pmid:27508061 Public

https://scm.piranha.sh/git/ada56728063306072cb24f17/sci-pmid-27508061 · at 08b58b82be4e

From reads to genes to pathways: differential expression analysis of RNA-Seq experiments using Rsubread and the edgeR quasi-likelihood pipeline

pmid:27508061 · revision 7 · F1000Research

Original: 2016
Created: 2026-11-03
Ingested: 2026-11-07

Paper record The research question, publication details and source material recorded for this paper.

In recent years, RNA sequencing (RNA-seq) has become a very widely used technology for profiling gene expression. One of the most common aims of RNA-seq profiling is to identify genes or molecular pathways that are differentially expressed (DE) between two or more biological conditions. This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland. The workflow uses R software packages from the open-source Bioconductor project and covers all steps of the analysis pipeline, including alignment of read sequences, data exploration, differential expression analysis, visualization and pathway analysis. Read alignment and count quantification is conducted using the Rsubread package and the statistical analyses are performed using the edgeR package. The differential expression analysis uses the quasi-likelihood functionality of edgeR.

Yunshun Chen, Aaron T. L. Lun, Gordon K. Smyth

DOI: 10.12688/f1000research.8987.2
PMID: 27508061
Journal: F1000Research
Published: 2016
Revision: 7
Format version: 1.5
Content hash: sha256:72abc1c558c8d6a3461ec0365234046ee2dc5f723b2f8b3b3ae0904ac6e4ab85
Opened from: pmid:27508061
Written: 2026-11-03T19:42:08Z
Updated: 2026-11-07T10:10:47Z
Made by: Corpus assay engine, MiniMax literature reader
Source run: sci-assay-array-2026-11-03

Data sources The sources the file names, with the access and the state the file records for each one.

manuscript · open · resolved

10.12688/f1000research.8987.2

https://doi.org/10.12688/f1000research.8987.2

xml · 60,617 bytes · sha256:3bf8a3f4c0135bde16e66f7f232937e6a89868783968461f69da3b9c8795dceb

Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.

raw · open · resolved

GSE60450

https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE60450

geo-series ·

Except for the targets file targets.txt, all data analyzed in the workflow is read automatically from public websites as part of the code. All software used is publicly available as part of Bioconductor 3.3, except for the fastq-dump utility, which can be downloaded from NCBI website as described in the text. The article includes the complete code necessary to reproduce the analyses shown.

raw · open · resolved

SRP045534

https://www.ncbi.nlm.nih.gov/sra/?term=SRP045534

sra-study ·

The twelve raw FASTQ runs the paper aligns, one per library, and the study they belong to.

supplementary · open · verified

GSE60450_Lactation-GenewiseCounts.txt.gz

https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE60450&format=file&file=GSE60450_Lactation-GenewiseCounts.txt.gz

geo-supplementary · 513,592 bytes · sha256:906b6ec4c33e95ca0ba454a3e0d07ad74e9cb7528ee38b89a9b122f5674a5f0d

The genewise read-count matrix the paper analyses: 27179 genes over twelve libraries, named by the repository. Fetched and hashed on 4 November 2026, and checked against the numbers the paper printed.

reference · open · verified

org.Mm.eg.db_3.3.0

https://bioconductor.org/packages/3.3/data/annotation/src/contrib/org.Mm.eg.db_3.3.0.tar.gz

bioconductor-package · 63,495,324 bytes · sha256:5dc93707b7ca319b295b5b19963c573d5a3817d836f458a3e30d635ddd4e2365

The annotation release the paper's own sessionInfo names, fetched and hashed on 4 November 2026 from the Bioconductor 3.3 archive. It decides which genes keep a symbol, and the paper discards the ones that do not, so it is an input to the filtering stage.

code · open · verified

targets.txt

http://bioinf.wehi.edu.au/edgeR/F1000Research2016/targets.txt

text/plain · 525 bytes · sha256:88ae42c0539403073f0bbbd53287dd9c9cf61ddd5b1a42856243d7d99113cb8b

The authors' own file, fetched and hashed on 3 November 2026. The publisher states no licence for the entry.

code · open · verified

edgeRQL.R

http://bioinf.wehi.edu.au/edgeR/F1000Research2016/edgeRQL.R

R source · 10,298 bytes · sha256:3b11478ac314c4456af8b4ba7af7992e938488ffc7bec88d3f73f42aed4c0bba

The authors' own file, fetched and hashed on 3 November 2026. The publisher states no licence for the entry.

code · open · verified

edgeRQL.Rnw

http://bioinf.wehi.edu.au/edgeR/F1000Research2016/edgeRQL.Rnw

Rnw source · 59,373 bytes · sha256:defd3acb73dcbfe885ca02209ac9437b785b4ccf12c7ba09a8a8bb311173902d

The authors' own file, fetched and hashed on 3 November 2026. The publisher states no licence for the entry.

code · open · verified

edgeRQL.pdf

http://bioinf.wehi.edu.au/edgeR/F1000Research2016/edgeRQL.pdf

PDF · 904,232 bytes · sha256:76ea4da65b151b1bb78ba42b0d80c0e864632df0e13219fe968525a43efd2276

The authors' own file, fetched and hashed on 3 November 2026. The publisher states no licence for the entry.

reference · open · declared

GCA_000001635.6_GRCm38.p4

fasta.gz ·

The mouse genome build the paper indexes and aligns to, as the paper names it.

The samples analysed The group sizes the file holds, and the group sizes the paper itself states. A run is only comparable when it used the same cohort.

In this file

Basal 18.5 dP: 2
Basal 2 dL: 2
Basal virgin: 2
Luminal 18.5 dP: 2
Luminal 2 dL: 2
Luminal virgin: 2

As the paper states them

B.lactating: 2
B.pregnant: 2
B.virgin: 2
L.lactating: 2
L.pregnant: 2
L.virgin: 2

12 samples in total.

Reference group: B.pregnant.

There are therefore six groups of RNA samples, one for each combination of cell type and mouse status. Two biological replicates were collected for each group.

Reproducibility map Follow the research stages and see which inputs each stage needs and what state the file records for it.

