GOSim - An R-package for computation of information theoretic GO similarities between terms and gene products

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Fröhlich, Holger ^a   Speer, Nora ^b   Poustka, Annemarie ^a   Beißbarth, Tim ^a  

^a GERMAN CANCER RESEARCH CENTER DKFZ   (Germany)

^b UNIVERSITY OF TÜBINGEN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL DATA; BIOLOGICAL FUNCTIONS; DNA MICROARRAY DATA; FREELY AVAILABLE SOFTWARE; FUNCTIONAL ANNOTATION; FUNCTIONAL SIMILARITY; HIGH-THROUGHPUT DATA; STATISTICAL COMPUTING;

INFORMATION THEORY; TOOLS;

GENE EXPRESSION;

GENE PRODUCT;

ARTICLE; BIOINFORMATICS; CLASSIFICATION; COMPUTER PROGRAM; CONCEPT ANALYSIS; DNA DETERMINATION; GENE CLUSTER; GENE FUNCTION; GENE IDENTIFICATION; GENETIC ALGORITHM; MATHEMATICAL ANALYSIS; MATHEMATICAL COMPUTING; NOMENCLATURE; SEQUENCE HOMOLOGY; COMPUTER LANGUAGE; DNA SEQUENCE; GENETIC DATABASE; INFORMATION RETRIEVAL; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE; REPRODUCIBILITY; SENSITIVITY AND SPECIFICITY; STATISTICAL ANALYSIS;

BASE SEQUENCE; DATA INTERPRETATION, STATISTICAL; DATABASES, GENETIC; INFORMATION STORAGE AND RETRIEVAL; MOLECULAR SEQUENCE DATA; PROGRAMMING LANGUAGES; REPRODUCIBILITY OF RESULTS; SENSITIVITY AND SPECIFICITY; SEQUENCE ANALYSIS, DNA; SOFTWARE;

EID: 34250764323     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-166     Document Type: Article

References (17)

1. Eisen M Spellman P Botstein D Brown P Cluster Analysis and Display of Genome-wide Expression Patterns Proceedings of the National Academy of Sciences, USA 1998 95 14863-14867 10.1073/pnas.95.25.14863
2. The Gene Ontology Consortium The Gene Ontology (GO) database and informatics resource Nucleic Acids Research 2004 32 D258-D261 308770 14681407 10.1093/nar/gkh036
3. Resnik P Using Information Content to Evaluate Semantic Similarity in a Taxonomy Proceedings of the 14th International Joint Conference on Artificial Intelligence, Montreal 1995 1 448-453
4. Resnik P Semantic Similarity in a Taxonomy: An information-based measure and its application to problems of ambigiguity in natural language Journal of Artificial Intelligence Research 1999 11 95-130
5. Lin D An information-theoretic definition of similarity Proceedings of the 15th International Conference on Machine Learning, San Francisco, CA Kaufmann M 1998 1 296-304
6. Jiang J Conrath D Semantic similarity based on corpus statistics and lexical taxonomy Proceedings of the International Conference on Research in Computational Linguistics, Taiwan 1998
7. Lord P Stevens R Brass A Goble C Semantic Similarity Measures as Tools for Exploring the Gene Ontology Proceedings of the Pacific Symposium on Biocomputing 2003 601-612
8. Couto F Silva M Coutinho P Implementation of a Functional Semantic Similarity Measure between Gene-Products Tech Rep DI/FCUL TR 03-29 Department of Informatics, University of Lisbon 2003
9. Couto F Silva M Coutinho P Semantic Similarity over the Gene Ontology: Family Correlation and Selecting Disjunctive Ancestors Conference in Information and Knowledge Management 2005
10. Speer N Fröhlich H Spieth C Zell A Functional Grouping of Genes Using Spectral Clustering and Gene Ontology Proc Int Joint Conf Neural Networks 2005 298-303
11. Fröhlich H Speer N Zell A Kernel Based Functional Gene Grouping Proc Int Joint Conf Neural Networks 2006 6886 6891
12. Beissbarth T Speed T GOstat: Finding statistically overexpressed Gene Ontologies within groups of genes Bioinformatics 2004 20 9 1464-1465 10.1093/bioinformatics/bth088 14962934
13. Schölkopf B Smola AJ Learning with Kernels Cambridge, MA: MIT Press 2002
14. Mehlhorn K Näher S The LEDA Platform of Combinatorial and Geometric Computing Cambridge University Press 1999
15. Rousseeuw P Silhouettes: A graphical aid to the interpretation and validation of cluster analysis J Comp and Applied Mathematics 1987 20 53-65 10.1016/0377-0427(87)90125-7
16. CRAN project http://www.r-project.org
17. Barth AS Kuner R Buness A Ruschhaupt M Merk S Zwermann L Kääb S Kreuzer E Steinbeck G Mansmann U Poustka A Nabauer M Sültmann H Identification of a Common Gene Expression Signature in Dilated Cardiomyopathy Across Independent Microarray Studies Journal of the American College of Cardiology 2006 48 8 17045896