Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Berlin, Germany.
Bioinformatics. 2011 Oct 15;27(20):2917-8. doi: 10.1093/bioinformatics/btr499. Epub 2011 Sep 4.
Pathway-level analysis is a powerful approach enabling interpretation of post-genomic data at a higher level than that of individual biomolecules. Yet, it is currently hard to integrate more than one type of omics data in such an approach. Here, we present a web tool 'IMPaLA' for the joint pathway analysis of transcriptomics or proteomics and metabolomics data. It performs over-representation or enrichment analysis with user-specified lists of metabolites and genes using over 3000 pre-annotated pathways from 11 databases. As a result, pathways can be identified that may be disregulated on the transcriptional level, the metabolic level or both. Evidence of pathway disregulation is combined, allowing for the identification of additional pathways with changed activity that would not be highlighted when analysis is applied to any of the functional levels alone. The tool has been implemented both as an interactive website and as a web service to allow a programming interface.
The web interface of IMPaLA is available at http://impala.molgen.mpg.de. A web services programming interface is provided at http://impala.molgen.mpg.de/wsdoc.
kamburov@molgen.mpg.de; r.cavill@imperial.ac.uk; h.keun@imperial.ac.uk
Supplementary data are available at Bioinformatics online.
通路水平分析是一种强大的方法，可在单个生物分子水平之上对后基因组数据进行解释。然而，目前很难在这种方法中整合超过一种类型的组学数据。在这里，我们介绍了一个名为‘IMPaLA’的网络工具，用于转录组学或蛋白质组学和代谢组学数据的联合通路分析。它使用来自 11 个数据库的超过 3000 个预先注释的通路，对用户指定的代谢物和基因列表进行过度表达或富集分析。结果，可以识别可能在转录水平、代谢水平或两者上失调的通路。失调通路的证据被组合在一起，允许识别出具有改变活性的其他通路，如果仅对任何一个功能水平进行分析，则不会突出显示这些通路。该工具已被实现为交互式网站和网络服务，以允许编程接口。
IMPaLA 的网络界面可在 http://impala.molgen.mpg.de 上获得。网络服务编程接口可在 http://impala.molgen.mpg.de/wsdoc 上获得。
kamburov@molgen.mpg.de; r.cavill@imperial.ac.uk; h.keun@imperial.ac.uk
补充数据可在 Bioinformatics 在线获得。
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