CASCADE_SCAN: mining signal transduction network from high-throughput data based on steepest descent method

BMC Bioinformatics

Research Article

Kejia Xu¹  Fuyan Hu¹  Kai Wang²  Ruili Feng²  Jing Li²  Tieqiao Wen²  Meng Jiang²  Hua Cheng² 

[1] Department of Mathematics, College of Sciences, Shanghai University, 200444, Shanghai, China;Laboratory of Molecular Neurobiology, School of Life Sciences and Institute of Systems Biology, Shanghai University, 200444, Shanghai, China;

关键词: Integer Linear Programming;    Seed Protein;    Steep Descent Method;    Depth First Search;    Functional Enrichment Analysis;   

DOI  :  10.1186/1471-2105-12-164

 received in 2010-12-08, accepted in 2011-05-17,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundSignal transduction is an essential biological process involved in cell response to environment changes, by which extracellular signaling initiates intracellular signaling. Many computational methods have been generated in mining signal transduction networks with the increasing of high-throughput genomic and proteomic data. However, more effective means are still needed to understand the complex mechanisms of signaling pathways.ResultsWe propose a new approach, namely CASCADE_SCAN, for mining signal transduction networks from high-throughput data based on the steepest descent method using indirect protein-protein interactions (PPIs). This method is useful for actual biological application since the given proteins utilized are no longer confined to membrane receptors or transcription factors as in existing methods. The precision and recall values of CASCADE_SCAN are comparable with those of other existing methods. Moreover, functional enrichment analysis of the network components supported the reliability of the results.ConclusionsCASCADE_SCAN is a more suitable method than existing methods for detecting underlying signaling pathways where the membrane receptors or transcription factors are unknown, providing significant insight into the mechanism of cellular signaling in growth, development and cancer. A new tool based on this method is freely available at http://www.genomescience.com.cn/CASCADE_SCAN/.

【 授权许可】

Unknown   
© Wang et al; licensee BioMed Central Ltd. 2011. This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.