Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis 英文参考文献.docVIP

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Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis 英文参考文献.doc

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Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis 英文参考文献

Open Access Me od 2007LiuVoluandmthe Ringnér8, Issue 5, Article R77 Revealing signaling pathway deregulation by using gene expression signatures and regulatory motif analysis Yingchun Liu* and Markus Ringnér? Addresses: *Computational Biology and Biological Physics, Department of Theoretical Physics, Lund University, SE-221 85, Sweden. ?Division of Oncology, Department of Clinical Sciences, Lund University, SE-221 85, Sweden. Correspondence: Markus Ringnér. Email: markus.ringner@med.lu.se Published: 11 May 2007 Received: 6 October 2006 Revised: 19 April 2007 Accepted: 11 May 2007 Genome Biology 2007, 8:R77 (doi:10.1186/gb-2007-8-5-r77) The electronic version of this article is the complete one and can be found online at /2007/8/5/R77 ? 2007 Liu and Ringnér; licensee BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. RevealingpA stratsignalinge y for idpathwayentifyingderegulationcell signaling pathways whose deregulation result in an observed expression signature is presented./p Abstract Gene expression signatures consisting of tens to hundreds of genes have been found to be informative for different biological states. Recently, many computational methods have been proposed for biological interpretation of such signatures. However, there is a lack of methods for identifying cell signaling pathways whose deregulation results in an observed expression signature. We present a strategy for identifying such signaling pathways and evaluate the strategy using six human and mouse gene expression signatures. Background Signal transduction is at the core of many regulatory systems. Cellular functions such as growth, proliferation, differentia- tion, and apoptosis are regulated by signaling pathways