title: Prediction of potential cancer-risk regions based on transcriptome data: towards a comprehensive view.
abstract: A novel integrative pipeline is presented for discovery of potential cancer-susceptibility regions (PCSRs) by calculating the number of altered genes at each chromosomal region, using expression microarray datasets of different human cancers (HCs). Our novel approach comprises primarily predicting PCSRs followed by identification of key genes in these regions to obtain potential regions harboring new cancer-associated variants. In addition to finding new cancer causal variants, another advantage in prediction of such risk regions is simultaneous study of different types of genomic variants in line with focusing on specific chromosomal regions. Using this pipeline we extracted numbers of regions with highly altered expression levels in cancer condition. Regulatory networks were also constructed for different types of cancers following the identification of altered mRNA and microRNAs. Interestingly, results showed that GAPDH, LIFR, ZEB2, mir-21, mir-30a, mir-141 and mir-200c, all located at PCSRs, are common altered factors in constructed networks. We found a number of clusters of altered mRNAs and miRNAs on predicted PCSRs (e.g.12p13.31) and their common regulators including KLF4 and SOX10. Large scale prediction of risk regions based on transcriptome data can open a window in comprehensive study of cancer risk factors and the other human diseases.
authors.affiliation: Department of Plant Breeding and Biotechnology, University of Shahrekord, Shahrekord, Iran.
authors.forename: Arghavan
authors.initials: A
authors.lastname: Alisoltani
authors.affiliation: Department of Biology, School of Sciences, Razi University, Kermanshah, Iran.
authors.forename: Hossein
authors.initials: H
authors.lastname: Fallahi
authors.affiliation: Department of Informatics, Saarland University, Saarbrucken, Germany.
authors.forename: Mahdi
authors.initials: M
authors.lastname: Ebrahimi
authors.affiliation: Bioinformatics Research Group and Department of Biology, University of Qom, Qom, Iran.
authors.forename: Mansour
authors.initials: M
authors.lastname: Ebrahimi
authors.affiliation: School of Molecular and Biomedical Science, The University of Adelaide, Adelaide, Australia.
authors.forename: Esmaeil
authors.initials: E
authors.lastname: Ebrahimie
mesh_terms: D002877:Chromosomes, Human; D020869:Gene Expression Profiling; D053263:Gene Regulatory Networks; D020022:Genetic Predisposition to Disease; D006801:Humans; D000090062:Kruppel-Like Factor 4; D035683:MicroRNAs; D009369:Neoplasms / Q000235:genetics*; D011401:Promoter Regions, Genetic; D012307:Risk Factors
chemical_list: C000715467:KLF4 protein, human; D000090062:Kruppel-Like Factor 4; D035683:MicroRNAs