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Theoretical Biology and Medical Modelling

, 6:12

First Online: 03 July 2009Received: 10 October 2008Accepted: 03 July 2009DOI: 10.1186-1742-4682-6-12

Cite this article as: Andersson, L., Petersen, G. & Ståhl, F. Theor Biol Med Model 2009 6: 12. doi:10.1186-1742-4682-6-12

Abstract

BackgroundRat models are frequently used to find genomic regions that contribute to complex diseases, so called quantitative trait loci QTLs. In general, the genomic regions found to be associated with a quantitative trait are rather large, covering hundreds of genes. To help selecting appropriate candidate genes from QTLs associated with type 2 diabetes models in rat, we have developed a web tool called Candidate Gene Capture CGC, specifically adopted for this disorder.

MethodsCGC combines diabetes-related genomic regions in rat with rat-human homology data, textual descriptions of gene effects and an array of 789 keywords. Each keyword is assigned values that reflect its co-occurrence with 24 different reference terms describing sub-phenotypes of type 2 diabetes for example -insulin resistance-. The genes are then ranked based on the occurrences of keywords in the describing texts.

ResultsCGC includes QTLs from type 2 diabetes models in rat. When comparing gene rankings from CGC based on one sub-phenotype, with manual gene ratings for four QTLs, very similar results were obtained. In total, 24 different sub-phenotypes are available as reference terms in the application and based on differences in gene ranking, they fall into separate clusters.

ConclusionThe very good agreement between the CGC gene ranking and the manual rating confirms that CGC is as a reliable tool for interpreting textual information. This, together with the possibility to select many different sub-phenotypes, makes CGC a versatile tool for finding candidate genes. CGC is publicly available at http:-ratmap.org-CGC.

Electronic supplementary materialThe online version of this article doi:10.1186-1742-4682-6-12 contains supplementary material, which is available to authorized users.

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Author: Lars Andersson - Greta Petersen - Fredrik Ståhl

Source: https://link.springer.com/







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