 | 41640324 | ENSMUSG00000028445 | 0.6153 | - | Enho | protein_coding | 1.19e-08 | 4.48e-06 | -3.405858 | 8.68e+00 | 7.43e+00 | 8.03e+00 | 8.89e+00 | 6.13e+00 | 9.56e+00 | 2.37e-01 | 9.93e-02 | 1.52e-01 | 2.75e-01 | 4.01e-02 | 4.37e-01 | 4.86e+00 | 4.32e+00 | 5.70e+00 | 1.63e-02 | 1.10e-02 | 2.96e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr16 | 91269772 | 91271933 | ENSMUSG00000046160 | 0.6105 | + | Olig1 | protein_coding | 1.41e-08 | 5.18e-06 | 2.909235 | 0.00e+00 | 2.00e+00 | 1.58e+00 | 1.58e+00 | 4.86e+00 | 0.00e+00 | 0.00e+00 | 1.32e-03 | 8.80e-04 | 8.80e-04 | 1.23e-02 | 0.00e+00 | 5.98e+00 | 5.70e+00 | 5.29e+00 | 2.73e-02 | 2.24e-02 | 1.67e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 122169893 | 122186207 | ENSMUSG00000030866 | 0.4982 | - | Ern2 | protein_coding | 2.07e-08 | 7.44e-06 | -5.386581 | 5.21e+00 | 5.25e+00 | 5.43e+00 | 5.75e+00 | 3.91e+00 | 6.00e+00 | 1.34e-02 | 1.37e-02 | 1.56e-02 | 1.97e-02 | 5.19e-03 | 2.34e-02 | 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 | | chr8 | 72204335 | 72212837 | ENSMUSG00000074240 | 0.4771 | - | Cib3 | protein_coding | 2.43e-08 | 8.59e-06 | -5.339850 | 6.13e+00 | 5.95e+00 | 6.51e+00 | 5.58e+00 | 6.88e+00 | 4.00e+00 | 5.20e-02 | 4.59e-02 | 6.78e-02 | 3.54e-02 | 8.81e-02 | 1.13e-02 | 1.00e+00 | 0.00e+00 | 1.00e+00 | 7.53e-04 | 0.00e+00 | 7.53e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for wt_vs_3308.Download the whole result list for wt_vs_3308.DEG table for the contrast wt_vs_3312The 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_3312. 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_3312 | log2_normalized_counts_IT3R40-wt1 | log2_normalized_counts_IT3R41-wt2 | log2_normalized_counts_IT3R42-wt5 | log2_normalized_counts_IT3R43-wt15 | log2_normalized_counts_IT3R44-wt16 | log2_normalized_counts_IT3R45-wt17 | rpgm_normalized_counts_IT3R40-wt1 | rpgm_normalized_counts_IT3R41-wt2 | rpgm_normalized_counts_IT3R42-wt5 | rpgm_normalized_counts_IT3R43-wt15 | rpgm_normalized_counts_IT3R44-wt16 | rpgm_normalized_counts_IT3R45-wt17 | log2_normalized_counts_IT3R35-3312-1 | log2_normalized_counts_IT3R36-3312-3 | rpgm_normalized_counts_IT3R35-3312-1 | rpgm_normalized_counts_IT3R36-3312-3 | LN | AR | MD | MN | QN | KN | CM | BT |
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| chr10 | 79890853 | 79892656 | ENSMUSG00000061780 | 0.5649 | + | Cfd | protein_coding | 1.13e-20 | 2.04e-16 | 4.321192 | 2.32e+00 | 1.00e+00 | 3.91e+00 | 2.32e+00 | 5.98e+00 | 3.00e+00 | 3.02e-03 | 7.55e-04 | 1.06e-02 | 3.02e-03 | 4.68e-02 | 5.29e-03 | 8.32e+00 | 8.38e+00 | 2.41e-01 | 2.51e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 104146382 | 104153870 | ENSMUSG00000066361 | 0.4806 | - | Serpina3c | protein_coding | 1.40e-17 | 1.26e-13 | -6.468470 | 1.11e+01 | 1.03e+01 | 1.08e+01 | 1.05e+01 | 1.04e+01 | 1.18e+01 | 1.06e+00 | 5.98e-01 | 8.57e-01 | 6.77e-01 | 6.25e-01 | 1.73e+00 | 4.46e+00 | 4.46e+00 | 9.98e-03 | 9.98e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 149411749 | 149431723 | ENSMUSG00000029659 | 0.4657 | + | Medag | protein_coding | 1.40e-14 | 6.62e-11 | -7.453956 | 0.00e+00 | 1.00e+00 | 1.58e+00 | 1.58e+00 | 4.86e+00 | 1.06e+01 | 0.00e+00 | 2.31e-04 | 4.63e-04 | 4.63e-04 | 6.48e-03 | 3.56e-01 | 1.00e+00 | 0.00e+00 | 2.31e-04 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 149368476 | 149430682 | ENSMUSG00000107314 | 0.4719 | + | Gm20488 | processed_transcript | 1.47e-14 | 6.62e-11 | -7.450295 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 4.86e+00 | 1.06e+01 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 7.97e-04 | 2.23e-02 | 1.23e+00 | 1.00e+00 | 0.00e+00 | 7.97e-04 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 142575529 | 142578143 | ENSMUSG00000000031 | 0.5583 | - | H19 | lincRNA | 1.74e-11 | 6.25e-08 | -4.965143 | 7.97e+00 | 8.93e+00 | 8.78e+00 | 9.83e+00 | 6.79e+00 | 5.67e+00 | 8.82e-02 | 1.73e-01 | 1.55e-01 | 3.22e-01 | 3.90e-02 | 1.77e-02 | 1.58e+00 | 4.39e+00 | 7.08e-04 | 7.08e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 94172664 | 94173568 | ENSMUSG00000031762 | 0.5569 | + | Mt2 | protein_coding | 2.25e-09 | 6.76e-06 | -3.749229 | 9.42e+00 | 1.03e+01 | 1.05e+01 | 1.16e+01 | 5.39e+00 | 7.72e+00 | 4.90e-01 | 8.79e-01 | 1.02e+00 | 2.17e+00 | 2.94e-02 | 1.51e-01 | 6.04e+00 | 6.61e+00 | 4.66e-02 | 6.95e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 61670177 | 61674136 | ENSMUSG00000078674 | 0.4104 | - | Mup18 | protein_coding | 1.06e-08 | 2.73e-05 | 2.425952 | 9.20e+00 | 8.29e+00 | 8.06e+00 | 6.69e+00 | 1.18e+01 | 1.11e+01 | 2.32e-01 | 1.24e-01 | 1.05e-01 | 4.04e-02 | 1.45e+00 | 8.90e-01 | 1.27e+01 | 1.26e+01 | 2.63e+00 | 2.46e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr14 | 55575617 | 55576952 | ENSMUSG00000022215 | 0.5808 | + | Fitm1 | protein_coding | 1.30e-08 | 2.93e-05 | 2.731406 | 4.91e+00 | 4.00e+00 | 5.00e+00 | 5.55e+00 | 5.81e+00 | 5.73e+00 | 2.27e-02 | 1.17e-02 | 2.42e-02 | 3.60e-02 | 4.30e-02 | 4.07e-02 | 7.68e+00 | 8.29e+00 | 1.59e-01 | 2.44e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 54286486 | 54341786 | ENSMUSG00000046167 | 0.4529 | + | Gldn | protein_coding | 3.28e-08 | 6.58e-05 | -4.906891 | 3.58e+00 | 7.99e+00 | 7.15e+00 | 7.32e+00 | 0.00e+00 | 7.23e+00 | 2.60e-03 | 6.01e-02 | 3.34e-02 | 3.76e-02 | 0.00e+00 | 3.53e-02 | 1.00e+00 | 2.58e+00 | 2.37e-04 | 1.18e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 60418046 | 60421952 | ENSMUSG00000078686 | 0.4116 | - | Mup9 | protein_coding | 5.74e-08 | 1.03e-04 | 2.111673 | 9.08e+00 | 8.01e+00 | 8.09e+00 | 7.56e+00 | 1.21e+01 | 1.11e+01 | 1.28e-01 | 6.11e-02 | 6.44e-02 | 4.47e-02 | 1.04e+00 | 5.16e-01 | 1.22e+01 | 1.27e+01 | 1.12e+00 | 1.55e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 94936224 | 94953042 | ENSMUSG00000001506 | 0.5392 | + | Col1a1 | protein_coding | 7.37e-08 | 1.21e-04 | -4.859165 | 1.58e+00 | 4.17e+00 | 3.17e+00 | 3.32e+00 | 6.51e+00 | 1.01e+01 | 3.11e-04 | 2.64e-03 | 1.24e-03 | 1.40e-03 | 1.40e-02 | 1.69e-01 | 3.58e+00 | 1.00e+00 | 1.71e-03 | 1.55e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 94179082 | 94180327 | ENSMUSG00000031765 | 0.5425 | + | Mt1 | protein_coding | 1.17e-07 | 1.76e-04 | -3.239120 | 9.24e+00 | 9.74e+00 | 1.00e+01 | 1.04e+01 | 6.70e+00 | 7.61e+00 | 2.79e-01 | 3.96e-01 | 4.83e-01 | 6.32e-01 | 4.78e-02 | 8.99e-02 | 6.04e+00 | 6.34e+00 | 3.01e-02 | 3.71e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 86581371 | 86695953 | ENSMUSG00000032418 | 0.4164 | - | Me1 | protein_coding | 2.54e-07 | 3.52e-04 | 2.726444 | 8.47e+00 | 8.16e+00 | 7.47e+00 | 7.26e+00 | 8.04e+00 | 7.22e+00 | 9.14e-02 | 7.36e-02 | 4.54e-02 | 3.92e-02 | 6.76e-02 | 3.82e-02 | 9.74e+00 | 1.11e+01 | 2.20e-01 | 5.67e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 93084206 | 93093727 | ENSMUSG00000111013 | 0.4194 | + | RP23-337J18.2 | lincRNA | 5.66e-07 | 7.28e-04 | 3.984893 | 3.17e+00 | 0.00e+00 | 0.00e+00 | 2.32e+00 | 0.00e+00 | 0.00e+00 | 3.19e-03 | 0.00e+00 | 0.00e+00 | 1.59e-03 | 0.00e+00 | 0.00e+00 | 5.04e+00 | 5.95e+00 | 1.28e-02 | 2.43e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 124430759 | 124464794 | ENSMUSG00000008153 | 0.4931 | - | Clstn3 | protein_coding | 8.39e-07 | 1.01e-03 | 1.769387 | 3.17e+00 | 2.81e+00 | 3.17e+00 | 3.58e+00 | 6.79e+00 | 4.81e+00 | 1.13e-03 | 8.45e-04 | 1.13e-03 | 1.55e-03 | 1.55e-02 | 3.80e-03 | 5.83e+00 | 7.16e+00 | 7.88e-03 | 2.00e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 61857321 | 61857876 | ENSMUSG00000081053 | 0.4442 | - | Mup-ps17 | unprocessed_pseudogene | 1.38e-06 | 1.45e-03 | 3.040157 | 2.81e+00 | 1.58e+00 | 0.00e+00 | 1.00e+00 | 3.00e+00 | 3.32e+00 | 4.78e-03 | 1.59e-03 | 0.00e+00 | 7.97e-04 | 5.58e-03 | 7.18e-03 | 4.64e+00 | 5.91e+00 | 1.91e-02 | 