1. Definitions Transcriptional Modules (TM) are groups of co-regulated genes and transcription factors regulating their expression –Basic building blocks of transcriptional networks –Higher organizational level of functionally related genes

2. DATA – Expression, ChIP-chip experiments and PWM scores Gene expression Array1 Array2 … ArrayN Gene Expression Measurements Gene1 Gene2 Gene3. GeneT ChIP - chip Tf1 Tf2 … TfM ChIP - chip P-values PWM Tf1 Tf2 … TfP PWM Scores

3. Context-Specific Infinite Bayesian Mixtures for Gene Expression, ChIP-chip Data and PWM Scores Y C B p(C|)p(C|) p(|)p(|) p(X|C,)p(X|C,) X Clustering p(Y|C,B)p(Y|C,B)   p(L|a) a L   p(B|)p(B|) Z R p(Z|C,R)p(Z|C,R)  p(B|)p(B|) Posterior pairwise probability of co-regulation Posterior probability of binding

4. Visualizing Transcriptional Modules

5. From Transcriptional Modules To Transcriptional Regulatory Networks First gene-expression then ChIP-chip Joint gene-expression and ChIP-chip analysis

6. Integrative Characterization of Transcriptional Modules Constructing Concept Maps Characterizing protein interactions within and between modules http://polyview.cchmc.org/polyview3d_new.html http://polyview.cchmc.org/polyview3d_new.html