Comparison of Gene Coexpression Profiles and Construction of Conserved Gene Networks to Find Functional Modules

PLoS One. 2015 Jul 6;10(7):e0132039. doi: 10.1371/journal.pone.0132039. eCollection 2015.

Abstract

Background: Computational approaches toward gene annotation are a formidable challenge, now that many genome sequences have been determined. Each gene has its own function, but complicated cellular functions are achieved by sets of genes. Therefore, sets of genes with strong functional relationships must be identified. For this purpose, the similarities of gene expression patterns and gene sequences have been separately utilized, although the combined information will provide a better solution.

Result & discussion: We propose a new method to find functional modules, by comparing gene coexpression profiles among species. A coexpression pattern is represented as a list of coexpressed genes with each guide gene. We compared two coexpression lists, one from a human guide gene and the other from a homologous mouse gene, and defined a measure to evaluate the similarity between the lists. Based on this coexpression similarity, we detected the highly conserved genes, and constructed human gene networks with conserved coexpression between human and mouse. Some of the tightly coupled genes (modules) showed clear functional enrichment, such as immune system and cell cycle, indicating that our method could identify functionally related genes without any prior knowledge. We also found a few functional modules without any annotations, which may be good candidates for novel functional modules. All of the comparisons are available at the http://v1.coxsimdb.info web database.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Animals
  • Databases, Genetic
  • Gene Expression Profiling
  • Gene Expression Regulation*
  • Gene Regulatory Networks*
  • Humans
  • Mice

Associated data

  • Dryad/10.5061/dryad.P15M6

Grant support

This research was supported by for Scientific Research (24570176) to KK from Ministry of Education, Culture, Sports, Science, and Technology (MEXT, http://www.mext.go.jp/english/) and for Innovative Area (24114005) to TO from MEXT, and also supported by the CREST research project of the Japan Science and Technology Agency (http://www.jst.go.jp/EN/index.html) (11102558) to TO. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.