4.70e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr13 | 64161866 | 64186536 | ENSMUSG00000021476 | 0.4626 | + | Habp4 | protein_coding | 1.45e-06 | 1.45e-03 | 2.247267 | 4.91e+00 | 4.46e+00 | 5.25e+00 | 7.22e+00 | 6.51e+00 | 7.02e+00 | 1.18e-02 | 8.53e-03 | 1.50e-02 | 6.01e-02 | 3.66e-02 | 5.24e-02 | 8.72e+00 | 8.26e+00 | 1.71e-01 | 1.24e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 108334377 | 108362231 | ENSMUSG00000021259 | 0.5217 | + | Cyp46a1 | protein_coding | 1.45e-06 | 1.45e-03 | -4.922832 | 5.91e+00 | 5.86e+00 | 1.58e+00 | 5.75e+00 | 7.88e+00 | 7.09e+00 | 3.28e-02 | 3.16e-02 | 1.11e-03 | 2.94e-02 | 1.30e-01 | 7.50e-02 | 2.00e+00 | 1.00e+00 | 1.67e-03 | 5.55e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr16 | 91269772 | 91271933 | ENSMUSG00000046160 | 0.6105 | + | Olig1 | protein_coding | 1.78e-06 | 1.69e-03 | 2.293500 | 0.00e+00 | 2.00e+00 | 1.58e+00 | 1.58e+00 | 4.86e+00 | 0.00e+00 | 0.00e+00 | 1.32e-03 | 8.80e-04 | 8.80e-04 | 1.23e-02 | 0.00e+00 | 4.39e+00 | 5.52e+00 | 8.80e-03 | 1.98e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr13 | 69573449 | 69611442 | ENSMUSG00000021594 | 0.4705 | - | Srd5a1 | protein_coding | 2.55e-06 | 2.28e-03 | 2.608941 | 5.04e+00 | 4.86e+00 | 4.39e+00 | 3.81e+00 | 5.13e+00 | 5.55e+00 | 7.64e-03 | 6.68e-03 | 4.77e-03 | 3.10e-03 | 8.12e-03 | 1.10e-02 | 7.75e+00 | 7.21e+00 | 5.13e-02 | 3.51e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 61515592 | 61519531 | ENSMUSG00000078675 | 0.4107 | - | Mup16 | protein_coding | 2.66e-06 | 2.28e-03 | 2.150088 | 1.04e+01 | 9.56e+00 | 9.49e+00 | 9.03e+00 | 1.25e+01 | 1.18e+01 | 4.52e-01 | 2.61e-01 | 2.48e-01 | 1.80e-01 | 1.96e+00 | 1.21e+00 | 1.31e+01 | 1.32e+01 | 3.08e+00 | 3.30e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for wt_vs_3312.Download the whole result list for wt_vs_3312.DEG table for the contrast wt_vs_3343The 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_3343. 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_3343 | log2_normalized_counts_IT3R40-wt1 | log2_normalized_counts_IT3R41-wt2 | log2_normalized_counts_IT3R42-wt5 | log2_normalized_counts_IT3R43-wt15 | log2_normalized_counts_IT3R44-wt16 | log2_normalized_counts_IT3R45-wt17 | rpgm_normalized_counts_IT3R40-wt1 | rpgm_normalized_counts_IT3R41-wt2 | rpgm_normalized_counts_IT3R42-wt5 | rpgm_normalized_counts_IT3R43-wt15 | rpgm_normalized_counts_IT3R44-wt16 | rpgm_normalized_counts_IT3R45-wt17 | log2_normalized_counts_IT3R37-3343-2 | log2_normalized_counts_IT3R38-3343-3 | log2_normalized_counts_IT3R39-3343-4 | rpgm_normalized_counts_IT3R37-3343-2 | rpgm_normalized_counts_IT3R38-3343-3 | rpgm_normalized_counts_IT3R39-3343-4 | LN | AR | MD | MN | QN | KN | CM | BT |
|---|
| chr12 | 104146382 | 104153870 | ENSMUSG00000066361 | 0.4806 | - | Serpina3c | protein_coding | 3.15e-24 | 5.68e-20 | -6.582127 | 1.11e+01 | 1.03e+01 | 1.08e+01 | 1.05e+01 | 1.04e+01 | 1.18e+01 | 1.06e+00 | 5.98e-01 | 8.57e-01 | 6.77e-01 | 6.25e-01 | 1.73e+00 | 4.25e+00 | 4.39e+00 | 4.39e+00 | 8.56e-03 | 9.51e-03 | 9.51e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 79890853 | 79892656 | ENSMUSG00000061780 | 0.5649 | + | Cfd | protein_coding | 2.10e-20 | 1.89e-16 | 4.071791 | 2.32e+00 | 1.00e+00 | 3.91e+00 | 2.32e+00 | 5.98e+00 | 3.00e+00 | 3.02e-03 | 7.55e-04 | 1.06e-02 | 3.02e-03 | 4.68e-02 | 5.29e-03 | 8.21e+00 | 7.83e+00 | 8.23e+00 | 2.23e-01 | 1.71e-01 | 2.26e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 149368476 | 149430682 | ENSMUSG00000107314 | 0.4719 | + | Gm20488 | processed_transcript | 1.03e-19 | 6.18e-16 | -7.298292 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 4.86e+00 | 1.06e+01 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 7.97e-04 | 2.23e-02 | 1.23e+00 | 1.00e+00 | 1.00e+00 | 0.00e+00 | 7.97e-04 | 7.97e-04 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 149411749 | 149431723 | ENSMUSG00000029659 | 0.4657 | + | Medag | protein_coding | 1.94e-18 | 8.75e-15 | -7.038919 | 0.00e+00 | 1.00e+00 | 1.58e+00 | 1.58e+00 | 4.86e+00 | 1.06e+01 | 0.00e+00 | 2.31e-04 | 4.63e-04 | 4.63e-04 | 6.48e-03 | 3.56e-01 | 1.58e+00 | 1.00e+00 | 0.00e+00 | 4.63e-04 | 2.31e-04 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr7 | 142575529 | 142578143 | ENSMUSG00000000031 | 0.5583 | - | H19 | lincRNA | 1.39e-14 | 5.00e-11 | -4.813140 | 7.97e+00 | 8.93e+00 | 8.78e+00 | 9.83e+00 | 6.79e+00 | 5.67e+00 | 8.82e-02 | 1.73e-01 | 1.55e-01 | 3.22e-01 | 3.90e-02 | 1.77e-02 | 4.46e+00 | 2.00e+00 | 3.81e+00 | 7.44e-03 | 1.06e-03 | 4.60e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr9 | 54286486 | 54341786 | ENSMUSG00000046167 | 0.4529 | + | Gldn | protein_coding | 4.89e-13 | 1.44e-09 | -5.906891 | 3.58e+00 | 7.99e+00 | 7.15e+00 | 7.32e+00 | 0.00e+00 | 7.23e+00 | 2.60e-03 | 6.01e-02 | 3.34e-02 | 3.76e-02 | 0.00e+00 | 3.53e-02 | 1.58e+00 | 1.00e+00 | 0.00e+00 | 4.73e-04 | 2.37e-04 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 61857321 | 61857876 | ENSMUSG00000081053 | 0.4442 | - | Mup-ps17 | unprocessed_pseudogene | 6.01e-13 | 1.44e-09 | 4.429508 | 2.81e+00 | 1.58e+00 | 0.00e+00 | 1.00e+00 | 3.00e+00 | 3.32e+00 | 4.78e-03 | 1.59e-03 | 0.00e+00 | 7.97e-04 | 5.58e-03 | 7.18e-03 | 6.52e+00 | 7.25e+00 | 6.49e+00 | 7.26e-02 | 1.20e-01 | 7.10e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 7197782 | 7202546 | ENSMUSG00000020429 | 0.4886 | + | Igfbp1 | protein_coding | 6.41e-13 | 1.44e-09 | -4.017974 | 8.74e+00 | 1.11e+01 | 9.56e+00 | 1.23e+01 | 7.31e+00 | 1.13e+01 | 2.39e-01 | 1.25e+00 | 4.22e-01 | 2.85e+00 | 8.86e-02 | 1.40e+00 | 6.71e+00 | 7.19e+00 | 6.54e+00 | 5.83e-02 | 8.13e-02 | 5.16e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr14 | 55575617 | 55576952 | ENSMUSG00000022215 | 0.5808 | + | Fitm1 | protein_coding | 4.35e-12 | 8.51e-09 | 3.180844 | 4.91e+00 | 4.00e+00 | 5.00e+00 | 5.55e+00 | 5.81e+00 | 5.73e+00 | 2.27e-02 | 1.17e-02 | 2.42e-02 | 3.60e-02 | 4.30e-02 | 4.07e-02 | 8.27e+00 | 8.62e+00 | 8.49e+00 | 2.40e-01 | 3.07e-01 | 2.80e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 94936224 | 94953042 | ENSMUSG00000001506 | 0.5392 | + | Col1a1 | protein_coding | 4.72e-12 | 8.51e-09 | -5.444127 | 1.58e+00 | 4.17e+00 | 3.17e+00 | 3.32e+00 | 6.51e+00 | 1.01e+01 | 3.11e-04 | 2.64e-03 | 1.24e-03 | 1.40e-03 | 1.40e-02 | 1.69e-01 | 3.46e+00 | 0.00e+00 | 1.00e+00 | 1.55e-03 | 0.00e+00 | 1.55e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 124430759 | 124464794 | ENSMUSG00000008153 | 0.4931 | - | Clstn3 | protein_coding | 1.32e-10 | 2.17e-07 | 2.456448 | 3.17e+00 | 2.81e+00 | 3.17e+00 | 3.58e+00 | 6.79e+00 | 4.81e+00 | 1.13e-03 | 8.45e-04 | 1.13e-03 | 1.55e-03 | 1.55e-02 | 3.80e-03 | 7.17e+00 | 7.60e+00 | 7.18e+00 | 2.01e-02 | 2.72e-02 | 2.03e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 64592542 | 64693054 | ENSMUSG00000037852 | 0.4269 | - | Cpe | protein_coding | 2.39e-10 | 3.59e-07 | -4.579226 | 6.48e+00 | 8.03e+00 | 8.52e+00 | 6.54e+00 | 0.00e+00 | 7.60e+00 | 2.03e-02 | 5.99e-02 | 8.40e-02 | 2.12e-02 | 0.00e+00 | 4.44e-02 | 1.58e+00 | 3.58e+00 | 2.58e+00 | 4.61e-04 | 2.53e-03 | 1.15e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 61591929 | 61595871 | ENSMUSG00000096688 | 0.4119 | - | Mup17 | protein_coding | 4.27e-10 | 5.92e-07 | 2.096240 | 8.28e+00 | 7.52e+00 | 7.55e+00 | 6.55e+00 | 1.17e+01 | 1.06e+01 | 1.22e-01 | 7.21e-02 | 7.40e-02 | 3.68e-02 | 1.34e+00 | 6.15e-01 | 1.19e+01 | 1.18e+01 | 1.22e+01 | 1.52e+00 | 1.43e+00 | 1.90e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 60418046 | 60421952 | ENSMUSG00000078686 | 0.4116 | - | Mup9 | protein_coding | 4.73e-10 | 6.08e-07 | 2.415731 | 9.08e+00 | 8.01e+00 | 8.09e+00 | 7.56e+00 | 1.21e+01 | 1.11e+01 | 1.28e-01 | 6.11e-02 | 6.44e-02 | 4.47e-02 | 1.04e+00 | 5.16e-01 | 1.27e+01 | 1.28e+01 | 1.28e+01 | 1.55e+00 | 1.70e+00 | 