Network enrichment analysis: extension of gene-set enrichment analysis to gene networks (Q34411128)

2 August 2017

title

Network enrichment analysis: extension of gene-set enrichment analysis to gene networks (English)

1 reference

2 August 2017

Maria Pernemalm

3

0 references

Andrey Alexeyenko

Andrey Alexeyenko

series ordinal

1

0 references

Janne Lehtiö

Janne Lehtiö

series ordinal

7

0 references

Yudi Pawitan

series ordinal

8

Yudi Pawitan

1 reference

2 August 2017

2

Woojoo Lee

1 reference

2 August 2017

5

Philippe Dessen

1 reference

2 August 2017

6

Vladimir Lazar

1 reference

2 August 2017

Justin Guegan

4

1 reference

2 August 2017

publication date

11 September 2012

1 reference

2 August 2017

1 reference

2 August 2017

volume

13

1 reference

2 August 2017

page(s)

226

1 reference

describes a project that uses

2 August 2017

limma

R package limma

2 references

22 June 2022

https://europepmc.org/article/PMC/3505158

based on heuristic

inferred from PubMed Central ID database lookup

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

Cytoscape

Cytoscape

1 reference

CZ Software Mentions: A large dataset of software mentions in the biomedical literature

cites work

Hallmarks of Cancer: The Next Generation

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

The STRING database in 2011: functional interaction networks of proteins, globally integrated and scored

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Exon-level microarray analyses identify alternative splicing programs in breast cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Network enrichment analysis in complex experiments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Dynamic zebrafish interactome reveals transcriptional mechanisms of dioxin toxicity

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

GOing Bayesian: model-based gene set analysis of genome-scale data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Automated network analysis identifies core pathways in glioblastoma

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Early pregnancy peripheral blood gene expression and risk of preterm delivery: a nested case control study

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Network-based Identification of novel cancer genes

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

COSMIC (the Catalogue of Somatic Mutations in Cancer): a resource to investigate acquired mutations in human cancer

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

How and when should interactome-derived clusters be used to predict functional modules and protein function?

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Comparative study of gene set enrichment methods.

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Exploring the human genome with functional maps

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Global networks of functional coupling in eukaryotes from comprehensive data integration

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Somatic mutations affect key pathways in lung adenocarcinoma

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Network-based analysis of affected biological processes in type 2 diabetes models

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Linear models and empirical bayes methods for assessing differential expression in microarray experiments

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Improved scoring of functional groups from gene expression data by decorrelating GO graph structure

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Oncogenic pathway signatures in human cancers as a guide to targeted therapies

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

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

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Prediction of protein function using protein-protein interaction data

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Cytoscape: a software environment for integrated models of biomolecular interaction networks

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Assortative Mixing in Networks

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Discovering regulatory and signalling circuits in molecular interaction networks

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Specificity and stability in topology of protein networks

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Random graphs with arbitrary degree distributions and their applications

6 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

Extensions to gene set enrichment

6 July 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/1471-2105-13-226

A global pathway crosstalk network

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/1471-2105-13-226

Bias in the estimation of false discovery rate in microarray studies

21 January 2018

1 reference

Crossref

https://api.crossref.org/works/10.1186/1471-2105-13-226

Genome-wide pathway analysis implicates intracellular transmembrane protein transport in Alzheimer disease.

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

False discovery rate, sensitivity and sample size for microarray studies.

27 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=3505158

27 October 2018

Identifiers

DOI

10.1186/1471-2105-13-226

1 reference

journals/bmcbi/AlexeyenkoLPGDLLP12

2 August 2017

DBLP publication ID

1 reference

DBLP Dataset 2021-01-02

Dimensions Publication ID

28 January 2021

0 references

1 reference

2 August 2017

1 reference