title: Identifying novel genes and chemicals related to nasopharyngeal cancer in a heterogeneous network.
abstract: Nasopharyngeal cancer or nasopharyngeal carcinoma (NPC) is the most common cancer originating in the nasopharynx. The factors that induce nasopharyngeal cancer are still not clear. Additional information about the chemicals or genes related to nasopharyngeal cancer will promote a better understanding of the pathogenesis of this cancer and the factors that induce it. Thus, a computational method NPC-RGCP was proposed in this study to identify the possible relevant chemicals and genes based on the presently known chemicals and genes related to nasopharyngeal cancer. To extensively utilize the functional associations between proteins and chemicals, a heterogeneous network was constructed based on interactions of proteins and chemicals. The NPC-RGCP included two stages: the searching stage and the screening stage. The former stage is for finding new possible genes and chemicals in the heterogeneous network, while the latter stage is for screening and removing false discoveries and selecting the core genes and chemicals. As a result, five putative genes, CXCR3, IRF1, CDK1, GSTP1, and CDH2, and seven putative chemicals, iron, propionic acid, dimethyl sulfoxide, isopropanol, erythrose 4-phosphate, β-D-Fructose 6-phosphate, and flavin adenine dinucleotide, were identified by NPC-RGCP. Extensive analyses provided confirmation that the putative genes and chemicals have significant associations with nasopharyngeal cancer.
authors.affiliation: College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun, China.
authors.forename: Zhandong
authors.initials: Z
authors.lastname: Li
authors.affiliation: Department of Otorhinolaryngology and Head &Neck, China-Japan Union Hospital attached to Jilin University, Changchun, China.
authors.forename: Lifeng
authors.initials: L
authors.lastname: An
authors.affiliation: College of Biology and Food Engineering, Jilin Engineering Normal University, Changchun, China.
authors.forename: Hao
authors.initials: H
authors.lastname: Li
authors.affiliation: School of Life Sciences, Shanghai University, Shanghai, China.
authors.forename: ShaoPeng
authors.initials: S
authors.lastname: Wang
authors.affiliation: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences &Shanghai Jiao Tong University School of Medicine, Shanghai, China.
authors.forename: You
authors.initials: Y
authors.lastname: Zhou
authors.affiliation: Institute of Health Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences &Shanghai Jiao Tong University School of Medicine, Shanghai, China.
authors.forename: Fei
authors.initials: F
authors.lastname: Yuan
authors.affiliation: Department of Otorhinolaryngology and Head &Neck, China-Japan Union Hospital attached to Jilin University, Changchun, China.
authors.forename: Lin
authors.initials: L
authors.lastname: Li
mesh_terms: D019840:2-Propanol / Q000633:toxicity; D015703:Antigens, CD / Q000235:genetics / Q000378:metabolism; D016203:CDC2 Protein Kinase / Q000235:genetics / Q000378:metabolism; D015820:Cadherins / Q000235:genetics / Q000378:metabolism; D002277:Carcinoma / Q000139:chemically induced / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D019295:Computational Biology / Q000379:methods*; D004121:Dimethyl Sulfoxide / Q000633:toxicity; D005182:Flavin-Adenine Dinucleotide / Q000633:toxicity; D005636:Fructosephosphates / Q000633:toxicity; D020869:Gene Expression Profiling; D015972:Gene Expression Regulation, Neoplastic; D059647:Gene-Environment Interaction; D051549:Glutathione S-Transferase pi / Q000235:genetics / Q000378:metabolism; D006801:Humans; D050856:Interferon Regulatory Factor-1 / Q000235:genetics / Q000378:metabolism; D007501:Iron / Q000633:toxicity; D000077274:Nasopharyngeal Carcinoma; D009303:Nasopharyngeal Neoplasms / Q000139:chemically induced / Q000235:genetics* / Q000378:metabolism / Q000473:pathology; D009305:Nasopharynx / Q000187:drug effects* / Q000378:metabolism / Q000473:pathology; D011422:Propionates / Q000633:toxicity; D054367:Receptors, CXCR3 / Q000235:genetics / Q000378:metabolism; D013403:Sugar Phosphates / Q000633:toxicity
chemical_list: D015703:Antigens, CD; C050361:CDH2 protein, human; C515187:CXCR3 protein, human; D015820:Cadherins; D005636:Fructosephosphates; C494257:IRF1 protein, human; D050856:Interferon Regulatory Factor-1; D011422:Propionates; D054367:Receptors, CXCR3; D013403:Sugar Phosphates; D005182:Flavin-Adenine Dinucleotide; C026959:erythrose 4-phosphate; C027618:fructose-6-phosphate; D007501:Iron; C496556:GSTP1 protein, human; D051549:Glutathione S-Transferase pi; D016203:CDC2 Protein Kinase; C528899:CDK1 protein, human; C029658:propionic acid; D019840:2-Propanol; D004121:Dimethyl Sulfoxide