title: ToxDBScan: Large-scale similarity screening of toxicological databases for drug candidates.
abstract: We present a new tool for hepatocarcinogenicity evaluation of drug candidates in rodents. ToxDBScan is a web tool offering quick and easy similarity screening of new drug candidates against two large-scale public databases, which contain expression profiles for substances with known carcinogenic profiles: TG-GATEs and DrugMatrix. ToxDBScan uses a set similarity score that computes the putative similarity based on similar expression of genes to identify chemicals with similar genotoxic and hepatocarcinogenic potential. We propose using a discretized representation of expression profiles, which use only information on up- or down-regulation of genes as relevant features. Therefore, only the deregulated genes are required as input. ToxDBScan provides an extensive report on similar compounds, which includes additional information on compounds, differential genes and pathway enrichments. We evaluated ToxDBScan with expression data from 15 chemicals with known hepatocarcinogenic potential and observed a sensitivity of 88 Based on the identified chemicals, we achieved perfect classification of the independent test set. ToxDBScan is publicly available from the ZBIT Bioinformatics Toolbox.
authors.affiliation: Center of Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72074, Germany. michael.roemer@uni-tuebingen.de.
authors.forename: Michael
authors.initials: M
authors.lastname: Römer
authors.affiliation: Center of Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72074, Germany. backert@informatik.uni-tuebingen.de.
authors.forename: Linus
authors.initials: L
authors.lastname: Backert
authors.affiliation: Center of Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72074, Germany. johannes.eichner@uni-tuebingen.de.
authors.forename: Johannes
authors.initials: J
authors.lastname: Eichner
authors.affiliation: Center of Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72074, Germany. andreas.zell@uni-tuebingen.de.
authors.forename: Andreas
authors.initials: A
authors.lastname: Zell
mesh_terms: D000818:Animals; D002273:Carcinogens / Q000633:toxicity*; D019295:Computational Biology / Q000379:methods; D016208:Databases, Factual; D015536:Down-Regulation / Q000187:drug effects; D004353:Drug Evaluation, Preclinical / Q000379:methods; D020869:Gene Expression Profiling / Q000379:methods; D008113:Liver Neoplasms / Q000139:chemically induced* / Q000235:genetics; D012377:Rodentia; D059467:Transcriptome / Q000187:drug effects / Q000235:genetics; D015854:Up-Regulation / Q000187:drug effects / Q000235:genetics
chemical_list: D002273:Carcinogens