This article demonstrates a computational workflow for the detection of DE genes and pathways from RNA-seq data by providing a complete analysis of an RNA-seq experiment profiling epithelial cell subsets in the mouse mammary gland.

1

Read the published estimate from the source

The claim, method and evidence span published with the source article.

in: source:pmid:27508061

out: the published estimate and its evidence

complete
other
2

Obtain the source data from the named repository

The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.

in: data:geo:GSE60450

out: the source data with its repository provenance

complete
data-preparation
3

Run the published analysis

Apply the paper's statistical method to the resolved series and compare the result with the published target.

in: data:geo:GSE60450

out: the replicated result and its comparison

blocked on method:rna_seq_read_alignment

blocked
analysis

The methods the paper publishes Each method as the paper states it, with the evidence the file holds for it.

Read alignment

not expressible

Rsubread align to the GRCm38/mm10 reference

aligner: Rsubread 1.4.4, align()
reference: GRCm38/mm10 (Dec 2011), GCA_000001635.6_GRCm38.p4
index: built with buildindex() from the genomic FASTA
reads: 100 bp single-end FASTQ, about 30 million per sample
mapped_reads: only reads with a unique mapping location are reported

operations still missing: rna_seq_read_alignment

Subread version 1.4.4 ( http://subread.sourceforge.net) was used to align the reads to the mouse mm10 genome and featureCounts was used to assign reads to Entrez Genes using RefSeq gene annotation.

Gene quantification

not expressible

Rsubread featureCounts against the inbuilt RefSeq annotation

tool: Rsubread featureCounts
annotation: NCBI RefSeq, built in to Rsubread for mm10
identifier: Entrez Gene ID
output: a matrix of read counts per gene per sample

operations still missing: gene_count_quantification

The read counts for each gene can be quantified using the featureCounts function in Rsubread.

Count filtering and normalisation

not expressible

low-count filtering by counts per million, then TMM normalisation

filter: keep genes with CPM above 0.5 in at least 2 libraries
keep.lib.sizes
normalisation: TMM, calcNormFactors()
genes_kept: 15653
genes_discarded: 10704

operations still missing: normalise_counts_tmm

For the current analysis, we keep genes that have CPM values above 0.5 in at least two libraries:

Differential expression

not expressible

edgeR quasi-likelihood F-test with Benjamini-Hochberg false discovery rate, and glmTreat against a fold-change threshold

contrast: B.lactating - B.pregnant
test: QL F-test, glmQLFTest()
false_discovery_rate: Benjamini-Hochberg, 5%
threshold_test: glmTreat(), lfc = log2(1.5) = 0.58
design: one-way layout, six groups, two biological replicates each

operations still missing: differential_expression_quasi_likelihood

We will use QL F-tests instead of the more usual likelihood ratio tests (LRT) as they give stricter error rate control by accounting for the uncertainty in dispersion estimation:

Pathway analysis

expressible

KEGG pathway enrichment with edgeR's kegga on the thresholded result

organism: Mm
pathways_printed: 15
term_truncated_at: 34
annotation: KEGG, read from the Internet each time the analysis runs
input: the glmTreat result

A KEGG analysis can be done exactly as for GO, but using the kegga function:

The numbers to reproduce The values the paper prints, with the tolerance each one is held to.

