Detection of lncRNA-mRNA interaction modules by integrating eQTL with weighted gene co-expression network analysis

作者：Mo, Xing-Bo; Wu, Long-Fei; Lu, Xin; Zhu, Xiao-Wei; Xia, Wei; Wang, Lan; He, Pei; Bing, Peng-Fei; Zhang, Yong-Hong; Deng, Fei-Yan; Lei, Shu-Feng^*

来源：Functional & Integrative Genomics, 2019, 19(2): 217-225.

DOI：10.1007/s10142-018-0638-4

• Long noncoding RNA
• eQTL
• Weighted gene co-expression network analysis
• Functional annotation
• HOTAIR

One major function of lncRNA is to regulate the expression of mRNA, but the patterns of their interactions were largely unknown. We attempted to construct lncRNA-mRNA interaction modules at a genome-wide scale. We performed a genome-wide lncRNA-mRNA eQTL analysis in peripheral blood mononuclear cells of 43 individuals, followed by weighted gene co-expression network analysis and functional enrichment analysis which sought to detect functional modules. There were 4627 significant cis lnc-eQTL pairs (P<1.4x10(-6)) and 1,587,128 significant trans lnc-eQTL pairs (P<3.46x10(-9)). We detected 11 eQTL modules for the lnc-eQTL networks. Among them, five modules showed significant enrichments in GO terms, and three modules showed significant enrichments in specific KEGG pathways (e.g., Toll-like receptor, PI3K-Akt, NF-kappa B, and TNF signaling pathways). lncRNA-protein interaction analysis showed that some well-known functional lncRNAs (HOTAIR, CCDC26, RHPN1-AS1, WT1-AS, and TCL6) in the eQTL module interacted with genes in focal adhesion and PI3K-Akt signaling pathway. We identified biologically functional lncRNA-mRNA interaction modules by integrating eQTL and weighted gene co-expression network analysis. Integrative analysis of lncRNA and mRNA data by applying eQTL analysis and weighted gene co-expression network analysis methods could be helpful for functional annotation of lncRNAs.

• 出版日期2019-3
• 单位苏州大学