| Literature DB >> 24158600 |
Robert Hoehndorf1, Tanya Hiebert, Nigel W Hardy, Paul N Schofield, Georgios V Gkoutos, Michel Dumontier.
Abstract
MOTIVATION: Methods for computational drug target identification use information from diverse information sources to predict or prioritize drug targets for known drugs. One set of resources that has been relatively neglected for drug repurposing is animal model phenotype.Entities:
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Year: 2013 PMID: 24158600 PMCID: PMC3933875 DOI: 10.1093/bioinformatics/btt613
Source DB: PubMed Journal: Bioinformatics ISSN: 1367-4803 Impact factor: 6.937
Fig. 1.The figure illustrates our basic workflow and the connections between the different datasets we exploit. We aim to infer inhibition actions between drugs and their targets based on the similarity between drug effect profiles and mouse model phenotypes resulting from single gene knockouts. We test the hypothesis whether the phenotypic effects of a perturbation of a gene/protein through a drug action bears some similarity to the phenotypic effects of a targeted mutation of that gene/protein observed in a model organism. As drugs often perturb multiple genes/proteins, we systematically compute how well a drug effect profile covers observed phenotypes in a mouse model using a non-symmetrical measure of semantic similarity
Fig. 2.The ROC curves for our three evaluation datasets. DrugBank consists of experimentally verified and manually annotated drug-target interactions. STITCH integrates drug-target relations from multiple databases (including DrugBank), applies text mining and network-based inference approaches to infer drug-target relations. We used human–mouse orthology available from the MGI database to map human proteins in the DrugBank and STITCH (human) dataset to mouse proteins
The ROCAUC values we obtain for different protein families, including the 95% confidence interval
| InterPro family | ROCAUC (STITCH mouse) | ROCAUC (STITCH human) | ROCAUC (DrugBank) |
|---|---|---|---|
| G protein-coupled receptor, rhodopsin-like ( | |||
| Peptidase S1A, chymotrypsin-type ( | |||
| Steroid hormone receptor ( | |||
| Voltage-dependent potassium channel ( | |||
| Neurotransmitter-gated ion-channel ( | |||
| NAD(P)-binding domain ( |
Note: We only analyzed protein families with > 5 positive drug-target associations.
Fig. 3.ROCAUC values obtained for STITCH (human) and STITCH (mouse) drug-target interactions grouped by protein family. GPCR-A stands for G protein-coupled receptor, rhodopsin-like (IPR000276), S1A for Peptidase S1A, chymotrypsin-type (IPR001314, SHR for Steroid hormone receptor (IPR001723), VdPC for voltage-dependent potassium channel (IPR003091), NgIC for Neurotransmitter-gated ion-channel (IPR006201) and NADP for NAD(P)-binding domain (IPR016040)