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Updated: Nov 6, 2025
High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions
Published on: March 5, 2022
Analysis of mRNA‑lncRNA and mRNA‑lncRNA-pathway co‑expression networks based on WGCNA in developing pediatric sepsis
Xiaojuan Zhang1, Yuqing Cui1, Xianfei Ding1
1General ICU, Zhengzhou Key Laboratory of Sepsis, Henan Engineering Research Center for Critical Care Medicine, the First Affiliated Hospital of Zhengzhou University, Henan Key Laboratory of Critical Care Medicine, Zhengzhou, China.
Insights
This study identifies key messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) as potential diagnostic markers for pediatric sepsis, offering new insights into its molecular mechanisms.
Area of Science:
- Genomics and Molecular Biology
- Pediatric Critical Care Medicine
- Bioinformatics
Background:
- Pediatric sepsis poses a significant global mortality risk, yet its underlying pathogenesis remains incompletely understood.
- Identifying molecular markers is crucial for early diagnosis and effective treatment of pediatric sepsis.
Purpose of the Study:
- To identify differentially expressed messenger RNAs (mRNAs) and long noncoding RNAs (lncRNAs) associated with pediatric sepsis.
- To explore co-expression networks and pathways involved in the molecular mechanisms of pediatric sepsis.
- To identify potential diagnostic markers for pediatric sepsis.
Main Methods:
- Utilized the Gene Expression Omnibus (GEO) database to identify differentially expressed mRNAs and lncRNAs.
- Applied weighted gene co-expression network analysis (WGCNA) to discover modules linked to pediatric sepsis.
- Conducted Gene Ontology (GO) and KEGG pathway analyses, alongside mRNA-lncRNA and mRNA-lncRNA-pathway co-expression network analyses.
Main Results:
- WGCNA identified a significant turquoise module associated with pediatric sepsis traits, involving 1941 mRNAs and 225 lncRNAs.
- GO and KEGG analyses revealed the involvement of mRNAs in vital biological processes within the turquoise module.
- Identified 15 hub mRNAs and 4 hub lncRNAs as potential diagnostic markers for pediatric sepsis.
Conclusions:
- The study successfully identified 15 mRNAs and 4 lncRNAs with potential diagnostic value for pediatric sepsis.
- These findings provide novel directions for investigating the complex molecular mechanisms underlying pediatric sepsis.
- The identified markers may contribute to improved diagnostic strategies for this life-threatening condition.
Abstract:
Pediatric sepsis is a great threat to death worldwide. However, the pathogenesis has not been clearly understood until now in sepsis. This study identified differentially expressed mRNAs and lncRNAs based on Gene Expression Omnibus (GEO) database. And the weighted gene co-expression network analysis (WGCNA) was performed to explore co-expression modules associated with pediatric sepsis. Then, Gene Ontology (GO), KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway, mRNA‑lncRNA and mRNA‑lncRNA-pathway co-expression network analysis was conducted in selected significant module. A total of 1941 mRNAs and 225 lncRNAs were used to conduct WGCNA. And turquoise module was selected as a significant module that was associated with particular traits. The mRNAs functions associated with many vital processes were also shown by GO and KEGG pathway analysis in the turquoise module. Finally, 15 mRNAs (MAPK14, ITGAM, HK3, ALOX5, CR1, HCK, NCF4, PYGL, FLOT1, CARD6, NLRC4, SH3GLB1, PGS1, RAB31, LTB4R) and 4 lncRNAs (GSEC, NONHSAT160878.1, XR_926068.1 and RARA-AS1) were selected as hub genes in mRNA‑lncRNA-Pathway co-expression network. We identified 15 mRNAs and 4 lncRNAs as diagnostic markers, which have potential functions in pediatric sepsis. Our study provides more directions to study the molecular mechanism of pediatric sepsis.Abbreviations: mRNA: messenger RNA; lncRNA: long noncoding RNAs; GEO: Gene Expression Omnibus; WGCNA: weighted gene co-expression network analysis; GO: Gene Ontology; KEGG: Kyoto Encyclopedia of Genes and Genomes; SIRS: systemic inflammatory response syndrome; TOM: topological overlap measure; BP: biological process; MF: molecular function; CC: cellular component; ROC: receiver operating characteristic curve; AUC: area under curve; MAPK14: Mitogen-activated protein kinase 14; ALI: acute lung injury; ITGAM: Integrin subunit alpha M; HK3: Hexokinase 3; LPS: lipopolysaccharide; 5-LO: 5-lipoxygenase; LTs: leukotrienes; LTB4R: leukotriene B4 receptor.
