FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.
FatiGO +: a functional profiling tool for genomic data. Integration of functional annotation, regulatory motifs and interaction data with microarray experiments.
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DOI：
10.1093/nar/gkm260
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发表时间：
2007-07
影响因子：
14.9
通讯作者：
Dopazo J
中科院分区：
文献类型：
--
作者：
Al-Shahrour F;Minguez P;Tárraga J;Medina I;Alloza E;Montaner D;Dopazo J
任何基因组规模实验的最终目标都是提供对数据的功能性解释，将现有信息与实验的假设联系起来。因此，功能分析方法在微阵列实验、蛋白质组学等多种场景中变得必不可少。我们提出了FatiGO+，一个基于网络的工具，用于基因组规模实验的功能分析，特别面向微阵列实验的解释。除了不同的功能注释（基因本体、KEGG通路、Interpro motif、Swissprot关键字和基于文本挖掘的与疾病和化合物相关的生物实体），FatiGO+还包括调控和结构信息。所使用的监管信息包括不同监管要素的目标预测（从Transfac和CisRed数据库获得）。此外，FatiGO+使用miRNA靶基序的预测来推断在研究的基因样本中哪些可以被激活或失活。最后，基因产物的特性与其在相互作用组中的相对位置和连接也被使用。此外，任何这些功能项的富集都可以在染色体坐标上直接分析。FatiGO+可以在http://www.fatigoplus.org和Babelomics环境http://www.babelomics.org中找到
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
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