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 gene´s 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.