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

@article{citeulike:1449483, abstract = {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.}, address = {Bioinformatics Department, Centro de Investigaci\'{o}n Pr\'{i}ncipe Felipe (CIPF), Valencia 46013, Spain and Functional Genomics Node, INB, CIPF, Valencia 46013, Spain.}, author = {Al-Shahrour, F\'{a}tima and Minguez, Pablo and T\'{a}rraga, Joaqu\'{i}n and Medina, Ignacio and Alloza, Eva and Montaner, David and Dopazo, Joaqu\'{i}n }, citeulike-article-id = {1449483}, issn = {1362-4962}, journal = {Nucleic Acids Research}, keywords = {gene\_ontology, tools}, month = {May}, pages = {W91--W96}, posted-at = {2008-02-15 09:18:35}, priority = {0}, title = {FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.}, url = {http://view.ncbi.nlm.nih.gov/pubmed/17478504}, volume = {35}, year = {2007} }

TY - JOUR ID - citeulike:1449483 L3 - citeulike-article-id:1449483 TI - FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. JF - Nucleic Acids Research VL - 35 SP - W91 EP - W96 AD - Bioinformatics Department, Centro de Investigación Príncipe Felipe (CIPF), Valencia 46013, Spain and Functional Genomics Node, INB, CIPF, Valencia 46013, Spain. SN - 1362-4962 N2 - 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. KW - gene_ontology KW - tools AU - Al-Shahrour, Fátima AU - Minguez, Pablo AU - Tárraga, Joaquín AU - Medina, Ignacio AU - Alloza, Eva AU - Montaner, David AU - Dopazo, Joaquín PY - 2007/05/03/ UR - http://view.ncbi.nlm.nih.gov/pubmed/17478504 ER -