Gene ontology (GO) and phylogenic similarity as approaches to functional module prediction have been explored by [20]. This work is based on the hypothesis that a pair of genes with high GO or phylogenic similarity score is likely in the same functional module (operon or regulon). In this study, we extend their work to include gene expression analysis, and focus on TRN construction. We show that GO and phylogenic similarity can be used to greatest advantage if they are based on a gene/TF interaction model.