TY - JOUR T1 - FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments. JF - Nucleic Acids Res Y1 - 2007 A1 - Al-Shahrour, Fátima A1 - Minguez, Pablo A1 - Tárraga, Joaquín A1 - Medina, Ignacio A1 - Alloza, Eva A1 - Montaner, David A1 - Dopazo, Joaquin KW - Amino Acid Motifs KW - Animals KW - Binding Sites KW - Computational Biology KW - Gene Expression Profiling KW - Genes KW - Genomics KW - Humans KW - Internet KW - Oligonucleotide Array Sequence Analysis KW - Programming Languages KW - Software KW - Systems Integration KW - Transcription Factors AB -

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.

VL - 35 IS - Web Server issue U1 - https://www.ncbi.nlm.nih.gov/pubmed/17478504?dopt=Abstract ER -