Investigating Dysregulated Sub-Pathways for Preeclampsia Infants Based on lncRNA-mRNA Expression Data and Pathway Network

• Published in: Annals of clinical and laboratory science Vol. 49; no. 5; pp. 598 - 607
• Main Authors: Jin, Xiaoxiao, Ma, Xia, Zhu, Ying
• Format: Journal Article
• Language: English
• Published: United States 01.09.2019
• Subjects: Female; Gene Expression Regulation; Gene Regulatory Networks; Humans; Pre-Eclampsia - genetics; Pregnancy; RNA Transport - genetics; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; RNA, Messenger - genetics; RNA, Messenger - metabolism; Signal Transduction - genetics; mRNA; lncRNA; preeclampsia infants; sub-pathway; network
• ISSN: 1550-8080

This study aimed to investigate dysregulated sub-pathways for preeclampsia (PE) infants based on lncRNA-mRNA expression profiles and pathway network. The inference of dysregulated sub-pathways consisted of four steps: extracting candidate lncRNA-mRNA interactions from validated lncRNA-miRNA and miRNA-mRNA interactions; capturing seed lncRNA-mRNA pairs from candidate lncRNA-mRNA interactions; embedding lncRNAs of seed lncRNA-mRNA pairs into significant pathways, and constructing a network for lncRNAs competing regulated pathways (LCRPs), followed by hub nodes identification; and exploring candidate sub-pathways based on the shortest path and estimating their significance by the Wallenius approximation method to select dysregulated sub-pathways for PE. 1,473 seed lncRNA-mRNA pairs involved 105 seed lncRNAs and 742 seed mRNAs were obtained. Based on them, we investigated 35 LCRPs for PE infants. The network for LCRPs was consisted of 532 nodes and 1,840 edges, of which 62 hub lncRNAs were identified. Further, a total of 38 dysregulated sub-pathways were determined from candidate sub-pathways under the condition of <1.00E-05. values for dysregulated sub-pathways were nearly zero, which indicated their great significance between PE infants and controls. Identifying competitively dysregulated sub-pathways could provide better understanding into the origin and development of PE, as well as assist in clarifying the functions of important lncRNAs.