NDLI: A graph model and an exact algorithm for finding transcription factor modules

Content Provider	ACM Digital Library
Author	Lu, Xinghua Lu, Songjian
Abstract	Systematically perturbing a cellular system and monitoring the effects of the perturbations on gene expression provide a powerful approach to study signal transduction in gene expression systems. A critical step of revealing a signal transduction pathway regulating gene expression is to identify transcription factors transmitting signals in the system. In this paper, we address the task of identifying modules of cooperative transcription factors based on results derived from systems-biology experiments at two levels: First, a graph algorithm is developed to identify a minimum set of co-operative TFs that covers the differentially expressed genes under each systematic perturbation. Second, using a clique-finding approach, modules of TFs that tend to consistently cooperate together under various perturbations are further identified. Our results indicate that this approach is capable of identifying many known TF modules at both the individual experiment level and at the systems level; thus we provide a novel graph-based method of identifying context-specific and highly reused TF-modules.
Starting Page	355
Ending Page	359
Page Count	5
File Format	PDF
ISBN	9781450307963
DOI	10.1145/2147805.2147850
Language	English
Publisher	Association for Computing Machinery (ACM)
Publisher Date	2011-08-01
Publisher Place	New York
Access Restriction	Subscribed
Content Type	Text
Resource Type	Article

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A graph model and an exact algorithm for finding transcription factor modules