Ranking candidate genes in rat models of type 2 diabetes.

Full Abstract

BACKGROUND: Rat 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. METHODS: CGC 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. RESULTS: CGC 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. CONCLUSION: The 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.

Author information

Author/s: Andersson, Lars (L); Petersen, Greta (G); Ståhl, Fredrik (F);

Affiliation: Department of Cell and Molecular Biology-Genetics, Göteborg University, Box 462, SE40530 Göteborg, Sweden. lars.andersson(-atsign-)gen.gu.se

Journal and publication information

Publication Type: Comparative Study; Evaluation Studies; Journal Article; Research Support, Non-U.S. Gov't

Journal: Theoretical biology & medical modelling (Theor Biol Med Model), published in England. (Language: eng)

Reference: 2009-; vol 6 (issue ) : pp 12

Dates: Created 2009/07/15; Completed 2009/10/01;

PMID: 19575795, status: MEDLINE (last retrieved date: 10/1/2009)

Sourced from the National Library of Medicine. Abstract text and other information may be subject to copyright.

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