eQED: an efficient method for interpreting eQTL associations using protein networks.

TitleeQED: an efficient method for interpreting eQTL associations using protein networks.
Publication TypeJournal Article
Year of Publication2008
AuthorsSuthram S, Beyer A, Karp RM, Eldar Y, Ideker T
JournalMol Syst Biol
Volume4
Pagination162
Date Published2008
ISSN1744-4292
KeywordsAnimals, Computational Biology, Fungal Proteins, Genotype, Humans, Linkage Disequilibrium, Models, Genetic, Models, Statistical, Oligonucleotide Array Sequence Analysis, Phenotype, Protein Interaction Mapping, Proteins, Quantitative Trait Loci, Reproducibility of Results, Systems Biology
Abstract

Analysis of expression quantitative trait loci (eQTLs) is an emerging technique in which individuals are genotyped across a panel of genetic markers and, simultaneously, phenotyped using DNA microarrays. Because of the spacing of markers and linkage disequilibrium, each marker may be near many genes making it difficult to finely map which of these genes are the causal factors responsible for the observed changes in the downstream expression. To address this challenge, we present an efficient method for prioritizing candidate genes at a locus. This approach, called 'eQTL electrical diagrams' (eQED), integrates eQTLs with protein interaction networks by modeling the two data sets as a wiring diagram of current sources and resistors. eQED achieved a 79% accuracy in recovering a reference set of regulator-target pairs in yeast, which is significantly higher than the performance of three competing methods. eQED also annotates 368 protein-protein interactions with their directionality of information flow with an accuracy of approximately 75%.

DOI10.1038/msb.2008.4
PubMed URLhttp://www.ncbi.nlm.nih.gov/pubmed/18319721?dopt=Abstract
PMCPMC2290938
Alternate JournalMol. Syst. Biol.
PubMed ID18319721