SICAGO: Semi-supervised cluster analysis using semantic distance between gene pairs in Gene Ontology

Bioinformatics

Volumn 26, Issue 10, 2010, Pages 1384-1385

  Kang, Bo Yeong ^a   Ko, Song ^b   Kim, Dae Won ^b  

^a Kyungpook National University   (South Korea)

^b Chung Ang University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; CLUSTER ANALYSIS; COMPUTER INTERFACE; COMPUTER PROGRAM; GENE EXPRESSION PROFILING; GENETIC DATABASE; METHODOLOGY;

ALGORITHMS; CLUSTER ANALYSIS; DATABASES, GENETIC; GENE EXPRESSION PROFILING; SOFTWARE; USER-COMPUTER INTERFACE;

EID: 77952793819     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btq133     Document Type: Article

References (14)

1. Azuaje, F. and Bodenreider, O. (2004) Incorporating ontology-driven similarity knowledge into functional genomics: an exploratory study. In Proceedings of the IEEE Fourth Symposium Bioinformatics and Bioengineering, Taichung, Taiwan.
2. Cheng, J. et al. (2004) A Knowledge-based clustering algorithm driven by Gene Ontology. J. Biopharm. Stat., 14, 687-700.
3. Cho, R.J. et al. (1998) A genome-wide transcriptional analysis of the mitotic cell cycle. Mol. Cell, 2, 65-73.
4. Eisen, M.B. et al. (1998) Cluster analysis display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA, 95, 14863-14868.
5. Fang, Z. et al. (2006) Knowledge guided analysis of microarray data. J. Biomed. Inform., 39, 401-411.
6. Huang, D. and Pan, W. (2006) Incorporating biological knowledge into distancebased clustering analysis of microarray gene expression data. Bioinformatics, 22, 1259-1268.
7. Jiang, J. and David, W. (1997) Semantic similarity based on corpus statistics and lexical taxonomy. In Proceedings of International Conference Research on Computational Linguistics, Tapei, Taiwan.
8. Kustra, R. and Zagdanski, A. (2006) Incorporating gene ontology in clustering gene exresspion data. In Proceedings of the 20th IEEE International Symposium on Computer-Based Medical Systems, Maribor, Slovenia.
9. Lin, D. (1998) An information-theoretic definition of similarity. In Proceeding of the [15th] International Conference on Machine Learning, Madison, Wisconsin, USA.
10. Lord, P.W. and Stevens, R.D. (2003) Investigating semantic semiliarity measures across the Gene Ontology: the relationship between sequence and annotation. Bioinformatics, 19, 1275-1283.
11. Resnik, P. (1995) Using information content to evaluate semantic similarity in a taxonomy. In Proceedings of the 14th International Joint Conference on Artificial Intelligence, Montreal, Canada.
12. Spellman, P.T. (1998) Comprehensive identification of cell cycle-regulated genes of the yeast Saccaromyces cerevisiae by microarray hybridization. Mol. Biol. Cell, 9, 3273-3297.
13. Sevilla, J.L. et al. (2005) Correlation between gene expression and GO semantic similarity. In IEEE Trans. Comput. Biol. Bioinform., 2, 330-338.
14. Whitfield, M.L. et al. (2002) Indentification of genes periodically expressed in the human cell cycle and their expression in tumors. Mol. Biol. Cell, 13, 1977-2000.