Characterizing gene sets with FuncAssociate - PubMed (original) (raw)
Comparative Study
. 2003 Dec 12;19(18):2502-4.
doi: 10.1093/bioinformatics/btg363.
Affiliations
- PMID: 14668247
- DOI: 10.1093/bioinformatics/btg363
Comparative Study
Characterizing gene sets with FuncAssociate
Gabriel F Berriz et al. Bioinformatics. 2003.
Abstract
Summary: FuncAssociate is a web-based tool to help researchers use Gene Ontology attributes to characterize large sets of genes derived from experiment. Distinguishing features of FuncAssociate include the ability to handle ranked input lists, and a Monte Carlo simulation approach that is more appropriate to determine significance than other methods, such as Bonferroni or idák p-value correction. FuncAssociate currently supports 10 organisms (Vibrio cholerae, Shewanella oneidensis, Saccharomyces cerevisiae, Schizosaccharomyces pombe, Arabidopsis thaliana, Caenorhaebditis elegans, Drosophila melanogaster, Mus musculus, Rattus norvegicus and Homo sapiens).
Availability: FuncAssociate is freely accessible at http://llama.med.harvard.edu/Software.html. Source code (in Perl and C) is freely available to academic users 'as is'.
Similar articles
- WILMA-automated annotation of protein sequences.
Prlić A, Domingues FS, Lackner P, Sippl MJ. Prlić A, et al. Bioinformatics. 2004 Jan 1;20(1):127-8. doi: 10.1093/bioinformatics/btg380. Bioinformatics. 2004. PMID: 14693821 - Using GOstats to test gene lists for GO term association.
Falcon S, Gentleman R. Falcon S, et al. Bioinformatics. 2007 Jan 15;23(2):257-8. doi: 10.1093/bioinformatics/btl567. Epub 2006 Nov 10. Bioinformatics. 2007. PMID: 17098774 - Identification and correction of abnormal, incomplete and mispredicted proteins in public databases.
Nagy A, Hegyi H, Farkas K, Tordai H, Kozma E, Bányai L, Patthy L. Nagy A, et al. BMC Bioinformatics. 2008 Aug 27;9:353. doi: 10.1186/1471-2105-9-353. BMC Bioinformatics. 2008. PMID: 18752676 Free PMC article. - Analysing gene expressions with GRANK.
de Boer WP, Oudejans JJ, Meijer CJ, Lankelma J. de Boer WP, et al. Bioinformatics. 2003 Oct 12;19(15):2000-1. doi: 10.1093/bioinformatics/btg267. Bioinformatics. 2003. PMID: 14555635 - Get ready to GO! A biologist's guide to the Gene Ontology.
Lomax J. Lomax J. Brief Bioinform. 2005 Sep;6(3):298-304. doi: 10.1093/bib/6.3.298. Brief Bioinform. 2005. PMID: 16212777 Review.
Cited by
- Pattern-driven neighborhood search for biclustering of microarray data.
Ayadi W, Elloumi M, Hao JK. Ayadi W, et al. BMC Bioinformatics. 2012 May 8;13 Suppl 7(Suppl 7):S11. doi: 10.1186/1471-2105-13-S7-S11. BMC Bioinformatics. 2012. PMID: 22594997 Free PMC article. - Local ancestry corrects for population structure in Saccharomyces cerevisiae genome-wide association studies.
Diao L, Chen KC. Diao L, et al. Genetics. 2012 Dec;192(4):1503-11. doi: 10.1534/genetics.112.144790. Epub 2012 Sep 28. Genetics. 2012. PMID: 23023004 Free PMC article. - FUNC: a package for detecting significant associations between gene sets and ontological annotations.
Prüfer K, Muetzel B, Do HH, Weiss G, Khaitovich P, Rahm E, Pääbo S, Lachmann M, Enard W. Prüfer K, et al. BMC Bioinformatics. 2007 Feb 6;8:41. doi: 10.1186/1471-2105-8-41. BMC Bioinformatics. 2007. PMID: 17284313 Free PMC article. - Integrated biclustering of heterogeneous genome-wide datasets for the inference of global regulatory networks.
Reiss DJ, Baliga NS, Bonneau R. Reiss DJ, et al. BMC Bioinformatics. 2006 Jun 2;7:280. doi: 10.1186/1471-2105-7-280. BMC Bioinformatics. 2006. PMID: 16749936 Free PMC article. - Partitioning the C. elegans genome by nucleosome modification, occupancy, and positioning.
Gu SG, Fire A. Gu SG, et al. Chromosoma. 2010 Feb;119(1):73-87. doi: 10.1007/s00412-009-0235-3. Epub 2009 Aug 25. Chromosoma. 2010. PMID: 19705140 Free PMC article.
Publication types
MeSH terms
Substances
LinkOut - more resources
Full Text Sources
Other Literature Sources
Molecular Biology Databases