1.69e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chrX | 52272426 | 52613950 | ENSMUSG00000055653 | 0.3967 | - | Gpc3 | protein_coding | 6.18e-10 | 7.42e-07 | -4.315269 | 6.44e+00 | 8.55e+00 | 8.32e+00 | 7.48e+00 | 8.62e+00 | 7.31e+00 | 2.60e-02 | 1.13e-01 | 9.64e-02 | 5.38e-02 | 1.19e-01 | 4.78e-02 | 3.81e+00 | 3.81e+00 | 3.32e+00 | 3.93e-03 | 3.93e-03 | 2.72e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 164214454 | 164221660 | ENSMUSG00000018211 | 0.4489 | - | Wfdc15b | protein_coding | 8.85e-10 | 9.96e-07 | -4.483816 | 6.70e+00 | 7.10e+00 | 8.11e+00 | 6.94e+00 | 4.86e+00 | 7.81e+00 | 7.38e-02 | 9.75e-02 | 1.98e-01 | 8.75e-02 | 2.01e-02 | 1.61e-01 | 2.58e+00 | 2.81e+00 | 2.81e+00 | 3.58e-03 | 4.30e-03 | 4.30e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 61670177 | 61674136 | ENSMUSG00000078674 | 0.4104 | - | Mup18 | protein_coding | 9.79e-10 | 1.04e-06 | 2.471171 | 9.20e+00 | 8.29e+00 | 8.06e+00 | 6.69e+00 | 1.18e+01 | 1.11e+01 | 2.32e-01 | 1.24e-01 | 1.05e-01 | 4.04e-02 | 1.45e+00 | 8.90e-01 | 1.27e+01 | 1.27e+01 | 1.26e+01 | 2.66e+00 | 2.71e+00 | 2.51e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 32384633 | 32388252 | ENSMUSG00000026822 | 0.5470 | - | Lcn2 | protein_coding | 1.07e-09 | 1.07e-06 | -3.571835 | 6.55e+00 | 9.46e+00 | 8.81e+00 | 7.97e+00 | 4.46e+00 | 6.88e+00 | 1.77e-02 | 1.34e-01 | 8.56e-02 | 4.76e-02 | 4.00e-03 | 2.23e-02 | 5.09e+00 | 2.58e+00 | 4.86e+00 | 6.29e-03 | 9.53e-04 | 5.34e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr13 | 56288647 | 56296551 | ENSMUSG00000021508 | 0.5293 | - | Cxcl14 | protein_coding | 1.56e-08 | 1.48e-05 | -4.625709 | 6.09e+00 | 6.86e+00 | 6.27e+00 | 5.55e+00 | 4.46e+00 | 6.02e+00 | 2.79e-02 | 4.79e-02 | 3.17e-02 | 1.92e-02 | 8.75e-03 | 2.67e-02 | 2.00e+00 | 1.00e+00 | 1.00e+00 | 1.25e-03 | 4.17e-04 | 4.17e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr18 | 34859823 | 34864984 | ENSMUSG00000038418 | 0.5777 | + | Egr1 | protein_coding | 2.35e-08 | 2.12e-05 | -3.090893 | 8.67e+00 | 8.82e+00 | 1.01e+01 | 9.06e+00 | 7.70e+00 | 8.06e+00 | 1.65e-01 | 1.83e-01 | 4.36e-01 | 2.16e-01 | 8.38e-02 | 1.08e-01 | 6.30e+00 | 4.70e+00 | 6.09e+00 | 3.16e-02 | 1.01e-02 | 2.71e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 90490737 | 90508907 | ENSMUSG00000054932 | 0.4053 | + | Afp | protein_coding | 4.67e-08 | 4.01e-05 | -2.914300 | 9.35e+00 | 9.78e+00 | 9.62e+00 | 9.53e+00 | 6.60e+00 | 9.11e+00 | 1.30e-01 | 1.75e-01 | 1.56e-01 | 1.47e-01 | 1.92e-02 | 1.10e-01 | 7.26e+00 | 5.75e+00 | 5.29e+00 | 3.03e-02 | 1.06e-02 | 7.58e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 113345055 | 113356658 | ENSMUSG00000096569 | 0.3466 | - | Amy2a2 | protein_coding | 7.83e-08 | 6.41e-05 | 3.819428 | 0.00e+00 | 0.00e+00 | 2.00e+00 | 0.00e+00 | 3.00e+00 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 9.12e-04 | 0.00e+00 | 2.13e-03 | 3.04e-04 | 1.00e+00 | 6.87e+00 | 0.00e+00 | 3.04e-04 | 3.53e-02 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr19 | 58670365 | 58681786 | ENSMUSG00000046008 | 0.4208 | + | Pnlip | protein_coding | 1.39e-07 | 1.09e-04 | 4.807355 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 6.36e+00 | 0.00e+00 | 0.00e+00 | 6.17e-02 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 20248264 | 20275733 | ENSMUSG00000011463 | 0.3814 | - | Cpb1 | protein_coding | 1.52e-07 | 1.14e-04 | 4.807355 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 6.36e+00 | 0.00e+00 | 0.00e+00 | 2.08e-02 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr1 | 79794197 | 79861180 | ENSMUSG00000026249 | 0.4461 | - | Serpine2 | protein_coding | 3.38e-07 | 2.44e-04 | 2.299241 | 4.64e+00 | 4.17e+00 | 4.52e+00 | 4.17e+00 | 5.61e+00 | 7.22e+00 | 2.88e-03 | 2.04e-03 | 2.64e-03 | 2.04e-03 | 5.76e-03 | 1.78e-02 | 7.94e+00 | 7.96e+00 | 7.64e+00 | 2.94e-02 | 2.98e-02 | 2.38e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr6 | 116650609 | 116652794 | ENSMUSG00000048489 | 0.5178 | + | 8430408G22Rik | protein_coding | 3.62e-07 | 2.46e-04 | -2.242176 | 1.01e+01 | 9.53e+00 | 9.03e+00 | 1.04e+01 | 7.31e+00 | 8.96e+00 | 3.60e-01 | 2.47e-01 | 1.74e-01 | 4.64e-01 | 5.29e-02 | 1.66e-01 | 6.70e+00 | 6.87e+00 | 7.92e+00 | 3.45e-02 | 3.88e-02 | 8.07e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr13 | 69573449 | 69611442 | ENSMUSG00000021594 | 0.4705 | - | Srd5a1 | protein_coding | 3.68e-07 | 2.46e-04 | 2.624709 | 5.04e+00 | 4.86e+00 | 4.39e+00 | 3.81e+00 | 5.13e+00 | 5.55e+00 | 7.64e-03 | 6.68e-03 | 4.77e-03 | 3.10e-03 | 8.12e-03 | 1.10e-02 | 7.27e+00 | 7.81e+00 | 7.43e+00 | 3.65e-02 | 5.35e-02 | 4.11e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr18 | 41875696 | 41951194 | ENSMUSG00000056671 | 0.4234 | - | Prelid2 | protein_coding | 4.30e-07 | 2.77e-04 | -3.863822 | 6.43e+00 | 6.85e+00 | 6.48e+00 | 6.74e+00 | 4.86e+00 | 6.11e+00 | 3.51e-02 | 4.70e-02 | 3.63e-02 | 4.37e-02 | 1.16e-02 | 2.81e-02 | 3.17e+00 | 2.00e+00 | 2.00e+00 | 3.30e-03 | 1.24e-03 | 1.24e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr12 | 108334377 | 108362231 | ENSMUSG00000021259 | 0.5217 | + | Cyp46a1 | protein_coding | 5.35e-07 | 3.32e-04 | -4.285402 | 5.91e+00 | 5.86e+00 | 1.58e+00 | 5.75e+00 | 7.88e+00 | 7.09e+00 | 3.28e-02 | 3.16e-02 | 1.11e-03 | 2.94e-02 | 1.30e-01 | 7.50e-02 | 2.58e+00 | 2.00e+00 | 2.00e+00 | 2.78e-03 | 1.67e-03 | 1.67e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 128908919 | 128912816 | ENSMUSG00000025351 | 0.5818 | + | Cd63 | protein_coding | 5.70e-07 | 3.42e-04 | -2.451341 | 1.10e+01 | 1.19e+01 | 1.12e+01 | 1.21e+01 | 7.38e+00 | 1.13e+01 | 1.56e+00 | 2.96e+00 | 1.72e+00 | 3.26e+00 | 1.24e-01 | 1.86e+00 | 9.60e+00 | 7.87e+00 | 8.61e+00 | 5.81e-01 | 1.75e-01 | 2.92e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr19 | 3851773 | 3894369 | ENSMUSG00000024843 | 0.4388 | + | Chka | protein_coding | 7.30e-07 | 4.23e-04 | -2.912585 | 7.09e+00 | 7.37e+00 | 6.73e+00 | 9.66e+00 | 7.04e+00 | 8.74e+00 | 6.73e-03 | 8.18e-03 | 5.24e-03 | 4.04e-02 | 6.53e-03 | 2.13e-02 | 5.78e+00 | 5.09e+00 | 4.86e+00 | 2.69e-03 | 1.65e-03 | 1.40e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 68880491 | 68907448 | ENSMUSG00000015568 | 0.4217 | + | Lpl | protein_coding | 7.51e-07 | 4.23e-04 | -2.411222 | 9.89e+00 | 1.05e+01 | 1.02e+01 | 1.17e+01 | 8.11e+00 | 1.00e+01 | 1.07e-01 | 1.58e-01 | 1.33e-01 | 3.71e-01 | 3.09e-02 | 1.17e-01 | 8.53e+00 | 7.09e+00 | 8.04e+00 | 4.13e-02 | 1.51e-02 | 2.95e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 61224307 | 61228286 | ENSMUSG00000089873 | 0.4121 | - | Mup13 | protein_coding | 1.03e-06 | 5.65e-04 | 1.845645 | 1.00e+01 | 8.73e+00 | 8.99e+00 | 8.13e+00 | 1.22e+01 | 1.11e+01 | 4.16e-01 | 1.68e-01 | 2.01e-01 | 1.11e-01 | 1.81e+00 | 8.56e-01 | 1.23e+01 | 1.23e+01 | 1.26e+01 | 1.99e+00 | 1.99e+00 | 2.42e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for wt_vs_3343.Download the whole result list for wt_vs_3343.DEG table for the contrast 3308_vs_3343The following table presents the top 5% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast 3308_vs_3343. 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_3308_vs_3343 | log2_normalized_counts_IT3R46-3308-1 | log2_normalized_counts_IT3R47-3308-2 | log2_normalized_counts_IT3R48-3308-4 | rpgm_normalized_counts_IT3R46-3308-1 | rpgm_normalized_counts_IT3R47-3308-2 | rpgm_normalized_counts_IT3R48-3308-4 | log2_normalized_counts_IT3R37-3343-2 | log2_normalized_counts_IT3R38-3343-3 | log2_normalized_counts_IT3R39-3343-4 | rpgm_normalized_counts_IT3R37-3343-2 | rpgm_normalized_counts_IT3R38-3343-3 | rpgm_normalized_counts_IT3R39-3343-4 | LN | AR | MD | MN | QN | KN | CM | BT |
|---|
