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. The eQTL technology is potentially very powerful, as it allows searching for transcriptional regulators for all genes probed on a microarray. However, a range of experimental and statistical problems compromise the interpretation of the results. Existing eQTL detection techniques search for only one correlated marker at a time. We propose models explicitly taking into account combinatorial effects of several regulators. 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. 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.