(Q42021385)

15 October 2017

Quantitative set analysis for gene expression: a method to quantify gene set differential expression including gene-gene correlations (English)

1 reference

15 October 2017

1

1 reference

15 October 2017

Christopher R Bolen

2

1 reference

PMCID

3794608

15 October 2017

Juilee Thakar

series ordinal

3

1 reference

PMCID

3794608

15 October 2017

Steven H Kleinstein

series ordinal

4

1 reference

15 October 2017

5 August 2013

1 reference

15 October 2017

Nucleic Acids Research

1 reference

15 October 2017

41

1 reference

15 October 2017

18

1 reference

15 October 2017

e170

1 reference

Creative Commons Attribution 3.0 Unported

15 October 2017

start time

4 October 2016

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

limma

1 reference

22 June 2022

https://europepmc.org/article/PMC/3794608

based on heuristic

inferred from PubMed Central ID database lookup

cites work

COXPRESdb: a database of comparative gene coexpression networks of eleven species for mammals.

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

The limitations of simple gene set enrichment analysis assuming gene independence

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

The blood transcriptional signature of chronic hepatitis C virus is consistent with an ongoing interferon-mediated antiviral response

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Quantifying selection in high-throughput Immunoglobulin sequencing data sets

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Camera: a competitive gene set test accounting for inter-gene correlation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Differential expression analysis of multifactor RNA-Seq experiments with respect to biological variation

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Temporal dynamics of host molecular responses differentiate symptomatic and asymptomatic influenza a infection

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Molecular signatures database (MSigDB) 3.0.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

The PathOlogist: an automated tool for pathway-centric analysis

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

A diverse range of gene products are effectors of the type I interferon antiviral response

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Differential expression analysis for sequence count data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Heading down the wrong pathway: on the influence of correlation within gene sets

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

The Generalization of `Student's' Problem when Several Different Population Variances are Involved

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

A review of statistical methods for preprocessing oligonucleotide microarrays.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Gene set enrichment analysis made simple

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

edgeR: a Bioconductor package for differential expression analysis of digital gene expression data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Comparative study of gene set enrichment methods.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

A brief bout of exercise alters gene expression and distinct gene pathways in peripheral blood mononuclear cells of early- and late-pubertal females

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Brief bout of exercise alters gene expression in peripheral blood mononuclear cells of early- and late-pubertal males

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Cyclic changes in gene expression induced by Peg-interferon alfa-2b plus ribavirin in peripheral blood monocytes (PBMC) of hepatitis C patients during the first 10 weeks of treatment

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Interferon signaling and treatment outcome in chronic hepatitis C

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

STAT3 mutations in the hyper-IgE syndrome

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Small-sample estimation of negative binomial dispersion, with applications to SAGE data

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Re-sampling strategy to improve the estimation of number of null hypotheses in FDR control under strong correlation structures

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Analyzing gene expression data in terms of gene sets: methodological issues

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Changes in gene expression during pegylated interferon and ribavirin therapy of chronic hepatitis C virus distinguish responders from nonresponders to antiviral therapy

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Significance analysis of microarrays applied to the ionizing radiation response

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

KEGG: kyoto encyclopedia of genes and genomes

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Erroneous analyses of interactions in neuroscience: a problem of significance.

5 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Cell-type specific gene expression signature in liver underlies response to interferon therapy in chronic hepatitis C infection.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Gene expression profiling of peripheral blood from patients with untreated new-onset systemic juvenile idiopathic arthritis reveals molecular heterogeneity that may predict macrophage activation syndrome.

17 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3794608

Correlation between gene expression levels and limitations of the empirical bayes methodology for finding differentially expressed genes

17 August 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23921631

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Prior biological knowledge-based approaches for the analysis of genome-wide expression profiles using gene sets and pathways

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/23921631

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/NAR/GKT660

1 reference

15 October 2017

1 reference

15 October 2017

1 reference

PMCID

3794608