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Int. J. Mol. Sci. 2014, 15(10), 19037-19055; doi:10.3390/ijms151019037

ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases for Drug Candidates

Center of Bioinformatics Tuebingen (ZBIT), University of Tuebingen, Tübingen 72074, Germany
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Received: 28 August 2014 / Revised: 5 September 2014 / Accepted: 25 September 2014 / Published: 21 October 2014
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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. View Full-Text
Keywords: TG-GATEs; DrugMatrix; carcinogenic; toxicogenomics; mRNA; microarrays; drug discovery; visualization; similarity; web application TG-GATEs; DrugMatrix; carcinogenic; toxicogenomics; mRNA; microarrays; drug discovery; visualization; similarity; web application
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This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. (CC BY 4.0).

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MDPI and ACS Style

Römer, M.; Backert, L.; Eichner, J.; Zell, A. ToxDBScan: Large-Scale Similarity Screening of Toxicological Databases for Drug Candidates. Int. J. Mol. Sci. 2014, 15, 19037-19055.

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