A sensitive method for computing GO-based functional similarities among genes with 'shallow annotation'

Gene

Volumn 509, Issue 1, 2012, Pages 131-135

  Chen, Xiujie ^a   Yang, Ruizhi ^a   Xu, Jiankai ^a   Ma, Hongzhe ^a   Chen, Sheng ^a   Bian, Xiusen ^a   Liu, Lei ^a  

^a HARBIN MEDICAL UNIVERSITY   (China)

Author keywords

Functional similarity; Gene Ontology; Information content; Semantic similarity

Indexed keywords

ARTICLE; CONTROLLED STUDY; GENE FUNCTION; GENE ONTOLOGY; GENETIC CORRELATION; INTERMETHOD COMPARISON; MATHEMATICAL COMPUTING; MOLECULAR GENETICS; PRIORITY JOURNAL; SEQUENCE HOMOLOGY;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; GENE EXPRESSION PROFILING; GENOME, FUNGAL; MOLECULAR SEQUENCE ANNOTATION; MULTIGENE FAMILY; SACCHAROMYCES CEREVISIAE; SOFTWARE; VOCABULARY, CONTROLLED;

EID: 84866182495     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2012.07.078     Document Type: Article

References (17)

1. Ashburner M., et al. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat. Genet. 2000, 25:25-29.
2. Cheng J., et al. A knowledge-based clustering algorithm driven by Gene Ontology. J. Biopharm. Stat. 2004, 14:687-700.
3. Guo X., Liu R., Shriver C.D., Hu H., Liebman M.N. Assessing semantic similarity measures for the characterization of human regulatory pathways. Bioinformatics 2006, 22:967-973.
4. Jiang J., Conrath D. Semantic similarity based on corpus statistics and lexical taxonomy. Proc Int'l Conf Research in Computational Linguistics 1997.
5. Lin D. An information-theoretic definition of similarity. Fifteenth International Conference on Machine Learning (ICML'98) Madison 1998.
6. Lord P.W., Stevens R.D., Brass A., Goble C.A. Semantic similarity measures as tools for exploring the gene ontology. Pac. Symp. Biocomput. 2003, 601-612.
7. Mistry M., Pavlidis P. Gene Ontology term overlap as a measure of gene functional similarity. BMC Bioinforma. 2008, 9:327.
8. Pesquita C., Faria D., Bastos H., Ferreira A.E., Falcao A.O., Couto F.M. Metrics for GO based protein semantic similarity: a systematic evaluation. BMC Bioinforma. 2008, 9(Suppl. 5):S4.
9. Pesquita C., Pessoa D., Faria D., Couto F. CESSM: Collaborative Evaluation of Semantic Similarity Measures. Proceedings of JB2009: Challenges in Bioinformatics Lisbon 2009.
10. Resnik P. Semantic similarity in a taxonomy: an information-based measure and its application to problems of ambiguity in natural language. J. Artif. Intell. Res. 1999, 11:95-130.
11. Ruths T., Ruths D., Nakhleh L. GS2: an efficiently computable measure of GO-based similarity of gene sets. Bioinformatics 2009, 25:1178-1184.
12. Schlicker A., Domingues F.S., Rahnenfuhrer J., Lengauer T. A new measure for functional similarity of gene products based on Gene Ontology. BMC Bioinforma. 2006, 7:302.
13. Sevilla J.L., et al. Correlation between gene expression and GO semantic similarity. IEEE/ACM Trans. Comput. Biol. Bioinf. 2005, 2:330-338.
14. Sheehan B., Quigley A., Gaudin B., Dobson S. A relation based measure of semantic similarity for Gene Ontology annotations. BMC Bioinforma. 2008, 9:468.
15. Wang J.Z., Du Z., Payattakool R., Yu P.S., Chen C.F. A new method to measure the semantic similarity of GO terms. Bioinformatics 2007, 23:1274-1281.
16. Wu H., Su Z., Mao F., Olman V., Xu Y. Prediction of functional modules based on comparative genome analysis and Gene Ontology application. Nucleic Acids Res. 2005, 33:2822-2837.
17. Yu H., Gao L., Tu K., Guo Z. Broadly predicting specific gene functions with expression similarity and taxonomy similarity. Gene 2005, 352:75-81.