Identification and evaluation of lncRNA and mRNA integrative modules in human peripheral blood mononuclear cells

Epigenomics. 2017 Jul;9(7):943-954. doi: 10.2217/epi-2016-0178. Epub 2017 Jun 16.

Abstract

Aim: To identify sets of functionally related long noncoding RNAs (lncRNAs) and mRNAs and to evaluate the importance of lncRNAs in an lncRNA-mRNA network.

Methods: We carried out weighted gene co-expression network analysis and enrichment analyses to identify functional modules of co-expressed lncRNAs and mRNAs in human peripheral blood mononuclear cells of 43 females.

Results: We identified seven modules and found hub lncRNAs in each module. Four of the seven modules had significant gene ontology enrichments. Some of the hub lncRNAs (e.g., SSX8, UCA1, HOXA-AS2, STARD4-AS1 and PCBP1-AS1) have known functions related with diseases such as cancers.

Conclusion: We identified seven biologically important lncRNA and mRNA integrative modules in females and showed that lncRNAs might play important roles in lncRNA-mRNA co-expression modules.

Keywords: PBMC; UCA1; cancer; co-expression; functional enrichment; integrative; lncRNA; module; weighted gene co-expression network.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Female
  • Gene Regulatory Networks*
  • Humans
  • Monocytes / metabolism
  • Oncogenes
  • RNA, Long Noncoding / genetics*
  • RNA, Long Noncoding / metabolism
  • RNA, Messenger / genetics*
  • RNA, Messenger / metabolism

Substances

  • RNA, Long Noncoding
  • RNA, Messenger