Paper · 19237447

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

Bindea G and 9 others. Bioinformatics, 2009. Cited by 5,010 papers, by iCite.

11 sourcespapers-2026-11-12-0.1.0

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ConductScience Library. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Papers, record 19237447. Release papers-2026-11-12-0.1.0, 12 Nov 2026. https://conductscience.org/library/papers/19237447

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Paper

PubMed's record of the paper, with iCite's citation figures. No abstract is shown.

Title: ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks.; PubMed
Journal: Bioinformatics; PubMed
Year: 2009; PubMed
Publication types: Journal Article, Research Support, Non-U.S. Gov't; PubMed
PubMed: https://pubmed.ncbi.nlm.nih.gov/19237447/; PubMed
DOI: https://doi.org/10.1093/bioinformatics/btp101; PubMed
PMC: https://pmc.ncbi.nlm.nih.gov/articles/PMC2666812/; PubMed
The journal: https://conductscience.org/library/journal-index/9808944; PubMed
Citations, by iCite: 5,010; iCite
Relative citation ratio, by iCite: 123; iCite
Revised in PubMed: 2022-11-09; PubMed

Authors10

The authors in the order PubMed's record lists them, with the ORCID iDs it states.

Order	Author	Forename
1	Bindea G	Gabriela
2	Mlecnik B	Bernhard
3	Hackl H	Hubert
4	Charoentong P	Pornpimol
5	Tosolini M	Marie
6	Kirilovsky A	Amos
7	Fridman WH	Wolf-Herman
8	Pagès F	Franck
9	Trajanoski Z	Zlatko
10	Galon J	Jérôme

Source PubMed

Topics6

NLM's MeSH indexing of the paper, its major topics first.

MeSH term	Major
Computational Biology	Major topic
Gene Regulatory Networks	Major topic
Software	Major topic
Databases, Genetic
Models, Biological
Multigene Family

Source PubMed

Grants0

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None in this release.

Trials0

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None in this release.

Comments and corrections0

PubMed's comments and corrections, NLM's own indexing: retractions first, then expressions of concern, errata and updates, and comments last.

None in this release.

References11

The papers the reference list in PubMed's record names, those in our copy of PubMed, in the list's order.

Order	PMID	Title	Journal	Year	In Papers	Source
1	11,752,249	The KEGG databases at GenomeNet.	Nucleic Acids Res	2002	https://conductscience.org/library/papers/11752249	PubMed
2	15,297,299	GO::TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes.	Bioinformatics	2004	https://conductscience.org/library/papers/15297299	PubMed
3	17,127,678	GOlorize: a Cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring.	Bioinformatics	2007	https://conductscience.org/library/papers/17127678	PubMed
4	14,597,658	Cytoscape: a software environment for integrated models of biomolecular interaction networks.	Genome Res	2003	https://conductscience.org/library/papers/14597658	PubMed
5	15,972,284	BiNGO: a Cytoscape plugin to assess overrepresentation of gene ontology categories in biological networks.	Bioinformatics	2005	https://conductscience.org/library/papers/15972284	PubMed
6	17,784,955	The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists.	Genome Biol	2007	https://conductscience.org/library/papers/17784955	PubMed
7	17,182,697	Enrichment or depletion of a GO category within a class of genes: which test?	Bioinformatics	2007	https://conductscience.org/library/papers/17182697	PubMed
8	18,635,572	The protein information and property explorer: an easy-to-use, rich-client web application for the management and functional analysis of proteomic data.	Bioinformatics	2008	https://conductscience.org/library/papers/18635572	PubMed
9	10,802,651	Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.	Nat Genet	2000	https://conductscience.org/library/papers/10802651	PubMed
10	12,702,209	GoMiner: a resource for biological interpretation of genomic and proteomic data.	Genome Biol	2003	https://conductscience.org/library/papers/12702209	PubMed

1 to 10 of 11

See all 11 references

Cited by3,707

The papers in our copy of PubMed whose reference list names this one, newest first. iCite, which reads more sources, counts 5,010 citations.

