Phenotype-Dependent Coexpression Gene Clusters: Application to Normal and Premature Ageing

IEEE/ACM Trans Comput Biol Bioinform. Jan-Feb 2015;12(1):30-9. doi: 10.1109/TCBB.2014.2359446.

Abstract

Hutchinson Gilford progeria syndrome (HGPS) is a rare genetic disease with symptoms of aging at a very early age. Its molecular basis is not entirely clear, although profound gene expression changes have been reported, and there are some known and other presumed overlaps with normal aging process. Identification of genes with agingor HGPS-associated expression changes is thus an important problem. However, standard regression approaches are currently unsuitable for this task due to limited sample sizes, thus motivating development of alternative approaches. Here, we report a novel iterative multiple regression approach that leverages co-expressed gene clusters to identify gene clusters whose expression co-varies with age and/or HGPS. We have applied our approach to novel RNA-seq profiles in fibroblast cell cultures at three different cellular ages, both from HGPS patients and normal samples. After establishing the robustness of our approach, we perform a comparative investigation of biological processes underlying normal aging and HGPS. Our results recapitulate previously known processes underlying aging as well as suggest numerous unique processes underlying aging and HGPS. The approach could also be useful in detecting phenotype-dependent co-expression gene clusters in other contexts with limited sample sizes.

Publication types

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

MeSH terms

  • Aging / genetics*
  • Aging / physiology
  • Algorithms
  • Cells, Cultured
  • Computational Biology / methods*
  • Fibroblasts
  • Gene Expression Profiling
  • Humans
  • Male
  • Multigene Family / genetics*
  • Phenotype
  • Progeria / genetics*
  • Progeria / physiopathology