Algorithm to identify frequent coupled modules from two-layered network series: application to study transcription and splicing coupling.
Current network analysis methods all focus on one or multiple networks of the same type. However, cells are organized by multi-layer networks (e.g., transcriptional regulatory networks, splicing regulatory networks, protein-protein interaction networks), which interact and influence each other. Elucidating the coupling mechanisms among those different types of networks is essential in understanding the functions and mechanisms of cellular activities. In this article, we developed the first computational method for pattern mining across many two-layered graphs, with the two layers representing different types yet coupled biological networks. We formulated the problem of identifying frequent coupled clusters between the two layers of networks into a tensor-based computation problem, and proposed an efficient solution to solve the problem. We applied the method to 38 two-layered co-transcription and co-splicing networks, derived from 38 RNA-seq datasets. With the identified atlas of coupled transcription-splicing modules, we explored to what extent, for which cellular functions, and by what mechanisms transcription-splicing coupling takes place.
Program in Computational Biology, Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
Wenyuan
W
Li
Chao
C
Dai
Chun-Chi
CC
Liu
Xianghong Jasmine
XJ
Zhou
D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D057225:Data Mining; D030561:Databases, Nucleic Acid; D053263:Gene Regulatory Networks; D006801:Humans; D060066:Protein Interaction Maps; D012326:RNA Splicing; D014158:Transcription, Genetic