Context-dependent transcriptional regulations between signal transduction pathways

BMC Bioinformatics

Research Article

Sohyun Hwang¹  Doheon Lee¹  Sangwoo Kim¹  Heesung Shin² 

[1] Department of Bio and Brain Engineering, KAIST, 373-1 Guseong-dong, Yuseong-gu, Deajeon, Republic of Korea;Department of Mathematics, Inha University, 253 Yonghyun-dong, Nam-gu, Incheon, Republic of Korea;

关键词: KEGG Pathway;    Cellular Context;    Dendritic Cell Maturation;    Expression Score;    Start Node;   

DOI  :  10.1186/1471-2105-12-19

 received in 2010-08-12, accepted in 2011-01-13,  发布年份 2011

来源: Springer

【 摘 要 】

BackgroundCells coordinate their metabolism, proliferation, and cellular communication according to environmental cues through signal transduction. Because signal transduction has a primary role in cellular processes, many experimental techniques and approaches have emerged to discover the molecular components and dynamics that are dependent on cellular contexts. However, omics approaches based on genome-wide expression analysis data comparing one differing condition (e.g. complex disease patients and normal subjects) did not investigate the dynamics and inter-pathway cross-communication that are dependent on cellular contexts. Therefore, we introduce a new computational omics approach for discovering signal transduction pathways regulated by transcription and transcriptional regulations between pathways in signaling networks that are dependent on cellular contexts, especially focusing on a transcription-mediated mechanism of inter-pathway cross-communication.ResultsApplied to dendritic cells treated with lipopolysaccharide, our analysis well depicted how dendritic cells respond to the treatment through transcriptional regulations between signal transduction pathways in dendritic cell maturation and T cell activation.ConclusionsOur new approach helps to understand the underlying biological phenomenon of expression data (e.g. complex diseases such as cancer) by providing a graphical network which shows transcriptional regulations between signal transduction pathways. The software programs are available upon request.

【 授权许可】

Unknown   
© Hwang 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.