Identification and Evaluation of lncRNA and mRNA Integrative Modules in Human Peripheral Blood Mononuclear Cells

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::

• cancer
• co-expression
• functional enrichment
• integrative
• lncRNA
• module
• PBMC
• UCA1
• weighted gene co-expression network

Supplementary data

To view the supplementary data that accompany this paper please visit the journal website at:www.tandfonline.com/doi/full/10.2217/epi-2016-0178

Financial & competing interests disclosure

The study was supported by Natural Science Foundation of China (31401079, 81473046, 31271336, 81373010, 81502868, 81401343, 81541068), the Natural Science Research Project of Jiangsu Provincial Higher Education (16KJA330001), the Natural Science Foundation of Jiangsu Province (BK20130300, BK20150346), the Project funded by China Post Doctoral Science Foundation (2014M551649), the Startup Fund from Soochow University (Q413900313, Q413900112, Q413900712) and a Project of the Priority Academic Program Development of Jiangsu Higher Education Institutions. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed.

No writing assistance was utilized in the production of this manuscript.

Ethical conduct of research

The authors state that they have obtained appropriate institutional review board approval or have followed the principles outlined in the Declaration of Helsinki for all human or animal experimental investigations. In addition, for investigations involving human subjects, informed consent has been obtained from the participants involved.

Additional information

Funding

The study was supported by Natural Science Foundation of China (31401079, 81473046, 31271336, 81373010, 81502868, 81401343, 81541068), the Natural Science Research Project of Jiangsu Provincial Higher Education (16KJA330001), the Natural Science Foundation of Jiangsu Province (BK20130300, BK20150346), the Project funded by China Post Doctoral Science Foundation (2014M551649), the Startup Fund from Soochow University (Q413900313, Q413900112, Q413900712) and a Project of the Priority Academic Program Development of Jiangsu Higher Education Institutions. The authors have no other relevant affiliations or financial involvement with any organization or entity with a financial interest in or financial conflict with the subject matter or materials discussed in the manuscript apart from those disclosed. No writing assistance was utilized in the production of this manuscript.