Differential network analysis for the identification of condition-specific pathway activity and regulation

• DOI: 10.1093/bioinformatics/btt290
• Publication Date: 2013-06-08T01:09:41Z
• Authors: Gennaro Gambardella; Maria Nicoletta M...; Rossella de Cegli; Luca Cardone; Adriano Peron; Diego di Bernardo
• Keywords: Gene regulatory network; Identification; Biological pathway; Metabolic pathway

Abstract Motivation: Identification of differential expressed genes has led to countless new discoveries. However, differentially are only a proxy for finding dysregulated pathways. The problem is identify how the network regulatory and physical interactions rewires in different conditions or disease. Results: We developed procedure named DINA (DIfferential Network Analysis), which able set genes, whose co-regulation condition-specific, starting from collection condition-specific gene expression profiles. also predict transcription factors (TFs) may be responsible pathway co-regulation. derived 30 tissue-specific networks human identified several metabolic pathways as most regulated across tissues. correctly TFs such Nuclear Receptors their main regulators demonstrated that with unknown function (YEATS2) acts negative regulator hepatocyte metabolism. Finally, we showed can used make hypotheses on during disease progression. By analyzing profiles primary transformed hepatocytes, hepatocarcinoma-specific transcriptional dysregulation. Availability: implemented an on-line web-tool http://dina.tigem.it enabling user apply signatures. Contact: [e-mail] Supplementary information: data available at Bioinformatics online.