Claim	Operation	Expected	Tolerance	State
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, logFC; printed 6.08.	differential_expression_fit	6.08 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, logCPM; printed 10.19.	differential_expression_fit	10.19 log2 counts per million	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, F; printed 421.	differential_expression_fit	421 F statistic	0	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, PValue; printed 4.78e-11.	differential_expression_fit	4.78E-11 p-value	5.0E-14	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Csn1s2b, FDR; printed 7.48e-07.	fdr_bh	7.48E-7 false discovery rate	5.0E-10	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, logFC; printed 5.15.	differential_expression_fit	5.15 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, logCPM; printed 2.75.	differential_expression_fit	2.75 log2 counts per million	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, F; printed 343.	differential_expression_fit	343 F statistic	0	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, PValue; printed 1.32e-10.	differential_expression_fit	1.32E-10 p-value	5.0E-13	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Mrgprf, FDR; printed 7.99e-07.	fdr_bh	7.99E-7 false discovery rate	5.0E-10	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Myof, logFC; printed 2.32.	differential_expression_fit	2.32 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Myof, logCPM; printed 6.45.	differential_expression_fit	6.45 log2 counts per million	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Myof, F; printed 322.	differential_expression_fit	322 F statistic	0	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Myof, PValue; printed 1.97e-10.	differential_expression_fit	1.97E-10 p-value	5.0E-13	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Myof, FDR; printed 7.99e-07.	fdr_bh	7.99E-7 false discovery rate	5.0E-10	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, logFC; printed 2.14.	differential_expression_fit	2.14 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, logCPM; printed 6.15.	differential_expression_fit	6.15 log2 counts per million	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, F; printed 320.	differential_expression_fit	320 F statistic	0	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, PValue; printed 2.04e-10.	differential_expression_fit	2.04E-10 p-value	5.0E-13	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Atp2b4, FDR; printed 7.99e-07.	fdr_bh	7.99E-7 false discovery rate	5.0E-10	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, logFC; printed -7.17.	differential_expression_fit	-7.17 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, logCPM; printed 6.06.	differential_expression_fit	6.06 log2 counts per million	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, F; printed 308.	differential_expression_fit	308 F statistic	0	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, PValue; printed 2.60e-10.	differential_expression_fit	2.6E-10 p-value	5.0E-13	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Muc4, FDR; printed 8.15e-07.	fdr_bh	8.15E-7 false discovery rate	5.0E-10	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, logFC; printed -2.25.	differential_expression_fit	-2.25 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, logCPM; printed 5.19.	differential_expression_fit	5.19 log2 counts per million	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, F; printed 282.	differential_expression_fit	282 F statistic	0	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, PValue; printed 4.41e-10.	differential_expression_fit	4.41E-10 p-value	5.0E-13	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Micall2, FDR; printed 1.15e-06.	fdr_bh	1.15E-6 false discovery rate	5.0E-9	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, logFC; printed -1.82.	differential_expression_fit	-1.82 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, logCPM; printed 6.77.	differential_expression_fit	6.77 log2 counts per million	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, F; printed 261.	differential_expression_fit	261 F statistic	0	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, PValue; printed 7.13e-10.	differential_expression_fit	7.13E-10 p-value	5.0E-13	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Wif1, FDR; printed 1.60e-06.	fdr_bh	1.6E-6 false discovery rate	5.0E-9	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, logFC; printed -5.32.	differential_expression_fit	-5.32 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, logCPM; printed 9.87.	differential_expression_fit	9.87 log2 counts per million	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, F; printed 298.	differential_expression_fit	298 F statistic	0	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, PValue; printed 9.12e-10.	differential_expression_fit	9.12E-10 p-value	5.0E-13	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Cldn4, FDR; printed 1.74e-06.	fdr_bh	1.74E-6 false discovery rate	5.0E-9	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, logFC; printed 5.75.	differential_expression_fit	5.75 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, logCPM; printed 3.86.	differential_expression_fit	3.86 log2 counts per million	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, F; printed 313.	differential_expression_fit	313 F statistic	0	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, PValue; printed 1.00e-09.	differential_expression_fit	1.0E-9 p-value	5.0E-12	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Tnni2, FDR; printed 1.74e-06.	fdr_bh	1.74E-6 false discovery rate	5.0E-9	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, logFC; printed 2.57.	differential_expression_fit	2.57 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, logCPM; printed 4.87.	differential_expression_fit	4.87 log2 counts per million	0.005	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, F; printed 240.	differential_expression_fit	240 F statistic	0	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, PValue; printed 1.17e-09.	differential_expression_fit	1.17E-9 p-value	5.0E-12	complete
claim-ql-differential-expression Section 12, the topTags printout of the quasi-likelihood F-test: Creb5, FDR; printed 1.83e-06.	fdr_bh	1.83E-6 false discovery rate	5.0E-9	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Csn1s2b, logFC; printed 6.08.	differential_expression_fit	6.08 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Csn1s2b, unshrunk.logFC; printed 6.09.	differential_expression_fit	6.09 log2 fold change, unshrunk (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Csn1s2b, logCPM; printed 10.19.	differential_expression_fit	10.19 log2 counts per million	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Csn1s2b, PValue; printed 5.94e-11.	differential_expression_fit	5.94E-11 p-value	5.0E-14	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Csn1s2b, FDR; printed 9.30e-07.	fdr_bh	9.3E-7 false discovery rate	5.0E-10	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Mrgprf, logFC; printed 5.15.	differential_expression_fit	5.15 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Mrgprf, unshrunk.logFC; printed 5.15.	differential_expression_fit	5.15 log2 fold change, unshrunk (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Mrgprf, logCPM; printed 2.75.	differential_expression_fit	2.75 log2 counts per million	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Mrgprf, PValue; printed 1.77e-10.	differential_expression_fit	1.77E-10 p-value	5.0E-13	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Mrgprf, FDR; printed 1.38e-06.	fdr_bh	1.38E-6 false discovery rate	5.0E-9	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Muc4, logFC; printed -7.17.	differential_expression_fit	-7.17 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Muc4, unshrunk.logFC; printed -7.34.	differential_expression_fit	-7.34 log2 fold change, unshrunk (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Muc4, logCPM; printed 6.06.	differential_expression_fit	6.06 log2 counts per million	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Muc4, PValue; printed 3.98e-10.	differential_expression_fit	3.98E-10 p-value	5.0E-13	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Muc4, FDR; printed 2.07e-06.	fdr_bh	2.07E-6 false discovery rate	5.0E-9	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Myof, logFC; printed 2.32.	differential_expression_fit	2.32 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Myof, unshrunk.logFC; printed 2.32.	differential_expression_fit	2.32 log2 fold change, unshrunk (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Myof, logCPM; printed 6.45.	differential_expression_fit	6.45 log2 counts per million	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Myof, PValue; printed 7.82e-10.	differential_expression_fit	7.82E-10 p-value	5.0E-13	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Myof, FDR; printed 2.69e-06.	