title: Indirect role of microRNAs and transcription factors in the regulation of important cancer genes: A network biology approach.
abstract: Cancer is one of the leading causes of death worldwide. Although the mechanisms of gene regulation in cancer have been the subject of intense investigation during the last decades, the precise role of regulatory processes in cancer is largely unknown. More specifically, it is not completely understood how microRNAs and transcription factors regulate and influence the cancer-related processes. In the present study, using cancer-specific biological networks we examine the role of microRNAs and transcription factors (TFs) in regulation of important cancer genes. The importance measures which are used in this study consider both network structure information and biological data on miRNA- and TF-based gene regulation. By analyzing cancer-specific PPI, signaling and metabolic networks, it was shown that microRNAs and transcription factors tend to regulate those genes which are in the neighborhood of important components of cancer-specific PPI, signaling, and metabolic networks. The role of microRNAs was found to be particularly important, which confirms our previously-published results on the importance of microRNAs in detecting important network components. Moreover, we highlight that the miRNAs appear to apply their function via regulating the "neighbors" of important cancer genes, which implies their indirect role in cancer, and presumably, in fine-tuning the effect of other cancer-related genes.
authors.affiliation: University of Tehran Institute of Biochemistry and Biophysics Tehran Iran.
authors.forename: M
authors.initials: M
authors.lastname: Ahmadi
authors.affiliation: Tarbiat Modares University Department of Nanobiotechnology, Faculty of Biological Sciences Tehran Iran.
authors.forename: R
authors.initials: R
authors.lastname: Jafari
authors.affiliation: University of Tehran Department of Biotechnology, College of Science Tehran Iran marashi&commat;ut.ac.ir.
authors.forename: S A
authors.initials: SA
authors.lastname: Marashi
authors.affiliation: University of Tehran School of Biology, College of Science Tehran Iran afarazmand&commat;khayam.ut.ac.ir.
authors.forename: A
authors.initials: A
authors.lastname: Farazmand
mesh_terms: D000818:Animals; D015972:Gene Expression Regulation, Neoplastic; D053263:Gene Regulatory Networks; D006801:Humans; D035683:MicroRNAs / Q000235:genetics / Q000378:metabolism*; D009154:Mutation; D009369:Neoplasms / Q000235:genetics*; D012984:Software; D014157:Transcription Factors / Q000235:genetics / Q000378:metabolism*
chemical_list: D035683:MicroRNAs; D014157:Transcription Factors