Title: Identifying cell cycle regulators and combinatorial interactions among transcription factors with microarray data and ChIP-chip data

Authors: Ting Chen, Feng Li

Addresses: Department of Electronic Engineering, Fudan University, Shanghai 200433, China. ' Department of Electronic Engineering, Fudan University, Shanghai 200433, China

Abstract: In this paper, we integrate transcriptional regulatory modelling with temporal correlation analysis between one Transcription Factor (TF) and its corresponding cell cycle-regulated targets to investigate Cell Cycle Regulators (CCRs) and combinatorial interactions among TFs across the cell cycle in Saccharomyces cerevisiae. Our method is developed based on the rationale that if one TF or one TF combinatorial interaction takes more possibilities of sharing common cell cycle-regulated targets with other TFs, this TF or TF combinatorial interaction is more likely to control the cell cycle. Our results reveal abundant CCRs and TF co-operativities supported by biological experiments or other computational methods.

Keywords: CCR; cell cycle regulators; combinatorial interactions; microarray data; ChIP-chip data; average composite expression; ACE profile; temporal correlation; statistical significance; bioinformatics; transcription factors.

DOI: 10.1504/IJBRA.2009.029043

International Journal of Bioinformatics Research and Applications, 2009 Vol.5 No.6, pp.625 - 646

Received: 30 Jun 2008
Accepted: 25 Nov 2008

Published online: 29 Oct 2009 *

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