fdr_bh	2.69E-6 false discovery rate	5.0E-9	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Atp2b4, logFC; printed 2.14.	differential_expression_fit	2.14 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Atp2b4, unshrunk.logFC; printed 2.14.	differential_expression_fit	2.14 log2 fold change, unshrunk (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Atp2b4, logCPM; printed 6.15.	differential_expression_fit	6.15 log2 counts per million	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Atp2b4, PValue; printed 1.01e-09.	differential_expression_fit	1.01E-9 p-value	5.0E-12	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Atp2b4, FDR; printed 2.69e-06.	fdr_bh	2.69E-6 false discovery rate	5.0E-9	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Cldn4, logFC; printed -5.32.	differential_expression_fit	-5.32 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Cldn4, unshrunk.logFC; printed -5.32.	differential_expression_fit	-5.32 log2 fold change, unshrunk (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Cldn4, logCPM; printed 9.87.	differential_expression_fit	9.87 log2 counts per million	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Cldn4, PValue; printed 1.14e-09.	differential_expression_fit	1.14E-9 p-value	5.0E-12	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Cldn4, FDR; printed 2.69e-06.	fdr_bh	2.69E-6 false discovery rate	5.0E-9	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Tnni2, logFC; printed 5.75.	differential_expression_fit	5.75 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Tnni2, unshrunk.logFC; printed 5.76.	differential_expression_fit	5.76 log2 fold change, unshrunk (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Tnni2, logCPM; printed 3.86.	differential_expression_fit	3.86 log2 counts per million	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Tnni2, PValue; printed 1.20e-09.	differential_expression_fit	1.2E-9 p-value	5.0E-12	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Tnni2, FDR; printed 2.69e-06.	fdr_bh	2.69E-6 false discovery rate	5.0E-9	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Micall2, logFC; printed -2.25.	differential_expression_fit	-2.25 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Micall2, unshrunk.logFC; printed -2.25.	differential_expression_fit	-2.25 log2 fold change, unshrunk (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Micall2, logCPM; printed 5.19.	differential_expression_fit	5.19 log2 counts per million	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Micall2, PValue; printed 1.90e-09.	differential_expression_fit	1.9E-9 p-value	5.0E-12	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Micall2, FDR; printed 3.71e-06.	fdr_bh	3.71E-6 false discovery rate	5.0E-9	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Creb5, logFC; printed 2.57.	differential_expression_fit	2.57 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Creb5, unshrunk.logFC; printed 2.57.	differential_expression_fit	2.57 log2 fold change, unshrunk (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Creb5, logCPM; printed 4.87.	differential_expression_fit	4.87 log2 counts per million	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Creb5, PValue; printed 3.55e-09.	differential_expression_fit	3.55E-9 p-value	5.0E-12	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Creb5, FDR; printed 6.18e-06.	fdr_bh	6.18E-6 false discovery rate	5.0E-9	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Igfbp6, logFC; printed 2.87.	differential_expression_fit	2.87 log2 fold change (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Igfbp6, unshrunk.logFC; printed 2.87.	differential_expression_fit	2.87 log2 fold change, unshrunk (basal lactating - basal pregnant)	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Igfbp6, logCPM; printed 3.68.	differential_expression_fit	3.68 log2 counts per million	0.005	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Igfbp6, PValue; printed 4.60e-09.	differential_expression_fit	4.6E-9 p-value	5.0E-12	complete
claim-glmtreat-threshold Section 13, the topTags printout of the glmTreat test: Igfbp6, FDR; printed 7.20e-06.	fdr_bh	7.2E-6 false discovery rate	5.0E-9	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Ppl, logFC; printed -4.62.	differential_expression_fit	-4.62 log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Ppl, logCPM; printed 6.96.	differential_expression_fit	6.96 log2 counts per million	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Ppl, F; printed 524.	differential_expression_fit	524 F statistic	0	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Ppl, PValue; printed 9.55e-12.	differential_expression_fit	9.55E-12 p-value	5.0E-15	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Ppl, FDR; printed 1.49e-07.	fdr_bh	1.49E-7 false discovery rate	5.0E-10	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Creb5, logFC; printed -5.61.	differential_expression_fit	-5.61 log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Creb5, logCPM; printed 4.87.	differential_expression_fit	4.87 log2 counts per million	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Creb5, F; printed 438.	differential_expression_fit	438 F statistic	0	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Creb5, PValue; printed 2.91e-11.	differential_expression_fit	2.91E-11 p-value	5.0E-14	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Creb5, FDR; printed 2.13e-07.	fdr_bh	2.13E-7 false discovery rate	5.0E-10	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc1a3, logFC; printed 5.03.	differential_expression_fit	5.03 log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc1a3, logCPM; printed 3.65.	differential_expression_fit	3.65 log2 counts per million	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc1a3, F; printed 415.	differential_expression_fit	415 F statistic	0	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc1a3, PValue; printed 4.09e-11.	differential_expression_fit	4.09E-11 p-value	5.0E-14	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc1a3, FDR; printed 2.13e-07.	fdr_bh	2.13E-7 false discovery rate	5.0E-10	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: BC006965, logFC; printed -3.88.	differential_expression_fit	-3.88 log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: BC006965, logCPM; printed 4.68.	differential_expression_fit	4.68 log2 counts per million	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: BC006965, F; printed 372.	differential_expression_fit	372 F statistic	0	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: BC006965, PValue; printed 8.11e-11.	differential_expression_fit	8.11E-11 p-value	5.0E-14	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: BC006965, FDR; printed 2.86e-07.	fdr_bh	2.86E-7 false discovery rate	5.0E-10	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Ggt1, logFC; printed 3.17.	differential_expression_fit	3.17 log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Ggt1, logCPM; printed 6.38.	differential_expression_fit	6.38 log2 counts per million	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Ggt1, F; printed 357.	differential_expression_fit	357 F statistic	0	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Ggt1, PValue; printed 1.04e-10.	differential_expression_fit	1.04E-10 p-value	5.0E-13	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Ggt1, FDR; printed 2.86e-07.	fdr_bh	2.86E-7 false discovery rate	5.0E-10	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc25a1, logFC; printed 3.47.	differential_expression_fit	3.47 log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc25a1, logCPM; printed 7.50.	differential_expression_fit	7.5 log2 counts per million	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc25a1, F; printed 354.	differential_expression_fit	354 F statistic	0	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc25a1, PValue; printed 1.10e-10.	differential_expression_fit	1.1E-10 p-value	5.0E-13	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc25a1, FDR; printed 2.86e-07.	fdr_bh	2.86E-7 false discovery rate	5.0E-10	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Sardh, logFC; printed 2.92.	differential_expression_fit	2.92 log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Sardh, logCPM; printed 5.11.	differential_expression_fit	5.11 log2 counts per million	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Sardh, F; printed 342.	differential_expression_fit	342 F statistic	0	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Sardh, PValue; printed 1.36e-10.	differential_expression_fit	1.36E-10 p-value	5.0E-13	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Sardh, FDR; printed 3.04e-07.	fdr_bh	3.04E-7 false discovery rate	5.0E-10	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Rbp1, logFC; printed -4.40.	differential_expression_fit	-4.4 log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Rbp1, logCPM; printed 6.83.	differential_expression_fit	6.83 log2 counts per million	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Rbp1, F; printed 337.	