Maximum-clique Algorithm: an Effective Method to Mine Large-scale Co-expressed Genes in Arabidopsis Anther
Beyond the co-expression knowledge between two genes, investigating the co-expression relationships among multiple target genes is more informative for understanding the basic working mechanisms in a cell. In this paper, all the Arabidopsis anther genes and every genes potential co-expressed partners were collected by cross-database search. By combining simple pair gene co-expression networks, a complex Arabidopsis anther co-expression network is constructed. Maximum-clique algorithm is then applied to mine the groups reflecting co-expression relationships among multiple Arabidopsis anther genes that are represented by fully connected graphs. As a result, 254 Arabidopsis anther co-expression groups are obtained and our analysis shows that all the genes in the same group have very high propensity to be functionally related and co-expressed together. We also demonstrate the efficacy of the proposed Maximum-clique algorithm by comparing its results with the known Arabidopsis genome pathways, K-means clustering algorithm derived results and randomized data. It is expected that the 254 Arabidopsis anther co-expression groups generated in this paper can be a valuable knowledge source for further studies of molecular mechanisms of anther and its transcription regulations.
JIAO Qing-Ju SHEN Hong-Bin
Department of Automation, Shanghai Jiao Tong University, and Key Laboratory of system Control and Information Processing, Ministry of Education of China, Shanghai 200240, P.R.China
国际会议
The 30th Chinese Control Conference(第三十届中国控制会议)
烟台
英文
1-6
2011-07-01（万方平台首次上网日期，不代表论文的发表时间）