CisModule swMATH ID: 35646 Software Authors: Zhou, Q.; Wong, W.H Description: CisModule: A Bayesian module sampler by hierachical mixture modeling. CisModule: De novo discovery of cis-regulatory modules by hierarchical mixture modeling. The regulatory information for a eukaryotic gene is encoded in cis-regulatory modules. The binding sites for a set of interacting transcription factors have the tendency to colocalize to the same modules. Current de novo motif discovery methods do not take advantage of this knowledge. We propose a hierarchical mixture approach to model the cis-regulatory module structure. Based on the model, a new de novo motif-module discovery algorithm, CisModule, is developed for the Bayesian inference of module locations and within-module motif sites. Dynamic programming-like recursions are developed to reduce the computational complexity from exponential to linear in sequence length. By using both simulated and real data sets, we demonstrate that CisModule is not only accurate in predicting modules but also more sensitive in detecting motif patterns and binding sites than standard motif discovery methods are. Homepage: http://www.stat.ucla.edu/%7Ezhou/CisModule/ Related Software: BioProspector; MCFDR; TRANSFAC; R; tsbridge; CATS; PhyME; TileMap; PipMaker Cited in: 4 Documents all top 5 Cited by 12 Authors 2 Wong, Wing Hung 1 Bickel, Peter John 1 Boley, Nathan 1 Brown, James B. 1 Ferkingstad, Egil 1 Holden, Lars 1 Huang, Haiyan 1 Ji, Hongkai 1 Kou, S. C. 1 Sandve, Geir Kjetil 1 Zhang, Nancy Ruonan 1 Zhou, Qing Cited in 4 Serials 1 The Annals of Statistics 1 Biometrics 1 Statistical Science 1 The Annals of Applied Statistics Cited in 5 Fields 4 Statistics (62-XX) 3 Biology and other natural sciences (92-XX) 2 Numerical analysis (65-XX) 1 Statistical mechanics, structure of matter (82-XX) 1 Information and communication theory, circuits (94-XX) Citations by Year