differential_expression_fit	337 F statistic	0	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Rbp1, PValue; printed 1.63e-10.	differential_expression_fit	1.63E-10 p-value	5.0E-13	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Rbp1, FDR; printed 3.18e-07.	fdr_bh	3.18E-7 false discovery rate	5.0E-10	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc39a8, logFC; printed 6.19.	differential_expression_fit	6.19 log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc39a8, logCPM; printed 5.07.	differential_expression_fit	5.07 log2 counts per million	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc39a8, F; printed 376.	differential_expression_fit	376 F statistic	0	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc39a8, PValue; printed 1.83e-10.	differential_expression_fit	1.83E-10 p-value	5.0E-13	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: Slc39a8, FDR; printed 3.18e-07.	fdr_bh	3.18E-7 false discovery rate	5.0E-10	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: F2rl1, logFC; printed -3.92.	differential_expression_fit	-3.92 log2 fold change ((L.lactating - L.pregnant) - (B.lactating - B.pregnant))	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: F2rl1, logCPM; printed 5.61.	differential_expression_fit	5.61 log2 counts per million	0.005	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: F2rl1, F; printed 302.	differential_expression_fit	302 F statistic	0	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: F2rl1, PValue; printed 2.93e-10.	differential_expression_fit	2.93E-10 p-value	5.0E-13	complete
claim-interaction Section 16, the topTags printout of the interaction contrast: F2rl1, FDR; printed 4.20e-07.	fdr_bh	4.2E-7 false discovery rate	5.0E-10	complete
claim-counts Section 4: dim(GenewiseCounts) is 27179 genes by 13 columns, the gene length column and the twelve libraries.	normalise_counts	27179 genes in the count matrix	0	complete
claim-counts Section 4: the count matrix carries one column per library, twelve of them, and one column of gene lengths.	normalise_counts	12 libraries in the count matrix	0	complete
claim-counts Section 6: the rule is CPM above 0.5 in at least two libraries, and it keeps 15653 genes.	normalise_counts	15653 genes kept by the filter	0	complete
claim-counts Section 6: the same rule discards 10704 genes.	normalise_counts	10704 genes discarded by the filter	0	complete
claim-ql-differential-expression Section 12: summary(decideTestsDGE) calls 2757 genes down.	differential_expression_fit	2757 genes called down	0	complete
claim-ql-differential-expression Section 12: summary(decideTestsDGE) calls 10408 genes none.	differential_expression_fit	10408 genes called none	0	complete
claim-ql-differential-expression Section 12: summary(decideTestsDGE) calls 2488 genes up.	differential_expression_fit	2488 genes called up	0	complete
claim-glmtreat-threshold Section 13: summary(decideTestsDGE) calls 723 genes down.	differential_expression_fit	723 genes called down	0	complete
claim-glmtreat-threshold Section 13: summary(decideTestsDGE) calls 14530 genes none.	differential_expression_fit	14530 genes called none	0	complete
claim-glmtreat-threshold Section 13: summary(decideTestsDGE) calls 400 genes up.	differential_expression_fit	400 genes called up	0	complete
claim-ql-differential-expression Section 12: the false discovery rate is controlled at 5% by the Benjamini-Hochberg method.	fdr_bh	0.05 exclusive false-discovery-rate threshold	0	complete
claim-ql-differential-expression Section 12: the paper states there are in fact more than 5000 differentially expressed genes in this comparison. The count is a lower bound, not a value.	differential_expression_fit	5000 genes (the paper states more than this)		partial
claim-glmtreat-threshold Section 13: glmTreat is called with lfc = log2(1.5), so the test asks whether the fold changes are significantly greater than 1.5.	differential_expression_fit	1.5 fold-change threshold	0	complete
claim-glmtreat-threshold Section 13: the paper states the threshold value of log 2(1.5) = 0.58.	differential_expression_fit	0.58 log2 fold-change threshold	0.005	complete
claim-glmtreat-threshold Section 13: about 1100 genes are detected as differentially expressed with a fold change significantly above 1.5 at a false discovery rate of 5%. The count is approximate.	differential_expression_fit	1100 genes (the paper states about this many)		partial
claim-glmtreat-threshold Section 13: all the statistically significant expression changes have logFC greater than 0.8. The value is a bound, not an estimate.	differential_expression_fit	0.8 log2 fold change, lower bound on the significant genes		partial
claim-glmtreat-threshold Section 13: almost all (97%) of the significant genes have logFC greater than 0.9. The value is a share read off the paper's own summary.	differential_expression_fit	97 percent of the significant genes with logFC above 0.9		partial
claim-normalisation Section 7: MCL1.DG, group B.virgin, lib.size 23139638 after the filter and the TMM normalisation.	normalise_counts	23139638 reads in the library after filtering	0	complete
claim-normalisation Section 7: MCL1.DG, group B.virgin, norm.factors 1.235.	normalise_counts	1.235 TMM normalisation factor	0.0005	complete
claim-normalisation Section 7: MCL1.DH, group B.virgin, lib.size 21689576 after the filter and the TMM normalisation.	normalise_counts	21689576 reads in the library after filtering	0	complete
claim-normalisation Section 7: MCL1.DH, group B.virgin, norm.factors 1.213.	normalise_counts	1.213 TMM normalisation factor	0.0005	complete
claim-normalisation Section 7: MCL1.DI, group B.pregnant, lib.size 23976634 after the filter and the TMM normalisation.	normalise_counts	23976634 reads in the library after filtering	0	complete
claim-normalisation Section 7: MCL1.DI, group B.pregnant, norm.factors 1.126.	normalise_counts	1.126 TMM normalisation factor	0.0005	complete
claim-normalisation Section 7: MCL1.DJ, group B.pregnant, lib.size 22546909 after the filter and the TMM normalisation.	normalise_counts	22546909 reads in the library after filtering	0	complete
claim-normalisation Section 7: MCL1.DJ, group B.pregnant, norm.factors 1.069.	normalise_counts	1.069 TMM normalisation factor	0.0005	complete
claim-normalisation Section 7: MCL1.DK, group B.lactating, lib.size 21422164 after the filter and the TMM normalisation.	normalise_counts	21422164 reads in the library after filtering	0	complete
claim-normalisation Section 7: MCL1.DK, group B.lactating, norm.factors 1.036.	normalise_counts	1.036 TMM normalisation factor	0.0005	complete
claim-normalisation Section 7: MCL1.DL, group B.lactating, lib.size 19918278 after the filter and the TMM normalisation.	normalise_counts	19918278 reads in the library after filtering	0	complete
claim-normalisation Section 7: MCL1.DL, group B.lactating, norm.factors 1.087.	normalise_counts	1.087 TMM normalisation factor	0.0005	complete
claim-normalisation Section 7: MCL1.LA, group L.virgin, lib.size 20276400 after the filter and the TMM normalisation.	normalise_counts	20276400 reads in the library after filtering	0	complete
claim-normalisation Section 7: MCL1.LA, group L.virgin, norm.factors 1.370.	normalise_counts	1.37 TMM normalisation factor	0.0005	complete
claim-normalisation Section 7: MCL1.LB, group L.virgin, lib.size 21571124 after the filter and the TMM normalisation.	normalise_counts	21571124 reads in the library after filtering	0	complete
claim-normalisation Section 7: MCL1.LB, group L.virgin, norm.factors 1.368.	normalise_counts	1.368 TMM normalisation factor	0.0005	complete
claim-normalisation Section 7: MCL1.LC, group L.pregnant, lib.size 22120647 after the filter and the TMM normalisation.	normalise_counts	22120647 reads in the library after filtering	0	complete
claim-normalisation Section 7: MCL1.LC, group L.pregnant, norm.factors 1.006.	normalise_counts	1.006 TMM normalisation factor	0.0005	complete
claim-normalisation Section 7: MCL1.LD, group L.pregnant, lib.size 21879947 after the filter and the TMM normalisation.	normalise_counts	21879947 reads in the library after filtering	0	complete
claim-normalisation Section 7: MCL1.LD, group L.pregnant, norm.factors 0.924.	normalise_counts	0.924 TMM normalisation factor	0.0005	complete
claim-normalisation Section 7: MCL1.LE, group L.lactating, lib.size 24660577 after the filter and the TMM normalisation.	normalise_counts	24660577 reads in the library after filtering	0	complete
claim-normalisation Section 7: MCL1.LE, group L.lactating, norm.factors 0.529.	normalise_counts	0.529 TMM normalisation factor	0.0005	complete
claim-normalisation Section 7: MCL1.LF, group L.lactating, lib.size 24602860 after the filter and the TMM normalisation.	normalise_counts	24602860 reads in the library after filtering	0	complete
claim-normalisation Section 7: MCL1.LF, group L.lactating, norm.factors 0.535.	normalise_counts	0.535 TMM normalisation factor	0.0005	complete
