Identification of functional modules based on transcriptional regulation structure

Identifying gene functional modules is an important step towards elucidating gene functions at a global scale. Clustering algorithms mostly rely on co-expression of genes, that is group together genes having similar expression profiles.

We propose to cluster genes by co-regulation rather than by co-expression. We therefore present an inference algorithm for detecting co-regulated groups from gene expression data and introduce a method to cluster genes given that inferred regulatory structure. Finally, we propose to validate the clustering through a score based on the GO enrichment of the obtained groups of genes.

We evaluate the methods on the stress response of S. Cerevisiae data and obtain better scores than clustering obtained directly from gene expression.