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Linking Variants from Genome-Wide Association Analysis to Function via Transcriptional Network Analysis

  • Benjamin J. KellerEmail author
  • Sebastian Martini
  • Viji Nair
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 910)

Abstract

We outline a strategy to use tissue-specific expression along with promoter module analysis to determine the putative functional context of candidate genes implicated in genome-wide association studies. First, genes are selected from candidate SNPs, followed by construction of a gene co-regulation network to expand the regulatory context of the candidate genes, functional analysis to determine putative functional roles, and subsequent analysis of regulatory elements. We describe these sub-strategies and variations, along with guidelines for alternatives in the overall analysis.

Key words

Genome-wide association study GWAS Gene expression Candidate gene Co-regulation network Functional analysis Gene regulation Promoter module Transcriptional analysis 

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Copyright information

© Springer Science+Business Media New York 2012

Authors and Affiliations

  • Benjamin J. Keller
    • 1
    Email author
  • Sebastian Martini
    • 2
  • Viji Nair
    • 2
  1. 1.Department of Computer ScienceEastern Michigan UniversityYpsilantiUSA
  2. 2.Nephrology Division, Department of Internal MedicineUniversity of MichiganAnn ArborUSA

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