Enrichment map: a network-based method for gene-set enrichment visualization and interpretation (Q33749961)

29 July 2017

Enrichment map: a network-based method for gene-set enrichment visualization and interpretation (English)

1 reference

29 July 2017

1 reference

Gary D Bader

5

0 references

Andrew Emili

series ordinal

4

object named as

Andrew Emili

1 reference

29 July 2017

2

Ruth Isserlin

1 reference

29 July 2017

1

Daniele Merico

1 reference

29 July 2017

Oliver Stueker

3

1 reference

PubMed ID

21085593

29 July 2017

language of work or name

English

0 references

publication date

15 November 2010

1 reference

29 July 2017

1 reference

29 July 2017

5

1 reference

29 July 2017

e13984

1 reference

29 July 2017

11

1 reference

Creative Commons Attribution 4.0 International

29 July 2017

start time

15 November 2010

1 reference

April 2022 Public Data File from Crossref

copyright status

copyrighted

0 references

describes a project that uses

Cytoscape

object named as

Cytoscape

2 references

9 June 2022

https://europepmc.org/search?query=(METHODS:'Cytoscape')

based on heuristic

inferred from PubMed Central ID database lookup

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

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Functional impact of global rare copy number variation in autism spectrum disorders

21 June 2018

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Pathway analysis of dilated cardiomyopathy using global proteomic profiling and enrichment maps

21 June 2018

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WhichGenes: a web-based tool for gathering, building, storing and exporting gene sets with application in gene set enrichment analysis

21 June 2018

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ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks

21 June 2018

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Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources

21 June 2018

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

21 June 2018

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A novel signaling pathway impact analysis.

21 June 2018

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An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors

21 June 2018

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Technologies for the global discovery and analysis of alternative splicing.

21 June 2018

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Gene-set approach for expression pattern analysis

21 June 2018

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Integration of biological networks and gene expression data using Cytoscape

21 June 2018

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Analysis and validation of proteomic data generated by tandem mass spectrometry

21 June 2018

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Improved detection of overrepresentation of Gene-Ontology annotations with parent child analysis

21 June 2018

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A systems biology approach for pathway level analysis

21 June 2018

1 reference

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The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists

21 June 2018

1 reference

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Role of chemokines in tumor growth

21 June 2018

1 reference

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Transcriptional recapitulation and subversion of embryonic colon development by mouse colon tumor models and human colon cancer

21 June 2018

1 reference

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Whole-genome cartography of estrogen receptor alpha binding sites

21 June 2018

1 reference

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Molecular concepts analysis links tumors, pathways, mechanisms, and drugs

21 June 2018

1 reference

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Identification of key processes underlying cancer phenotypes using biologic pathway analysis

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Enrichment or depletion of a GO category within a class of genes: which test?

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Using GOstats to test gene lists for GO term association

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Grouping Gene Ontology terms to improve the assessment of gene set enrichment in microarray data.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Cancer's molecular sweet tooth and the Warburg effect.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Microarray data analysis: from disarray to consolidation and consensus

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

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

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

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

21 June 2018

1 reference

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WebGestalt: an integrated system for exploring gene sets in various biological contexts

21 June 2018

1 reference

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BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Effects of threshold choice on biological conclusions reached during analysis of gene expression by DNA microarrays

21 June 2018

1 reference

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Pathway information for systems biology

21 June 2018

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Staging of colorectal cancer: past, present, and future

21 June 2018

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Reactome: a knowledgebase of biological pathways

21 June 2018

1 reference

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Role of cytochromes P450 in chemical toxicity and oxidative stress: studies with CYP2E1.

21 June 2018

1 reference

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Detection of activity centers in cellular pathways using transcript profiling

21 June 2018

1 reference

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Bioconductor: open software development for computational biology and bioinformatics

21 June 2018

1 reference

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Molecular characterizations of derivatives of HCT116 colorectal cancer cells that are resistant to the chemotherapeutic agent 5-fluorouracil.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Estrogen and antiestrogen regulation of cell cycle progression in breast cancer cells

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

DAVID: Database for Annotation, Visualization, and Integrated Discovery

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Global functional profiling of gene expression.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

FunSpec: a web-based cluster interpreter for yeast

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Discovering regulatory and signalling circuits in molecular interaction networks

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Computational analysis of microarray data

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Gene ontology: tool for the unification of biology

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Systematic determination of genetic network architecture

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

KEGG: Kyoto Encyclopedia of Genes and Genomes

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

A susceptibility gene set for early onset colorectal cancer that integrates diverse signaling pathways: implication for tumorigenesis.

21 June 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

Profiling Gene Expression Using Onto-Express

30 October 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=2981572

A NAD(P)H:quinone oxidoreductase 1 polymorphism is a risk factor for human colon cancer

30 October 2018

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21085593

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Microsomal glutathione S-transferase gene polymorphisms and colorectal cancer risk in a Han Chinese population

1 reference

PubMed

https://pubmed.ncbi.nlm.nih.gov/21085593

inferred from PubMed ID database lookup

12 December 2020

based on heuristic

Identifiers

DOI

10.1371/JOURNAL.PONE.0013984

1 reference

29 July 2017

0 references

1 reference

29 July 2017

1 reference

PubMed ID

21085593