claim-alignment Section 27: SRR1552450, num total 30109290. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		30109290 reads in the library		partial
claim-alignment Section 27: SRR1552450, num mapped 26577308. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		26577308 reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552450, PropMapped 0.883. The paper states that the proportion of mapped reads should ideally be above 80%.		0.883 proportion of reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552451, num total 28322351. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		28322351 reads in the library		partial
claim-alignment Section 27: SRR1552451, num mapped 24794251. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		24794251 reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552451, PropMapped 0.875. The paper states that the proportion of mapped reads should ideally be above 80%.		0.875 proportion of reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552452, num total 31688348. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		31688348 reads in the library		partial
claim-alignment Section 27: SRR1552452, num mapped 27937620. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		27937620 reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552452, PropMapped 0.882. The paper states that the proportion of mapped reads should ideally be above 80%.		0.882 proportion of reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552453, num total 29614284. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		29614284 reads in the library		partial
claim-alignment Section 27: SRR1552453, num mapped 26074034. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		26074034 reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552453, PropMapped 0.880. The paper states that the proportion of mapped reads should ideally be above 80%.		0.88 proportion of reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552454, num total 27225012. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		27225012 reads in the library		partial
claim-alignment Section 27: SRR1552454, num mapped 24381742. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		24381742 reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552454, PropMapped 0.896. The paper states that the proportion of mapped reads should ideally be above 80%.		0.896 proportion of reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552455, num total 25433157. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		25433157 reads in the library		partial
claim-alignment Section 27: SRR1552455, num mapped 22813815. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		22813815 reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552455, PropMapped 0.897. The paper states that the proportion of mapped reads should ideally be above 80%.		0.897 proportion of reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552444, num total 27919481. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		27919481 reads in the library		partial
claim-alignment Section 27: SRR1552444, num mapped 23927833. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		23927833 reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552444, PropMapped 0.857. The paper states that the proportion of mapped reads should ideally be above 80%.		0.857 proportion of reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552445, num total 29731031. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		29731031 reads in the library		partial
claim-alignment Section 27: SRR1552445, num mapped 25487822. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		25487822 reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552445, PropMapped 0.857. The paper states that the proportion of mapped reads should ideally be above 80%.		0.857 proportion of reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552446, num total 29879070. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		29879070 reads in the library		partial
claim-alignment Section 27: SRR1552446, num mapped 25500318. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		25500318 reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552446, PropMapped 0.853. The paper states that the proportion of mapped reads should ideally be above 80%.		0.853 proportion of reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552447, num total 29245388. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		29245388 reads in the library		partial
claim-alignment Section 27: SRR1552447, num mapped 25187577. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		25187577 reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552447, PropMapped 0.861. The paper states that the proportion of mapped reads should ideally be above 80%.		0.861 proportion of reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552448, num total 31425424. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		31425424 reads in the library		partial
claim-alignment Section 27: SRR1552448, num mapped 27326500. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		27326500 reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552448, PropMapped 0.870. The paper states that the proportion of mapped reads should ideally be above 80%.		0.87 proportion of reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552449, num total 31276061. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		31276061 reads in the library		partial
claim-alignment Section 27: SRR1552449, num mapped 27204156. No DSL operation covers alignment to a reference genome, and the figure is the paper's own run: it depends on the aligner version and the reference build, so it is published and not compared numerically.		27204156 reads mapped to a unique location		partial
claim-alignment Section 27: SRR1552449, PropMapped 0.870. The paper states that the proportion of mapped reads should ideally be above 80%.		0.87 proportion of reads mapped to a unique location		partial
claim-pathway Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., n 75. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	75 genes in the pathway		partial
claim-pathway Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., up 1. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1 genes up in the pathway		partial
claim-pathway Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., down 19. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	19 genes down in the pathway		partial
claim-pathway Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., p_up 4.04e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	0.404 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu03008 Ribosome biogenesis in eukaryot..., p_down 3.23e-19. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	3.23E-19 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu01100 Metabolic pathways, n 1030. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1030 genes in the pathway		partial
claim-pathway Section 19: path:mmu01100 Metabolic pathways, up 28. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	28 genes up in the pathway		partial
claim-pathway Section 19: path:mmu01100 Metabolic pathways, down 51. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	51 genes down in the pathway		partial
claim-pathway Section 19: path:mmu01100 Metabolic pathways, p_up 3.42e-10. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	3.42E-10 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu01100 Metabolic pathways, p_down 1.11e-15. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1.11E-15 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu04110 Cell cycle, n 120. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	120 genes in the pathway		partial
claim-pathway Section 19: path:mmu04110 Cell cycle, up 1. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1 genes up in the pathway		partial
claim-pathway Section 19: path:mmu04110 Cell cycle, down 19. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	19 genes down in the pathway		partial
claim-pathway Section 19: path:mmu04110 Cell cycle, p_up 5.63e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	0.563 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu04110 Cell cycle, p_down 3.78e-15. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	3.78E-15 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu00230 Purine metabolism, n 152. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	152 genes in the pathway		partial
claim-pathway Section 19: path:mmu00230 Purine metabolism, up 2. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	2 genes up in the pathway		partial
claim-pathway Section 19: path:mmu00230 Purine metabolism, down 18. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	18 genes down in the pathway		partial