| chr7 | 26307169 | 26315088 | ENSMUSG00000074254 | 0.4619 | + | Cyp2a4 | protein_coding | 3.90e-11 | 7.02e-07 | 4.187832 | 5.93e+00 | 5.21e+00 | 4.95e+00 | 4.12e-02 | 2.47e-02 | 2.06e-02 | 1.07e+01 | 7.89e+00 | 8.98e+00 | 1.10e+00 | 1.63e-01 | 3.46e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 24223517 | 24302790 | ENSMUSG00000020000 | 0.4041 | + | Moxd1 | protein_coding | 4.96e-09 | 4.47e-05 | 5.108524 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 2.73e-04 | 0.00e+00 | 0.00e+00 | 6.63e+00 | 3.17e+00 | 4.91e+00 | 2.67e-02 | 2.18e-03 | 7.90e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 31125306 | 31129646 | ENSMUSG00000024029 | 0.5139 | - | Tff3 | protein_coding | 1.01e-08 | 6.06e-05 | 3.257388 | 3.58e+00 | 4.17e+00 | 1.00e+00 | 7.69e-03 | 1.19e-02 | 6.99e-04 | 7.58e+00 | 4.75e+00 | 6.46e+00 | 1.33e-01 | 1.82e-02 | 6.08e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 90490737 | 90508907 | ENSMUSG00000054932 | 0.4053 | + | Afp | protein_coding | 4.12e-08 | 1.86e-04 | 3.550197 | 2.81e+00 | 0.00e+00 | 3.70e+00 | 1.20e-03 | 0.00e+00 | 2.39e-03 | 7.26e+00 | 5.75e+00 | 5.29e+00 | 3.03e-02 | 1.06e-02 | 7.58e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 98666547 | 98667301 | ENSMUSG00000075014 | 0.3563 | - | Gm10800 | protein_coding | 1.94e-07 | 7.00e-04 | -3.700440 | 7.62e+00 | 5.04e+00 | 8.67e+00 | 1.56e-01 | 2.55e-02 | 3.24e-01 | 2.58e+00 | 5.39e+00 | 0.00e+00 | 3.99e-03 | 3.27e-02 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr19 | 44293676 | 44306864 | ENSMUSG00000025203 | 0.4912 | + | Scd2 | protein_coding | 4.83e-06 | 1.45e-02 | 3.191141 | 2.58e+00 | 2.32e+00 | 2.00e+00 | 1.02e-03 | 8.13e-04 | 6.10e-04 | 6.17e+00 | 3.32e+00 | 5.78e+00 | 1.44e-02 | 1.83e-03 | 1.10e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr3 | 113345055 | 113356658 | ENSMUSG00000096569 | 0.3466 | - | Amy2a2 | protein_coding | 1.33e-05 | 3.18e-02 | 4.906891 | 1.00e+00 | 0.00e+00 | 0.00e+00 | 3.04e-04 | 0.00e+00 | 0.00e+00 | 1.00e+00 | 6.87e+00 | 0.00e+00 | 3.04e-04 | 3.53e-02 | 0.00e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 94172664 | 94173568 | ENSMUSG00000031762 | 0.5569 | + | Mt2 | protein_coding | 1.41e-05 | 3.18e-02 | 2.419883 | 4.25e+00 | 6.58e+00 | 7.89e+00 | 1.29e-02 | 6.81e-02 | 1.70e-01 | 9.58e+00 | 9.42e+00 | 8.78e+00 | 5.47e-01 | 4.91e-01 | 3.14e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 41569775 | 41638158 | ENSMUSG00000061322 | 0.4783 | + | Dnaic1 | protein_coding | 2.89e-05 | 5.00e-02 | 2.617913 | 4.86e+00 | 4.32e+00 | 5.70e+00 | 1.94e-02 | 1.32e-02 | 3.54e-02 | 7.91e+00 | 7.48e+00 | 7.65e+00 | 1.67e-01 | 1.23e-01 | 1.39e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr4 | 41638144 | 41640324 | ENSMUSG00000028445 | 0.6153 | - | Enho | protein_coding | 2.89e-05 | 5.00e-02 | 2.617913 | 4.86e+00 | 4.32e+00 | 5.70e+00 | 1.63e-02 | 1.10e-02 | 2.96e-02 | 7.91e+00 | 7.48e+00 | 7.65e+00 | 1.39e-01 | 1.03e-01 | 1.16e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr10 | 6885796 | 7052478 | ENSMUSG00000064065 | 0.4093 | - | Ipcef1 | protein_coding | 3.05e-05 | 5.00e-02 | 3.584963 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 0.00e+00 | 4.39e+00 | 3.17e+00 | 2.58e+00 | 1.75e-03 | 7.02e-04 | 4.39e-04 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 39843013 | 39846341 | ENSMUSG00000097971 | 0.6912 | + | Gm26917 | lincRNA | 3.86e-05 | 5.80e-02 | -1.987927 | 1.01e+01 | 7.24e+00 | 7.46e+00 | 8.15e-01 | 1.11e-01 | 1.30e-01 | 6.46e+00 | 7.06e+00 | 7.12e+00 | 6.44e-02 | 9.78e-02 | 1.02e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for 3308_vs_3343.Download the whole result list for 3308_vs_3343.DEG table for the contrast 3312_vs_3343The following table presents the top 5% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast 3312_vs_3343. 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_3312_vs_3343 | log2_normalized_counts_IT3R35-3312-1 | log2_normalized_counts_IT3R36-3312-3 | rpgm_normalized_counts_IT3R35-3312-1 | rpgm_normalized_counts_IT3R36-3312-3 | log2_normalized_counts_IT3R37-3343-2 | log2_normalized_counts_IT3R38-3343-3 | log2_normalized_counts_IT3R39-3343-4 | rpgm_normalized_counts_IT3R37-3343-2 | rpgm_normalized_counts_IT3R38-3343-3 | rpgm_normalized_counts_IT3R39-3343-4 | LN | AR | MD | MN | QN | KN | CM | BT |
