Skip to main content
Article thumbnail
Location of Repository

POEM: Identifying joint additive effects on regulatory circuits

By Maya eBotzman, Aharon eNachshon, Avital eBrodt and Irit eGat-Viks


Motivation: Expression Quantitative Trait Locus (eQTL) mapping tackles the problem of identifying variation in DNA sequence that have an effect on the transcriptional regulatory network. Major computational efforts are aimed at characterizing the joint effects of several eQTLs acting in concert to govern the expression of the same genes. Yet, progress towards a comprehensive prediction of such joint effects is limited. For example, existing eQTL methods commonly discover interacting loci affecting the expression levels of a module of co-regulated genes. Such ‘modularization’ approaches, however, are focused on epistatic relations and thus have limited utility for the case of additive (non-epistatic) effects.Results: Here we present POEM (Pairwise effect On Expression Modules), a methodology for identifying pairwise eQTL effects on gene modules. POEM is specifically designed to achieve high performance in the case of additive joint effects. We applied POEM to transcription profiles measured in bone marrow-derived dendritic cells across a population of genotyped mice. Our study reveals widespread additive, trans-acting pairwise effects on gene modules, characterizes their organizational principles, and highlights high-order interconnections between modules within the immune signaling network. These analyses elucidate the central role of additive pairwise effect in regulatory circuits, and provide computational tools for future investigations into the interplay between eQTLs.Availability: The software described in this article is available at

Topics: eQTL, Additive effects, Gene modules, pairwise effects, immune signaling netwrok, Genetics, QH426-470
Publisher: Frontiers Media S.A.
Year: 2016
DOI identifier: 10.3389/fgene.2016.00048
OAI identifier:
Download PDF:
Sorry, we are unable to provide the full text but you may find it at the following location(s):
  • (external link)
  • (external link)
  • (external link)
  • Suggested articles

    To submit an update or takedown request for this paper, please submit an Update/Correction/Removal Request.