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Systematic analysis of co-expression network and gene expression profile of differentially expressed lncRNA-mRNA one week after spinal cord injury

Authors :
Yi Kang
Yijie Song
Zhongju Shi
Qiang Li
Yigang Lv
Mengfan Hou
Cui Ding
Jing Xie
Yongfu Lou
Chi Zhang
Huan Jian
Xueying Li
Hengxing Zhou
Shiqing Feng
Source :
All Life, Vol 17, Iss 1 (2024)
Publication Year :
2024
Publisher :
Taylor & Francis Group, 2024.

Abstract

Spinal cord injury (SCI) is a severe event that occurs in the central nervous system (CNS). Long noncoding RNAs (lncRNAs) have already been proven to play key roles in different diseases of the CNS. Nevertheless, the roles of messenger RNAs (mRNAs) and lncRNAs one week after SCI remain to be elucidated. We established a rat model of SCI and examined the differential levels of mRNAs and lncRNAs, and then, the differentially expressed mRNAs (DE mRNAs) and lncRNAs (DE lncRNAs) were investigated. Gene Ontology (GO) functional enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses of DE lncRNAs and mRNAs were subsequently carried out to explore crucial biological processes and signaling pathways. Moreover, we constructed protein–protein interaction (PPI) networks, the STRING database, and identified the 10 high degree core nodes. We also established a co-expression network by calculating the correlation between lncRNA expression profile and mRNA expression profile. The identified DE lncRNAs and DE mRNAs may potentially be critical targets for the diagnosis and treatment of SCI in the future. Abbreviations: SCI: spinal cord injury; CNS: central nervous system; YLDs: years of life lived with disability; lncRNAs: long noncoding RNAs; mRNAs: messenger RNAs; DE: differentially expressed; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; GSEA: gene set enrichment analysis; RIN: Renewable Identification Number; PCA: principal component analysis; PPI: protein–protein interaction; MF, molecular function; BP: biological process; CC: cellular component; MCODE: molecular complex detection

Details

Language :
English
ISSN :
26895307 and 26895293
Volume :
17
Issue :
1
Database :
Directory of Open Access Journals
Journal :
All Life
Publication Type :
Academic Journal
Accession number :
edsdoj.66d9eab497f4c3fa0911cc4f6b529f4
Document Type :
article
Full Text :
https://doi.org/10.1080/26895293.2024.2350185