PMID	Title	Journal	Year	In Papers	Source
42,985,003	A whole-blood transcriptomic analysis of shared molecular mechanisms between subclinical atherosclerosis and hypothyroidism in women.	Front Bioinform	2026	https://conductscience.org/library/papers/42985003	PubMed
42,984,818	Decoding the phosphorylation landscape of ITPR3 across calcium signaling and regulatory networks in cancer.	Front Bioinform	2026	https://conductscience.org/library/papers/42984818	PubMed
42,967,595	Long-Term Post-Mitotic Culture of Human Fibroblasts Recapitulates and Accelerates Features of In Vivo Aging and Enables Dynamic Testing of Anti-Aging Compounds.	Aging Cell	2026	https://conductscience.org/library/papers/42967595	PubMed
42,963,768	Breed and housing system shape jejunal transcriptome and digesta microbiota in German Landrace and Saddleback pigs.	Anim Microbiome	2026	https://conductscience.org/library/papers/42963768	PubMed
42,949,911	Automated plate-to-peptide protocol for mass spectrometry sample preparation.	STAR Protoc	2026	https://conductscience.org/library/papers/42949911	PubMed
42,946,706	Single-nucleus transcriptomics reveals disrupted pathways in the prefrontal cortex of Scn2a-deficient mice.	Transl Psychiatry	2026	https://conductscience.org/library/papers/42946706	PubMed
42,943,265	Machine Learning for Screening Bioactive Compounds in Traditional Chinese Medicine: Computational Prediction, Multi-Omics Integration, and Clinical Translation Potential.	Pharmaceuticals (Basel)	2026	https://conductscience.org/library/papers/42943265	PubMed
42,940,181	Stage-Stratified Explainable Machine Learning Identifies a Reproducible Transcriptomic Classifier with Stage-Dependent Feature Importance in Colorectal Cancer: A Multi-Cohort Study with Saudi Population Contextualisation.	Biomedicines	2026	https://conductscience.org/library/papers/42940181	PubMed
42,927,188	The smooth muscle titin filament system regulates uterus contractility and implantation.	iScience	2026	https://conductscience.org/library/papers/42927188	PubMed
42,895,604	Evaluation of Methylmercury-Induced Motor Dysfunction and Proteomic Analysis of Cerebrospinal Fluid in Common Marmosets (Callithrix jacchus).	Neurotox Res	2026	https://conductscience.org/library/papers/42895604	PubMed

1 to 10 of 3,707

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None in this release.

Drugs0

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None in this release.

Data0

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None in this release.

Data dates

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PubMed: 2026-11-06; PubMed
iCite: 2026-11-05; iCite
PMC's ID file: 2026-11-05; PMC's ID file
NIH RePORTER's grant and paper links: 2026-11-01; NIH RePORTER's grant and paper links
Trials: 2026-11-12
Gene search: 2026-11-11
Pipelines: 2026-09-18

Sources 11

ChEMBL, through Open TargetsCC BY-SA 3.0
ClinicalTrials.govNo license stated
HGNCCC0
iCiteCC BY 4.0
NCBI GenePublic domain (US government)
NIH RePORTER's grant and paper linksPublic domain
Open TargetsCC0 1.0
PMC's ID filePublic domain (US government)
PubMedNLM's terms
PubTator 3Public domain
UniProtCC BY 4.0

Each source's terms

ChEMBL, through Open TargetsCC BY-SA 3.0, for the parts from ChEMBL. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
ClinicalTrials.govnone stated
HGNCCC0: https://www.genenames.org/about/license/
iCiteCC BY 4.0
NCBI GeneNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
NIH RePORTER's grant and paper linksPublic domain (NIH RePORTER)
Open TargetsCC0 1.0. Open Targets asks that users cite its latest paper: Buniello et al. 2025, Open Targets Platform: facilitating therapeutic hypotheses building in drug discovery, Nucleic Acids Research 53(D1):D1467, PMID 39657122. Read on 8 Nov 2026 at https://platform-docs.opentargets.org/licence
PMC's ID fileNone named for the file. NCBI says information created by or for the US government on its site is in the public domain, and asks that NLM be acknowledged: https://www.ncbi.nlm.nih.gov/home/about/policies/
PubMedNLM's terms
PubTator 3Public domain
UniProtCC BY 4.0. UniProt's licence file: "All databases and documents in the UniProt FTP directory may be copied and redistributed freely, without advance permission, provided that this copyright statement is reproduced with each copy." UniProt asks that users cite its latest paper: The UniProt Consortium, UniProt: the Universal Protein Knowledgebase in 2025, Nucleic Acids Research 53:D609-D617, https://doi.org/10.1093/nar/gkae1010. Read on 9 Nov 2026 at https://www.uniprot.org/help/license

ClinicalTrials.gov's data carry an international copyright outside the United States: https://clinicaltrials.gov/about-site/terms-conditions.

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