title: TARGETgene: a tool for identification of potential therapeutic targets in cancer.
abstract: The vast array of in silico resources and data of high throughput profiling currently available in life sciences research offer the possibility of aiding cancer gene and drug discovery process. Here we propose to take advantage of these resources to develop a tool, TARGETgene, for efficiently identifying mutation drivers, possible therapeutic targets, and drug candidates in cancer. The simple graphical user interface enables rapid, intuitive mapping and analysis at the systems level. Users can find, select, and explore identified target genes and compounds of interest (e.g., novel cancer genes and their enriched biological processes), and validate predictions using user-defined benchmark genes (e.g., target genes detected in RNAi screens) and curated cancer genes via TARGETgene. The high-level capabilities of TARGETgene are also demonstrated through two applications in this paper. The predictions in these two applications were then satisfactorily validated by several ways, including known cancer genes, results of RNAi screens, gene function annotations, and target genes of drugs that have been used or in clinical trial in cancer treatments. TARGETgene is freely available from the Biomedical Simulations Resource web site (http://bmsr.usc.edu/Software/TARGET/TARGET.html).
authors.affiliation: Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America. perwu777@gmail.com
authors.forename: Chia-Chin
authors.initials: CC
authors.lastname: Wu
authors.forename: David
authors.initials: D
authors.lastname: D'Argenio
authors.forename: Shahab
authors.initials: S
authors.lastname: Asgharzadeh
authors.forename: Timothy
authors.initials: T
authors.lastname: Triche
mesh_terms: D000970:Antineoplastic Agents / Q000494:pharmacology; D015415:Biomarkers / Q000378:metabolism; D001943:Breast Neoplasms / Q000188:drug therapy; D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D015195:Drug Design; D015894:Genome, Human; D023281:Genomics / Q000379:methods; D006801:Humans; D009369:Neoplasms / Q000235:genetics* / Q000628:therapy*; D010641:Phenotype; D040901:Proteomics / Q000379:methods; D034622:RNA Interference; D012372:ROC Curve; D012984:Software; D049490:Systems Biology
chemical_list: D000970:Antineoplastic Agents; D015415:Biomarkers