Nelson, Ronald
- Department of Clinical Sciences, Swedish University of Agricultural Sciences
Abstract
Selection of candidate genes is an important step in the exploration of complex genetic architecture. The number of gene networks available is increasing and these can provide information to help with candidate gene selection. It is currently common to use the degree of connectedness in gene networks as validation in Genome Wide Association (GWA) and Quantitative Trait Locus (QTL) mapping studies. However, it can cause misleading results if not validated properly. Here we present a method and tool for validating the gene pairs from GWA studies given the context of the network they co-occur in. It ensures that proposed interactions and gene associations are not statistical artefacts inherent to the specific gene network architecture. The CandidateBacon package provides an easy and efficient method to calculate the average degree of separation (DoS) between pairs of genes to currently available gene networks. We show how these empirical estimates of average connectedness are used to validate candidate gene pairs. Validation of interacting genes by comparing their connectedness with the average connectedness in the gene network will provide support for said interactions by utilising the growing amount of gene network information available. (C) 2014 Elsevier Ltd. All rights reserved.
Keywords
Candidate genes; Network analysis; GWAS; Degree of separation; Gene-gene interaction
Published in
Computers in Biology and Medicine
2014, volume: 55, pages: 49-52
Publisher: PERGAMON-ELSEVIER SCIENCE LTD
SLU Authors
Pettersson, Mats
- Department of Clinical Sciences, Swedish University of Agricultural Sciences
- Department of Clinical Sciences, Swedish University of Agricultural Sciences
UKÄ Subject classification
Bioinformatics (Computational Biology)
Genetics and Genomics
Publication identifier
- DOI: https://doi.org/10.1016/j.compbiomed.2014.10.004
Permanent link to this page (URI)
https://res.slu.se/id/publ/67137