multi-species integrative biclustering综合biclustering大型化.pdfVIP

Waltman et al. Genome Biology 2010, 11:R96 /2010/11/9/R96 METHOD Open Access Multi-species integrative biclustering 1,2† 3† 3 4 5 3* Peter Waltman , Thadeous Kacmarczyk , Ashley R Bate , Daniel B Kearns , David J Reiss , Patrick Eichenberger , Richard Bonneau1,2,3* Abstract We describe an algorithm, multi-species cMonkey, for the simultaneous biclustering of heterogeneous multiple- species data collections and apply the algorithm to a group of bacteria containing Bacillus subtilis, Bacillus anthracis, and Listeria monocytogenes. The algorithm reveals evolutionary insights into the surprisingly high degree of conser- vation of regulatory modules across these three species and allows data and insights from well-studied organisms to complement the analysis of related but less well studied organisms. Background methods that require genes to participate in mutually The rapidly increasing volume of genome scale data has exclusive clusters, such as hierarchical agglomerative enabled global regulatory network inference and gen- clustering [1], k-means clustering [2] and singular value ome-wide prediction of gene function within single decomposition derived methods [3-5]. Because most organisms. In this work, we exploit another advantage genes are unlikely to be co-regulated under every possi- of the growing quantity of genomics data: by comparing ble condition (for instance, bacterial genes can have genome-wide datasets for closely related organisms, we more