Gene set enrichment analysis: performance evaluation and usage guidelines. (Q35977457)

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

review article

1 reference

title

Gene set enrichment analysis: performance evaluation and usage guidelines (English)

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

1 reference

1

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

author name string

Tun-Hsiang Yang

2

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

Zhenjun Hu

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

Zhiping Weng

4

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

Charles DeLisi

5

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

publication date

7 September 2011

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

Briefings in Bioinformatics

12 February 2020

published in

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

volume

13

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

issue

3

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

page(s)

281-291

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

Identification of functional modules that correlate with phenotypic difference: the influence of network topology.

12 February 2020

cites work

1 reference

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Comparative analysis of missing value imputation methods to improve clustering and interpretation of microarray experiments

2 October 2017

1 reference

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Normalization and gene p-value estimation: issues in microarray data processing

2 October 2017

1 reference

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A parsimony approach to biological pathway reconstruction/inference for genomes and metagenomes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

A general modular framework for gene set enrichment analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

A novel signaling pathway impact analysis.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Gene-set analysis and reduction

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Mapping and quantifying mammalian transcriptomes by RNA-Seq

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Gene-set approach for expression pattern analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Which missing value imputation method to use in expression profiles: a comparative study and two selection schemes

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

A rescue strategy for multimapping short sequence tags refines surveys of transcriptional activity by CAGE.

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

A systems biology approach for pathway level analysis

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Computation of significance scores of unweighted Gene Set Enrichment Analyses

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Human endometriosis is associated with plasma cells and overexpression of B lymphocyte stimulator

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

KAAS: an automatic genome annotation and pathway reconstruction server

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Towards the uniform distribution of null P values on Affymetrix microarrays

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Absolute enrichment: gene set enrichment analysis for homeostatic systems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

A multivariate approach for integrating genome-wide expression data and biological knowledge

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

JProGO: a novel tool for the functional interpretation of prokaryotic microarray data using Gene Ontology information

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Normalization and quantification of differential expression in gene expression microarrays

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Calculating the statistical significance of changes in pathway activity from gene expression data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

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

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Discovering statistically significant pathways in expression profiling studies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Ontological analysis of gene expression data: current tools, limitations, and open problems

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

PAGE: parametric analysis of gene set enrichment

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

A sequence-based identification of the genes detected by probesets on the Affymetrix U133 plus 2.0 array

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Significance analysis of functional categories in gene expression studies: a structured permutation approach

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Improving the scaling normalization for high-density oligonucleotide GeneChip expression microarrays

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

LSimpute: accurate estimation of missing values in microarray data with least squares methods

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Exploration, normalization, and summaries of high density oligonucleotide array probe level data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Statistical significance for genomewide studies

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Summaries of Affymetrix GeneChip probe level data

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Proteomic survey of metabolic pathways in rice

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Controlling the false discovery rate in behavior genetics research

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Gene set enrichment analysis made simple

2 October 2017

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

RNA-Seq gene expression estimation with read mapping uncertainty

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

A comparison of meta-analysis methods for detecting differentially expressed genes in microarray experiments.

11 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

GEAR: genomic enrichment analysis of regional DNA copy number changes.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Nonparametric bayesian estimation of positive false discovery rates.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Extensions to gene set enrichment.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Meta-analytic methods, the Rorschach, and the MMPI.

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Transcriptional regulation and function during the human cell cycle

24 September 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3357488

Multiple Hypothesis Testing

24 September 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR049

The positive false discovery rate: a Bayesian interpretation and the q -value

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR049

Calibration ofρValues for Testing Precise Null Hypotheses

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR049

ADAPT: a database of affymetrix probesets and transcripts

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FBIB%2FBBR049

Quantitative proteomics analysis of the secretory pathway

21 January 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21900207

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Biochemical networking contributes more to genetic buffering in human and mouse metabolic pathways than does gene duplication

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21900207

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1093/BIB/BBR049

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

DBLP publication ID

journals/bib/HungYHWD12

1 reference

DBLP Dataset 2021-01-02

28 January 2021

1 reference

https://www.ebi.ac.uk/europepmc/webservices/rest/search?query=EXT_ID:21900207%20AND%20SRC:MED&resulttype=core&format=json

12 February 2020

1 reference