Discovering Transcriptional Regulation by Integrating Protein-Protein Interaction, Gene Ezpression and Transcriptional Interaction Data
Understanding transcriptional regulation (TR) principles and mechanisms is a hot topic in the genomics and transcriptome research. Many experimental and computational methods have been proposed to investigate this problem. However, perhaps partially because the high complexity in the transcriptional regulation mechanism, or partially because the noise in the high-throughput detection experiments, integrative approaches are demanded to discover underlying TRs which could be missed when only single source of information is considered. In this paper, we explore the biological ideas behind co-regulated protein complexes to study this problem. Co-regulated protein complex has three remarkable characteristics: coding genes of member proteins share the same transcription factor, coding genes usually express coordinately and member proteins intensively interact and form a complex to implement a common biological function. It implies close relationships among co-regulation, co-expression and intensive interaction at the levels of transcriptional regulation, gene expression and protein-protein interaction. Based on these ideas, we integrate protein-protein interaction (PPI), gene expression (GE) and transcriptional interaction (TI) data and use them to form a framework to discover new Tr relationships. Experiments on the yeast in three conditions of cell cycle, diauxic shift and DNA damaging were conducted, and 20 novel TRs were predicted and explained.
Transcription Regulation Gene Ezpression Protein-Protein Interaction
Fei Luo Jinyan Li
School of Computer Engineering,Nanyang Technological University,Singapore
国际会议
The 3rd International Symposium on Optimization and System Biology(第三届最优化与系统生物学国际会议 OSB09)
张家界
英文
109-116
2009-09-20（万方平台首次上网日期，不代表论文的发表时间）