|---|
| chr8 | 94172664 | 94173568 | ENSMUSG00000031762 | 0.5569 | + | Mt2 | protein_coding | 2.43e-06 | 0.0438 | 2.940892 | 6.04e+00 | 6.61e+00 | 4.66e-02 | 6.95e-02 | 9.58e+00 | 9.42e+00 | 8.78e+00 | 5.47e-01 | 4.91e-01 | 3.14e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 35439155 | 35443773 | ENSMUSG00000060550 | 0.5373 | + | H2-Q7 | protein_coding | 2.75e-05 | 0.2477 | -2.383004 | 7.43e+00 | 7.73e+00 | 4.61e-02 | 5.68e-02 | 2.58e+00 | 3.17e+00 | 6.58e+00 | 1.34e-03 | 2.14e-03 | 2.55e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr2 | 181018380 | 181043546 | ENSMUSG00000027577 | 0.5268 | - | Chrna4 | protein_coding | 8.81e-05 | 0.5294 | -2.754888 | 6.00e+00 | 7.41e+00 | 8.29e-03 | 2.22e-02 | 5.00e+00 | 2.00e+00 | 4.00e+00 | 4.08e-03 | 3.95e-04 | 1.97e-03 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr8 | 94179082 | 94180327 | ENSMUSG00000031765 | 0.5425 | + | Mt1 | protein_coding | 2.14e-04 | 0.8426 | 2.229386 | 6.04e+00 | 6.34e+00 | 3.01e-02 | 3.71e-02 | 8.68e+00 | 8.63e+00 | 7.83e+00 | 1.89e-01 | 1.84e-01 | 1.05e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for 3312_vs_3343.Download the whole result list for 3312_vs_3343.DEG table for the contrast 3308_vs_3312The following table presents the top 5% statistically significant genes (use the download links below the table to retrieve the whole list) for the contrast 3308_vs_3312. 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_3308_vs_3312 | log2_normalized_counts_IT3R46-3308-1 | log2_normalized_counts_IT3R47-3308-2 | log2_normalized_counts_IT3R48-3308-4 | rpgm_normalized_counts_IT3R46-3308-1 | rpgm_normalized_counts_IT3R47-3308-2 | rpgm_normalized_counts_IT3R48-3308-4 | log2_normalized_counts_IT3R35-3312-1 | log2_normalized_counts_IT3R36-3312-3 | rpgm_normalized_counts_IT3R35-3312-1 | rpgm_normalized_counts_IT3R36-3312-3 | LN | AR | MD | MN | QN | KN | CM | BT |
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| chr7 | 26307169 | 26315088 | ENSMUSG00000074254 | 0.4619 | + | Cyp2a4 | protein_coding | 7.56e-12 | 1.36e-07 | 4.644527 | 5.93e+00 | 5.21e+00 | 4.95e+00 | 4.12e-02 | 2.47e-02 | 2.06e-02 | 8.99e+00 | 1.07e+01 | 3.48e-01 | 1.13e+00 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr5 | 90490737 | 90508907 | ENSMUSG00000054932 | 0.4053 | + | Afp | protein_coding | 9.01e-10 | 8.12e-06 | 4.327071 | 2.81e+00 | 0.00e+00 | 3.70e+00 | 1.20e-03 | 0.00e+00 | 2.39e-03 | 5.32e+00 | 7.91e+00 | 7.78e-03 | 4.79e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr11 | 7197782 | 7202546 | ENSMUSG00000020429 | 0.4886 | + | Igfbp1 | protein_coding | 1.79e-08 | 1.00e-04 | 3.556023 | 4.95e+00 | 4.91e+00 | 5.52e+00 | 1.68e-02 | 1.63e-02 | 2.52e-02 | 6.79e+00 | 9.51e+00 | 6.17e-02 | 4.08e-01 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr19 | 44293676 | 44306864 | ENSMUSG00000025203 | 0.4912 | + | Scd2 | protein_coding | 2.22e-08 | 1.00e-04 | 4.104337 | 2.58e+00 | 2.32e+00 | 2.00e+00 | 1.02e-03 | 8.13e-04 | 6.10e-04 | 5.43e+00 | 7.01e+00 | 8.54e-03 | 2.60e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | | chr17 | 31125306 | 31129646 | ENSMUSG00000024029 | 0.5139 | - | Tff3 | protein_coding | 1.52e-07 | 5.49e-04 | 3.092757 | 3.58e+00 | 4.17e+00 | 1.00e+00 | 7.69e-03 | 1.19e-02 | 6.99e-04 | 6.36e+00 | 6.64e+00 | 5.66e-02 | 6.92e-02 | 0 | 0 | 0 | 0 | 0 | 0 | 0 | 0 |
Download the DEG result list for 3308_vs_3312.Download the whole result list for 3308_vs_3312.Download the raw read counts table for the experiment.Download the normalized read counts table for the experiment.
References
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