claim-pathway Section 19: path:mmu00230 Purine metabolism, p_up 2.80e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	0.28 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu00230 Purine metabolism, p_down 3.45e-12. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	3.45E-12 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu00240 Pyrimidine metabolism, n 96. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	96 genes in the pathway		partial
claim-pathway Section 19: path:mmu00240 Pyrimidine metabolism, up 0. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	0 genes up in the pathway		partial
claim-pathway Section 19: path:mmu00240 Pyrimidine metabolism, down 15. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	15 genes down in the pathway		partial
claim-pathway Section 19: path:mmu00240 Pyrimidine metabolism, p_up 1.00e+00. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu00240 Pyrimidine metabolism, p_down 3.86e-12. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	3.86E-12 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu05150 Staphylococcus aureus infection, n 30. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	30 genes in the pathway		partial
claim-pathway Section 19: path:mmu05150 Staphylococcus aureus infection, up 0. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	0 genes up in the pathway		partial
claim-pathway Section 19: path:mmu05150 Staphylococcus aureus infection, down 10. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	10 genes down in the pathway		partial
claim-pathway Section 19: path:mmu05150 Staphylococcus aureus infection, p_up 1.00e+00. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu05150 Staphylococcus aureus infection, p_down 4.78e-12. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	4.78E-12 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu04510 Focal adhesion, n 191. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	191 genes in the pathway		partial
claim-pathway Section 19: path:mmu04510 Focal adhesion, up 13. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	13 genes up in the pathway		partial
claim-pathway Section 19: path:mmu04510 Focal adhesion, down 9. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	9 genes down in the pathway		partial
claim-pathway Section 19: path:mmu04510 Focal adhesion, p_up 7.22e-10. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	7.22E-10 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu04510 Focal adhesion, p_down 1.34e-03. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	0.00134 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., n 167. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	167 genes in the pathway		partial
claim-pathway Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., up 9. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	9 genes up in the pathway		partial
claim-pathway Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., down 16. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	16 genes down in the pathway		partial
claim-pathway Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., p_up 2.34e-06. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	2.34E-6 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu04060 Cytokine-cytokine receptor inte..., p_down 1.35e-09. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1.35E-9 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu04514 Cell adhesion molecules (CAMs), n 112. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	112 genes in the pathway		partial
claim-pathway Section 19: path:mmu04514 Cell adhesion molecules (CAMs), up 2. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	2 genes up in the pathway		partial
claim-pathway Section 19: path:mmu04514 Cell adhesion molecules (CAMs), down 13. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	13 genes down in the pathway		partial
claim-pathway Section 19: path:mmu04514 Cell adhesion molecules (CAMs), p_up 1.79e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	0.179 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu04514 Cell adhesion molecules (CAMs), p_down 4.72e-09. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	4.72E-9 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu04972 Pancreatic secretion, n 63. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	63 genes in the pathway		partial
claim-pathway Section 19: path:mmu04972 Pancreatic secretion, up 8. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	8 genes up in the pathway		partial
claim-pathway Section 19: path:mmu04972 Pancreatic secretion, down 4. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	4 genes down in the pathway		partial
claim-pathway Section 19: path:mmu04972 Pancreatic secretion, p_up 1.14e-08. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1.14E-8 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu04972 Pancreatic secretion, p_down 1.10e-02. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	0.011 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu04970 Salivary secretion, n 63. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	63 genes in the pathway		partial
claim-pathway Section 19: path:mmu04970 Salivary secretion, up 8. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	8 genes up in the pathway		partial
claim-pathway Section 19: path:mmu04970 Salivary secretion, down 7. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	7 genes down in the pathway		partial
claim-pathway Section 19: path:mmu04970 Salivary secretion, p_up 1.14e-08. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1.14E-8 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu04970 Salivary secretion, p_down 2.45e-05. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	2.45E-5 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu04610 Complement and coagulation casc..., n 47. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	47 genes in the pathway		partial
claim-pathway Section 19: path:mmu04610 Complement and coagulation casc..., up 2. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	2 genes up in the pathway		partial
claim-pathway Section 19: path:mmu04610 Complement and coagulation casc..., down 9. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	9 genes down in the pathway		partial
claim-pathway Section 19: path:mmu04610 Complement and coagulation casc..., p_up 4.14e-02. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	0.0414 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu04610 Complement and coagulation casc..., p_down 1.32e-08. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1.32E-8 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu05166 HTLV-I infection, n 245. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	245 genes in the pathway		partial
claim-pathway Section 19: path:mmu05166 HTLV-I infection, up 5. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	5 genes up in the pathway		partial
claim-pathway Section 19: path:mmu05166 HTLV-I infection, down 17. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	17 genes down in the pathway		partial
claim-pathway Section 19: path:mmu05166 HTLV-I infection, p_up 2.71e-02. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	0.0271 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu05166 HTLV-I infection, p_down 5.39e-08. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	5.39E-8 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu00100 Steroid biosynthesis, n 18. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	18 genes in the pathway		partial
claim-pathway Section 19: path:mmu00100 Steroid biosynthesis, up 5. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	5 genes up in the pathway		partial
claim-pathway Section 19: path:mmu00100 Steroid biosynthesis, down 0. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	0 genes down in the pathway		partial
claim-pathway Section 19: path:mmu00100 Steroid biosynthesis, p_up 1.13e-07. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1.13E-7 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu00100 Steroid biosynthesis, p_down 1.00e+00. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1 KEGG p-value, down-regulated genes		partial
claim-pathway Section 19: path:mmu04114 Oocyte meiosis, n 101. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	101 genes in the pathway		partial
claim-pathway Section 19: path:mmu04114 Oocyte meiosis, up 2. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	2 genes up in the pathway		partial
claim-pathway Section 19: path:mmu04114 Oocyte meiosis, down 11. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	11 genes down in the pathway		partial
claim-pathway Section 19: path:mmu04114 Oocyte meiosis, p_up 1.53e-01. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	0.153 KEGG p-value, up-regulated genes		partial
claim-pathway Section 19: path:mmu04114 Oocyte meiosis, p_down 1.43e-07. The paper states that the kegga function reads the latest KEGG annotation each time it runs, so the p-values are not comparable across runs.	pathway_enrich	1.43E-7 KEGG p-value, down-regulated genes		partial

