title: A gene browser of colorectal cancer with literature evidence and pre-computed regulatory information to identify key tumor suppressors and oncogenes.
abstract: Colorectal cancer (CRC) is a cancer of growing incidence that associates with a high mortality rate worldwide. There is a poor understanding of the heterogeneity of CRC with regard to causative genetic mutations and gene regulatory mechanisms. Previous studies have identified several susceptibility genes in small-scale experiments. However, the information has not been comprehensively and systematically compiled and interpreted. In this study, we constructed the gbCRC, the first literature-based gene resource for investigating CRC-related human genes. The features of our database include: (i) manual curation of experimentally-verified genes reported in the literature; (ii) comprehensive integration of five reliable data sources; and (iii) pre-computed regulatory patterns involving transcription factors, microRNAs and long non-coding RNAs. In total, 2067 genes associating with 2819 PubMed abstracts were compiled. Comprehensive functional annotations associated with all the genes, including gene expression profiles, homologous genes in other model species, protein-protein interactions, somatic mutations, and potential methylation sites. These comprehensive annotations and this pre-computed regulatory information highlighted the importance of the gbCRC with regard to the unexplored regulatory network of CRC. This information is available in a plain text format that is free to download.
authors.affiliation: School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia.
authors.forename: Min
authors.initials: M
authors.lastname: Zhao
authors.affiliation: School of Engineering, Faculty of Science, Health, Education and Engineering, University of the Sunshine Coast, Maroochydore DC, Queensland 4558, Australia.
authors.forename: Yining
authors.initials: Y
authors.lastname: Liu
authors.affiliation: Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, P.R. China.
authors.forename: Fuda
authors.initials: F
authors.lastname: Huang
authors.affiliation: Center for Bioinformatics, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, P.R. China.
authors.forename: Hong
authors.initials: H
authors.lastname: Qu
mesh_terms: D015179:Colorectal Neoplasms / Q000235:genetics* / Q000473:pathology*; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D016147:Genes, Tumor Suppressor; D006801:Humans; D009857:Oncogenes; D057089:Pathology, Molecular / Q000379:methods*