报告题目: Incorporating motif analysis into gene co-expression networks reveals novel modular expression pattern and new signaling pathways

　　报 告 人: Dr. Shisong Ma, Section of Plant Biology, University of California, Davis

　　报告时间: 2013年12月19日(星期四), 上午9:00

　　报告地点: 遗传发育所1号楼B210报告厅

　　联系人：焦雨铃（64807656）

　　摘要：

　　Understanding of gene regulatory networks requires discovery of expression modules within gene co-expression networks and identification of promoter motifs and corresponding transcription factors that regulate their expression. Here, we describe a novel bottom-up approach to identify gene expression modules driven by known cis-regulatory motifs in the gene promoters. For a specific motif, genes in the co-expression network are ranked according to their probability of belonging to an expression module regulated by that motif. The ranking is conducted via motif enrichment or motif position bias analysis. Sub-networks containing the top ranked genes are extracted and analyzed for inherent gene expression modules. This approach identified novel expression modules for the G-box, W-box, site II, and MYB motifs from an Arabidopsis thaliana gene co-expression network based on the graphical Gaussian model. The novel expression modules include those involved in house-keeping functions, primary and secondary metabolism, and abiotic and biotic stress responses. To associate transcription factors that regulate genes in these co-expression modules, we developed a novel reporter system. Using this approach, we evaluated MYB transcription factor-promoter interactions within MYB motif modules. At the same tim, plant protein microarrays were also developed and employed to probe for protein interactions between transcription factors. These interactions might be important for regulating TF activities.