The assays in this file Each assay the file names, with the operations it needs and the definition it was read from.

rna-seq-read-alignment

unsupported

assay:1 · data_generation · version 0.1.0

needs: rna_seq_read_alignment

sha256:781215e3b5e462988c0f0a214b7462f32b5e18c58a59ff0e7366fdf7059c67a9

Subread version 1.4.4 ( http://subread.sourceforge.net) was used to align the reads to the mouse mm10 genome and featureCounts was used to assign reads to Entrez Genes using RefSeq gene annotation.

rna-seq-gene-quantification

unsupported

assay:2 · data_generation · version 0.1.0

needs: gene_count_quantification

depends on: assay:1

sha256:a7731347e0ac054f8756d31ba6f586cb68a0e381b1946dfec53ef72bcddb1407

The read counts for each gene can be quantified using the featureCounts function in Rsubread.

rna-seq-count-filtering-and-normalisation

partial

assay:3 · normalisation · version 0.1.0

needs: normalise_counts, normalise_counts_tmm

depends on: assay:2

sha256:029f48150fdbe3973df58cc1d9a63ea34bd5ba35c319469ee1cfd1249101c0fe

For the current analysis, we keep genes that have CPM values above 0.5 in at least two libraries:

rna-seq-differential-expression

partial

assay:4 · analysis · version 0.1.0

needs: differential_expression_fit, fdr_bh, differential_expression_quasi_likelihood

depends on: assay:3

sha256:dfda866165c72d6cd1517a23e85867cdaa0adc1df88f9977b642792bdcdc7278

The workflow uses edgeR’s quasi-likelihood pipeline (edgeR-quasi) for differential expression.

rna-seq-pathway-enrichment

supported

assay:5 · analysis · version 0.1.0

needs: pathway_enrich

depends on: assay:4

sha256:13560e312926f7eb0829d4fcf69d3ebb6bc2af081c63ea341def7d3ca69a1e27

Another popular annotation database is the Kyoto Encyclopedia of Genes and Genomes (KEGG). Much smaller than GO, this is a curated database of molecular pathways and disease signatures. A KEGG analysis can be done exactly as for GO, but using the kegga function:

Can this run here What the file says about running this experiment, and what still stands in the way.

State: blocked · tier R4
Blocked on: method:rna_seq_read_alignment

can run: normalise_counts, differential_expression_fit, fdr_bh, pathway_enrich

Still to build

rna_seq_read_alignment
gene_count_quantification
normalise_counts_tmm
differential_expression_quasi_likelihood

method

The DSL catalogue has no operation for: rna_seq_read_alignment, gene_count_quantification, normalise_counts_tmm, differential_expression_quasi_likelihood. The catalogue's normalise_counts is counts per million and its differential_expression_fit is a Welch t-test, so neither is edgeR's TMM normalisation nor its quasi-likelihood F-test.

capability

The corpus capability table owns computational analysis.

data

The GEO series resolves, its twelve samples are listed, and the twelve SRA runs resolve. No dataset was downloaded and no licence was read.

The result not_run What has run against this file, and the review the file carries.

Runs

Nothing has run against this file

The file records no execution. It is the paper's own definition of its experiment, read and held by the journal.

Review carried by the file

partial

Reader: MiniMax-M3.1-Flash (minimax)
Calls: 8

No person has reviewed this file. The reader's assessment is an opinion and not a decision.

Scope and limitations What this file does not cover, as the file itself states it.

asset:data:geo:GSE60450 licence not read
asset:data:geo:GSE60450 not downloaded
asset:data:sra:SRP045534 licence not read
asset:data:sra:SRP045534 not downloaded
asset:reference:mm10 not downloaded
data.licence_not_stated_in_the_repository_record
execution.not_run
method.rna_seq_read_alignment
review.human_critique
review.independent_reader
review.machine_critique
step:run_analysis blocked on method:rna_seq_read_alignment
target.alignment_figures_not_comparable_across_runs
target.count_matrix_cells_not_published
target.fry_and_camera_results_not_published
target.gene_ontology_results_not_published
target.kegg_p_values_not_comparable_across_runs

experiment

step:run_analysis blocked on method:rna_seq_read_alignment

data

asset:data:geo:GSE60450 licence not read
asset:data:geo:GSE60450 not downloaded
asset:data:sra:SRP045534 licence not read
asset:data:sra:SRP045534 not downloaded
asset:reference:mm10 not downloaded
data.licence_not_stated_in_the_repository_record

analysis

method.rna_seq_read_alignment
target.alignment_figures_not_comparable_across_runs
target.count_matrix_cells_not_published
target.fry_and_camera_results_not_published
target.gene_ontology_results_not_published
target.kegg_p_values_not_comparable_across_runs

readiness

method:rna_seq_read_alignment

review

review.independent_reader
review.machine_critique
review.human_critique

execution

execution.not_run

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