BayGO: Bayesian analysis of ontology term enrichment in microarray data

BMC Bioinformatics
Ricardo Z N VêncioCarlos A de B Pereira

Abstract

The search for enriched (aka over-represented or enhanced) ontology terms in a list of genes obtained from microarray experiments is becoming a standard procedure for a system-level analysis. This procedure tries to summarize the information focussing on classification designs such as Gene Ontology, KEGG pathways, and so on, instead of focussing on individual genes. Although it is well known in statistics that association and significance are distinct concepts, only the former approach has been used to deal with the ontology term enrichment problem. BayGO implements a Bayesian approach to search for enriched terms from microarray data. The R source-code is freely available at http://blasto.iq.usp.br/~tkoide/BayGO in three versions: Linux, which can be easily incorporated into pre-existent pipelines; Windows, to be controlled interactively; and as a web-tool. The software was validated using a bacterial heat shock response dataset, since this stress triggers known system-level responses. The Bayesian model accounts for the fact that, eventually, not all the genes from a given category are observable in microarray data due to low intensity signal, quality filters, genes that were not spotted and so on. Moreover, BayGO allows one ...Continue Reading

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Citations

Oct 31, 2006·Omics : a Journal of Integrative Biology·Joaquín Dopazo
Jun 3, 2008·Nucleic Acids Research·Fátima Al-ShahrourJoaquín Dopazo
May 12, 2009·Nucleic Acids Research·Choong-Hyun SunGwan-Su Yi
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Jun 8, 2010·BMC Bioinformatics·Jiye AiDavid T Wong
Feb 4, 2012·BMC Bioinformatics·H Robert Frost, Alexa T McCray
Oct 16, 2007·BMC Bioinformatics·Ricardo Z N Vêncio, Ilya Shmulevich
Jan 6, 2007·Genome Biology·Pedro Carmona-SaezAlberto Pascual-Montano
Nov 22, 2007·PloS One·Henrik HornshøjChristian Bendixen
Jan 1, 2009·PloS One·Alessandro de Mello VaraniMarie-Anne Van Sluys
Mar 25, 2014·Biotechnology for Biofuels·Lilian Dos Santos CastroRoberto Nascimento Silva
Mar 1, 2006·BMC Bioinformatics·Ricardo Z N VêncioCarlos A de B Pereira
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Sep 16, 2008·Artificial Intelligence in Medicine·Joaquin Dopazo

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Datasets Mentioned

BETA
GSE3044

Methods Mentioned

BETA
Protein folding

Software Mentioned

Gene
LACK
Perl
Linux
GO
HTML
OntologyTraverser
: TermFinder
R language
Onto

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