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Context-dependent transcriptional regulations between signal transduction pathways

 Sohyun Hwang  ;  Sangwoo Kim  ;  Heesung Shin  ;  Doheon Lee 
 BMC BIOINFORMATICS, Vol.12(19) : 1-10, 2011 
Journal Title
Issue Date
Algorithms ; Computational Biology/methods* ; Dendritic Cells/metabolism ; Gene Expression Regulation* ; Gene Regulatory Networks* ; Humans ; Signal Transduction* ; Transcription, Genetic
KEGG Pathway ; Cellular Context ; Dendritic Cell Maturation ; Expression Score ; Start Node
BACKGROUND: Cells 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. RESULTS: Applied 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. CONCLUSIONS: Our 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.
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1. College of Medicine (의과대학) > BioMedical Science Institute (의생명과학부) > 1. Journal Papers
Yonsei Authors
Kim, Sangwoo(김상우) ORCID logo https://orcid.org/0000-0001-5356-0827
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