Transcriptional regulatory network discovery via multiple method integration: application to e. coli K12

Motivation: Transcriptional regulatory network (TRN) discovery from one method (e.g. microarray analysis, gene ontology, phylogenic similarity) does not seem feasible due to lack of sufficient information, resulting in the construction of spurious or incomplete TRNs. We develop a methodology, TRND, that integrates a preliminary TRN, microarray data, gene ontology and phylogenic similarity to accurately discover TRNs and apply the method to E.coli K12. The approach can easily be extended to include other methodologies. Results: Although gene ontology and phylogenic similarity have been used in the context of gene-gene networks, we show that more information can be extracted when gene-gene scores are transformed to gene-transcription factor (TF) scores using a preliminary TRN. This seems to be preferable over the construction of genegene interaction networks in light of the observed fact that gene expression and activity of a TF made of a component encoded by that gene is often out of p...

• Type: Journal
• Year: 2007
• Where: ALMOB
• Authors: Jingjun Sun, Kagan Tuncay, Alaa Abi Haidar, Lisa Ensman, Frank Stanley, Michael Trelinski, Peter J. Ortoleva
• Keywords: ALMOB 2007, Gene Ontology, Phylogenic Similarity, Preliminary Trn