ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks - PubMed (original) (raw)

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

Gabriela Bindea et al. Bioinformatics. 2009.

Abstract

We have developed ClueGO, an easy to use Cytoscape plug-in that strongly improves biological interpretation of large lists of genes. ClueGO integrates Gene Ontology (GO) terms as well as KEGG/BioCarta pathways and creates a functionally organized GO/pathway term network. It can analyze one or compare two lists of genes and comprehensively visualizes functionally grouped terms. A one-click update option allows ClueGO to automatically download the most recent GO/KEGG release at any time. ClueGO provides an intuitive representation of the analysis results and can be optionally used in conjunction with the GOlorize plug-in.

PubMed Disclaimer

Figures

Fig. 1.

ClueGO example analysis of up- and down-regulated NK cell genes in peripheral blood from healthy human donors. (a) GO/pathway terms specific for upregulated genes. The bars represent the number of genes associated with the terms. The percentage of genes per term is shown as bar label. (b) Overview chart with functional groups including specific terms for upregulated genes. (c) Functionally grouped network with terms as nodes linked based on their kappa score level (≥0.3), where only the label of the most significant term per group is shown. The node size represents the term enrichment significance. Functionally related groups partially overlap. Not grouped terms are shown in white. (d) The distribution of two clusters visualized on network (c). Terms with up/downregulated genes are shown in red/green, respectively. The color gradient shows the gene proportion of each cluster associated with the term. Equal proportions of the two clusters are represented in white.

Similar articles

• Comprehensive functional analysis of large lists of genes and proteins.
  Mlecnik B, Galon J, Bindea G. Mlecnik B, et al. J Proteomics. 2018 Jan 16;171:2-10. doi: 10.1016/j.jprot.2017.03.016. Epub 2017 Mar 22. J Proteomics. 2018. PMID: 28343001
• Automated exploration of gene ontology term and pathway networks with ClueGO-REST.
  Mlecnik B, Galon J, Bindea G. Mlecnik B, et al. Bioinformatics. 2019 Oct 1;35(19):3864-3866. doi: 10.1093/bioinformatics/btz163. Bioinformatics. 2019. PMID: 30847467 Free PMC article.
• Gene Ontology analysis in multiple gene clusters under multiple hypothesis testing framework.
  Zhong S, Xie D. Zhong S, et al. Artif Intell Med. 2007 Oct;41(2):105-15. doi: 10.1016/j.artmed.2007.08.002. Artif Intell Med. 2007. PMID: 17913480
• Ontology annotation: mapping genomic regions to biological function.
  Thomas PD, Mi H, Lewis S. Thomas PD, et al. Curr Opin Chem Biol. 2007 Feb;11(1):4-11. doi: 10.1016/j.cbpa.2006.11.039. Epub 2007 Jan 5. Curr Opin Chem Biol. 2007. PMID: 17208035 Review.
• A survey of current software for network analysis in molecular biology.
  Thomas S, Bonchev D. Thomas S, et al. Hum Genomics. 2010 Jun;4(5):353-60. doi: 10.1186/1479-7364-4-5-353. Hum Genomics. 2010. PMID: 20650822 Free PMC article. Review.

Cited by

• In Silico Insights Reveal Fibronectin 1 as a Theranostic Marker in Gastric Cancer.
  Millapán T, Gutiérrez Á, Rosas K, Buchegger K, Ili CG, Brebi P. Millapán T, et al. Int J Mol Sci. 2024 Oct 16;25(20):11113. doi: 10.3390/ijms252011113. Int J Mol Sci. 2024. PMID: 39456895 Free PMC article.
• Short loop functional commonality identified in leukaemia proteome highlights crucial protein sub-networks.
  Chung SS, Ng JCF, Laddach A, Thomas NSB, Fraternali F. Chung SS, et al. NAR Genom Bioinform. 2021 Mar 1;3(1):lqab010. doi: 10.1093/nargab/lqab010. eCollection 2021 Mar. NAR Genom Bioinform. 2021. PMID: 33709075 Free PMC article.
• Conditional knockout of Tsc1 in RORγt-expressing cells induces brain damage and early death in mice.
  Deng Y, Yang Q, Yang Y, Li Y, Peng H, Wu S, Zhang S, Yao B, Li S, Gao Y, Li X, Li L, Deng Y. Deng Y, et al. J Neuroinflammation. 2021 May 6;18(1):107. doi: 10.1186/s12974-021-02153-8. J Neuroinflammation. 2021. PMID: 33957945 Free PMC article.
• Proteome changes underpin improved meat quality and yield of chickens (Gallus gallus) fed the probiotic Enterococcus faecium.
  Zheng A, Luo J, Meng K, Li J, Zhang S, Li K, Liu G, Cai H, Bryden WL, Yao B. Zheng A, et al. BMC Genomics. 2014 Dec 23;15(1):1167. doi: 10.1186/1471-2164-15-1167. BMC Genomics. 2014. PMID: 25532559 Free PMC article.
• Protein signatures from blood plasma and urine suggest changes in vascular function and IL-12 signaling in elderly with a history of chronic diseases compared with an age-matched healthy cohort.
  Yu Y, Singh H, Kwon K, Tsitrin T, Petrini J, Nelson KE, Pieper R. Yu Y, et al. Geroscience. 2021 Apr;43(2):593-606. doi: 10.1007/s11357-020-00269-y. Epub 2020 Sep 24. Geroscience. 2021. PMID: 32974878 Free PMC article.

References

1. 1. Ashburner M, et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000;25:25–29. - PMC - PubMed
2. 1. Boyle EI, et al. 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;20:3710–3715. - PMC - PubMed
3. 1. Garcia O, et al. GOlorize: a cytoscape plug-in for network visualization with Gene Ontology-based layout and coloring. Bioinformatics. 2007;23:394–396. - PubMed
4. 1. Huang DW, et al. The DAVID Gene Functional Classification Tool: a novel biological module-centric algorithm to functionally analyze large gene lists. Genome Biol. 2007;8:R183–R183. - PMC - PubMed
5. 1. Kanehisa M, et al. The KEGG databases at GenomeNet. Nucleic Acids Res. 2002;30:42–46. - PMC - PubMed

Publication types

MeSH terms

LinkOut - more resources

• Full Text Sources

  • Europe PubMed Central
  • Ovid Technologies, Inc.
  • PubMed Central
  • Silverchair Information Systems

• Other Literature Sources

  • The Lens - Patent Citations Database