Integrative approach to pain genetics identifies pain sensitivity loci across diseases

PLoS Comput Biol. 2012;8(6):e1002538. doi: 10.1371/journal.pcbi.1002538. Epub 2012 Jun 7.


Identifying human genes relevant for the processing of pain requires difficult-to-conduct and expensive large-scale clinical trials. Here, we examine a novel integrative paradigm for data-driven discovery of pain gene candidates, taking advantage of the vast amount of existing disease-related clinical literature and gene expression microarray data stored in large international repositories. First, thousands of diseases were ranked according to a disease-specific pain index (DSPI), derived from Medical Subject Heading (MESH) annotations in MEDLINE. Second, gene expression profiles of 121 of these human diseases were obtained from public sources. Third, genes with expression variation significantly correlated with DSPI across diseases were selected as candidate pain genes. Finally, selected candidate pain genes were genotyped in an independent human cohort and prospectively evaluated for significant association between variants and measures of pain sensitivity. The strongest signal was with rs4512126 (5q32, ABLIM3, P = 1.3×10⁻¹⁰) for the sensitivity to cold pressor pain in males, but not in females. Significant associations were also observed with rs12548828, rs7826700 and rs1075791 on 8q22.2 within NCALD (P = 1.7×10⁻⁴, 1.8×10⁻⁴, and 2.2×10⁻⁴ respectively). Our results demonstrate the utility of a novel paradigm that integrates publicly available disease-specific gene expression data with clinical data curated from MEDLINE to facilitate the discovery of pain-relevant genes. This data-derived list of pain gene candidates enables additional focused and efficient biological studies validating additional candidates.

Publication types

  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
  • Research Support, U.S. Gov't, Non-P.H.S.
  • Twin Study

MeSH terms

  • Cohort Studies
  • Cold Temperature / adverse effects
  • Computational Biology
  • Databases, Genetic
  • Disease / genetics
  • Female
  • Gene Expression Profiling
  • Genome-Wide Association Study
  • Humans
  • Integrative Medicine
  • LIM Domain Proteins / genetics
  • Male
  • Models, Genetic
  • Neurocalcin / genetics
  • Pain / etiology
  • Pain / genetics*
  • Systems Biology


  • LIM Domain Proteins
  • NCALD protein, human
  • Neurocalcin