FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments

The ultimate goal of any genome-scale experiment is to provide a functional interpretation of the data, relating the available information with the hypotheses that originated the experiment. Thus, functional profiling methods have become essential in diverse scenarios such as microarray experiments,...

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Bibliographic Details
Published in:Nucleic acids research Vol. 35; no. suppl-2; pp. W91 - W96
Main Authors: Al-Shahrour, Fátima, Minguez, Pablo, Tárraga, Joaquín, Medina, Ignacio, Alloza, Eva, Montaner, David, Dopazo, Joaquín
Format: Journal Article
Language:English
Published: England Oxford University Press 01.07.2007
Subjects:
Amino Acid Motifs
Animals
Binding Sites
Computational Biology - methods
Gene Expression Profiling
Genes
Genomics - methods
Humans
Internet
Oligonucleotide Array Sequence Analysis
Programming Languages
Software
Systems Integration
Transcription Factors - metabolism
ISSN:0305-1048, 1362-4962, 1362-4962
Online Access:Get full text
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Summary:The ultimate goal of any genome-scale experiment is to provide a functional interpretation of the data, relating the available information with the hypotheses that originated the experiment. Thus, functional profiling methods have become essential in diverse scenarios such as microarray experiments, proteomics, etc. We present the FatiGO+, a web-based tool for the functional profiling of genome-scale experiments, specially oriented to the interpretation of microarray experiments. In addition to different functional annotations (gene ontology, KEGG pathways, Interpro motifs, Swissprot keywords and text-mining based bioentities related to diseases and chemical compounds) FatiGO+ includes, as a novelty, regulatory and structural information. The regulatory information used includes predictions of targets for distinct regulatory elements (obtained from the Transfac and CisRed databases). Additionally FatiGO+ uses predictions of target motifs of miRNA to infer which of these can be activated or deactivated in the sample of genes studied. Finally, properties of gene products related to their relative location and connections in the interactome have also been used. Also, enrichment of any of these functional terms can be directly analysed on chromosomal coordinates. FatiGO+ can be found at: http://www.fatigoplus.org and within the Babelomics environment http://www.babelomics.org
Bibliography:http://www.nar.oupjournals.org/
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SourceType-Scholarly Journals-1
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ISSN:0305-1048
1362-4962
1362-4962
DOI:10.1093/nar/gkm260