title: ccmGDB: a database for cancer cell metabolism genes.
abstract: Accumulating evidence has demonstrated that rewiring of metabolism in cells is an important hallmark of cancer. The percentage of patients killed by metabolic disorder has been estimated to be 30% of the advanced-stage cancer patients. Thus, a systematic annotation of cancer cell metabolism genes is imperative. Here, we present ccmGDB (Cancer Cell Metabolism Gene DataBase), a comprehensive annotation database for cell metabolism genes in cancer, available at http://bioinfo.mc.vanderbilt.edu/ccmGDB. We assembled, curated, and integrated genetic, genomic, transcriptomic, proteomic, biological network and functional information for over 2000 cell metabolism genes in more than 30 cancer types. In total, we integrated over 260 000 somatic alterations including non-synonymous mutations, copy number variants and structural variants. We also integrated RNA-Seq data in various primary tumors, gene expression microarray data in over 1000 cancer cell lines and protein expression data. Furthermore, we constructed cancer or tissue type-specific, gene co-expression based protein interaction networks and drug-target interaction networks. Using these systematic annotations, the ccmGDB portal site provides 6 categories: gene summary, phenotypic information, somatic mutations, gene and protein expression, gene co-expression network and drug pharmacological information with a user-friendly interface for browsing and searching. ccmGDB is developed and maintained as a useful resource for the cancer research community.
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.
authors.forename: Pora
authors.initials: P
authors.lastname: Kim
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.
authors.forename: Feixiong
authors.initials: F
authors.lastname: Cheng
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA.
authors.forename: Junfei
authors.initials: J
authors.lastname: Zhao
authors.affiliation: Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN 37203, USA Department of Cancer Biology, Vanderbilt University School of Medicine, Nashville, TN 37232, USA Department of Psychiatry, Vanderbilt University School of Medicine, Nashville, TN 37212, USA zhongming.zhao@vanderbilt.edu.
authors.forename: Zhongming
authors.initials: Z
authors.lastname: Zhao
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D030541:Databases, Genetic; D015870:Gene Expression; D053263:Gene Regulatory Networks; D052138:Genes, Neoplasm; D023281:Genomics; D006801:Humans; D008660:Metabolism / Q000235:genetics; D058977:Molecular Sequence Annotation; D009154:Mutation; D009363:Neoplasm Proteins / Q000378:metabolism; D009369:Neoplasms / Q000235:genetics* / Q000378:metabolism*; D040901:Proteomics
chemical_list: D000970:Antineoplastic Agents; D009363:Neoplasm Proteins