Protein melting curves were obtained from samples aliquoted in 96 well plates u

The CPS module is based on the assumption that com mon phenotypes are associated with proteins INK 128 溶解度 that partici pate in the same protein complex or biochemical pathway. Such systems biology methods are currently favored in candidate gene prediction because of the attractiveness of their basic thesis. Their weakness is the lack of coverage of the underlying systems biology knowledge bases. Many tools attempt to ameliorate the deficits of the human systems biology knowledge base by extensive extrapolation of data from other species. Examples are GeneSeeker, ToppGene and Endeavour. Gentrepid CPS uses only human data to reduce the num ber of predicted false positives i. e. it makes fewer predic tions which are more often correct compared to other prediction systems.<br><br> The other module, CMP, is a novel sequence analysis approach based on the principle that candidate genes have similar functions to disease genes already determined for the phenotype. KU-57788 溶解度 Gentrepid CMP differs from most candidate gene prediction systems which describe func tional similarity via keywords, a procedure which also lacks good coverage of the human genome. In CMP, sequences are parsed at the domain level, linking them directly to function. Although CMPs performance was disappointing in our original benchmark using a set of nine oligogenic diseases with Mendelian inheritance, it produced a surprising number of statistically significant results when confronted with the GWAS data on seven complex diseases. This result was robust when com pared with simulations using random SNPs, and may arise from an important underlying role for homologous genes in complex diseases.<br><br> Drug gene target data set We compiled the drug gene target data set from three publicly available drug databases, DrugBank, PharmGKB and TTD. Snapshots of these data bases were taken in June 2012. DrugBank is a freely available online database that combines detailed drug data and indication Linsitinib ic50 information with comprehensive drug target associations. From this database, we retrieved Drugbank IDs and drug names to represent drugs, and the unique gene symbols to represent protein targets. We extracted 6,711 drug entries active against 3,410 unique drug targets from several species. We used the G profiler conversion tool to separate human drug targets repre sented by official HUGO gene symbols, yielding 2,022 human drug targets associated with 3,910 drugs.<br><br> The Pharmacogenomics Knowledgebase is a drug knowledge base maintained by Stanford Uni versity, USA and funded by the US National Institute of Health. PharmGKB captures information about drugs, diseases phenotypes and targeted genes. From this database, we extracted the drug associated genes field along with description which contains the disease information. This database contains around 3,097 drugs and 26,961 human genes, but not all these genes are associated with drugs. We retrieved 382 drugs for 566 human drug targets. For the PharmGKB data base, the number of drug targets exceeds the number of drugs because some drugs target multiple genes. The Therapeutic Target Database is also a freely available online drug database which integrates drug data with therapeutic targets.