Disease gene identification based on generic and disease-specific genome networks

SUMMARY: Immune diseases have a strong genetic component with Mendelian patterns of inheritance. While the tight association has been a major understanding in the underlying pathophysiology for the category of immune diseases, the common features of these diseases remain unclear. Based on the potential commonality among immune genes, we design Gene Ranker for key gene identification. Gene Ranker is a network-based gene scoring algorithm that initially constructs a backbone network based on protein interactions. Patient gene expression networks are added into the network. An add-on process screens the networks of weighted gene co-expression network analysis (WGCNA) on the samples of immune patients. Gene Ranker is disease-specific; however, any WGCNA network that passes the screening procedure can be added on. With the constructed network, it employs the semi-supervised learning for gene scoring. RESULTS: The proposed method was applied to immune diseases. Based on the resulting scores, Gene Ranker identified potential key genes in immune diseases. In scoring validation, an average area under the receiver operating characteristic curve of 0.82 was achieved, which is a significant increase from the reference average of 0.76. Highly ranked genes were verified through retrieval and review of 27 million PubMed literatures. As a typical case, 20 potential key genes in rheumatoid arthritis were identified: 10 were de facto genes and the remaining were novel. AVAILABILITY AND IMPLEMENTATION: Gene Ranker is available at http://www.alphaminers.net/GeneRanker/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.