Revigo summarizes and visualizes long lists of gene ontology terms

PLoS ONE

Volumn 6, Issue 7, 2011, Pages

  Supek, Fran ^a,b   Bošnjak, Matko ^a   Škunca, Nives ^a   Šmuc, Tomislav ^a  

^a RUDER BO KOVI INSTITUTE   (Croatia)

^b CENTRE FOR GENOMIC REGULATION CRG   (Spain)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSCRIPTION FACTOR; TRANSCRIPTION FACTOR ZNF417; TRANSCRIPTION FACTOR ZNF587; UNCLASSIFIED DRUG;

ANALYTICAL ERROR; ARTICLE; BRAIN DEVELOPMENT; CLUSTER ANALYSIS; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; GENE FUNCTION; GENETIC ALGORITHM; HIGH THROUGHPUT SCREENING; INTERMETHOD COMPARISON; NERVE CELL DIFFERENTIATION; NOMENCLATURE; ONLINE ANALYSIS; PROCESS MODEL; REDUNDANCY ANALYSIS; ALGORITHM; BIOLOGY; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE EXPRESSION REGULATION; GENETICS; HUMAN; INTERNET; METABOLISM; METHODOLOGY; MOLECULAR GENETICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; GENE EXPRESSION REGULATION; HUMANS; INTERNET; MOLECULAR SEQUENCE ANNOTATION; SOFTWARE; TRANSCRIPTION FACTORS; USER-COMPUTER INTERFACE;

EID: 79960610118     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0021800     Document Type: Article

References (26)

1. Rivals I, Personnaz L, Taing L, Potier M-C, (2007) Enrichment or depletion of a GO category within a class of genes: which test? Bioinformatics 23: 401-407.
2. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, et al. (2000) Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 25: 25-29.
3. Newman JC, Weiner AM, (2005) L2L: a simple tool for discovering the hidden significance in microarray expression data. Genome Biol 6: R81-R81.
4. Al-Shahrour F, Minguez P, Tárraga J, Medina I, Alloza E, et al. (2007) FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. Nucleic Acids Res 35: W91-W96.
5. Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z, (2009) GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists. BMC Bioinformatics 10: 48.
6. Du Z, Zhou X, Ling Y, Zhang Z, Su Z, (2010) agriGO: a GO analysis toolkit for the agricultural community. Nucleic Acids Res 38: W64-W70.
7. Zeeberg B, Liu H, Kahn A, Ehler M, Rajapakse V, et al. (2011) RedundancyMiner: De-replication of redundant GO categories in microarray and proteomics analysis. BMC Bioinformatics 12: 52.
8. Pesquita C, Faria D, Falcão AO, Lord P, Couto FM, (2009) Semantic Similarity in Biomedical Ontologies. PLoS Comput Biol 5: e1000443.
9. Schlicker A, Albrecht M, (2007) FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res 36: D434-D439.
10. Saitou N, Nei M, (1987) The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4: 406-425.
11. Schlicker A, Domingues F, Rahnenfuhrer J, Lengauer T, (2006) A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinformatics 7: 302.
12. Lopes CT, Franz M, Kazi F, Donaldson SL, Morris Q, et al. (2010) Cytoscape Web: an interactive web-based network browser. Bioinformatics 26: 2347-2348.
13. Cline MS, Smoot M, Cerami E, Kuchinsky A, Landys N, et al. (2007) Integration of biological networks and gene expression data using Cytoscape. Nat Protoc 2: 2366-2382.
14. Nowick K, Hamilton AT, Zhang H, Stubbs L, (2010) Rapid Sequence and Expression Divergence Suggest Selection for Novel Function in Primate-Specific KRAB-ZNF Genes. Mol Biol Evol 27: 2606-2617.
15. Supek F, Škunca N, Repar J, Vlahoviček K, Šmuc T, (2010) Translational Selection Is Ubiquitous in Prokaryotes. PLoS Genet 6: e1001004.
16. Ester K, Supek F, Majsec K, Marjanović M, Lembo D, et al. (2010) Putative mechanisms of antitumor activity of cyano-substituted heteroaryles in HeLa cells. Invest New Drugs doi:10.1007/s10637-010-9571-7.
17. van't Veer LJ, Dai H, van de Vijver MJ, He YD, Hart AAM, et al. (2002) Gene expression profiling predicts clinical outcome of breast cancer. Nature 415: 530-536.
18. Zeeberg B, Qin H, Narasimhan S, Sunshine M, Cao H, et al. (2005) High-Throughput GoMiner, an "industrial-strength" integrative gene ontology tool for interpretation of multiple-microarray experiments, with application to studies of Common Variable Immune Deficiency (CVID). BMC Bioinformatics 6: 168.
19. Pich C, (2009) MDSJ: Java Library for Multidimensional Scaling (Version 0.2). Available at: http://www.inf.uni-konstanz.de/algo/software/mdsj/. Accessed 2010 Nov 2.
20. Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, et al. (2009) The GOA database in 2009-an integrated Gene Ontology Annotation resource. Nucleic Acids Res 37: D396-403.
21. Maere S, Heymans K, Kuiper M, (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics 21: 3448-3449.
22. Herrmann C, Bérard S, Tichit L, (2009) SimCT: a generic tool to visualize ontology-based relationships for biological objects. Bioinformatics 25: 3197-3198.
23. Bauer S, Grossmann S, Vingron M, Robinson PN, (2008) Ontologizer 2.0-a multifunctional tool for GO term enrichment analysis and data exploration. Bioinformatics 24: 1650-1651.
24. Grossmann S, Bauer S, Robinson PN, Vingron M, (2007) Improved detection of overrepresentation of Gene-Ontology annotations with parent-child analysis. Bioinformatics 23: 3024-3031.
25. Bauer S, Gagneur J, Robinson PN, (2010) GOing Bayesian: model-based gene set analysis of genome-scale data. Nucleic Acids Res 38: 3523-3532.
26. Pehkonen P, Wong G, Törönen P, Theme discovery from gene lists for identification and viewing of multiple functional groups. BMC Bioinformatics 6: 162-162.