ORIGINAL RESEARCH article
Front. Genet.
Sec. Computational Genomics
Hyperlipidemia-associated specific modules and hub genes revealed by integrative methods of WGCNA and MetaDE
Provisionally accepted
- 1The First Hospital of Jilin University, Changchun, China
- 2Northeast Normal University Hospital, Changchun, China
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Background and Objectives: This study aimed to screen the specific modules and hub genes of hyperlipidemia. Methods: Three microarray datasets (GSE3059, GSE1010 and GSE13985) were obtained from the Gene Expression Omnibus database. Weighted Gene Co-expression Network Analysis (WGCNA) was used to screen stable gene modules across the three datasets. The MetaDE method was used to screen differentially expressed genes (DEGs) based on GSE1010 and GSE13985 datasets. The Cytoscape software was 3 utilized for protein-protein interaction (PPI) network visualization, and the DAVID was employed to perform Kyoto Encyclopedia of Genes and Genomes (KEGG) signaling pathway analysis on the DEG nodes in the interaction network. Results: Based on the WGCNA algorithm, eleven hyperlipidemia-related modules were screened, and a total of 1149 DEGs were screened by the metaDE method. 288 overlapping genes were used to establish a PPI network. Finally, a total of four overlapping KEGG pathways were obtained, including Fc gamma R-mediated phagocytosis (ARPC1A, GAB2, LYN, HCK, RAF1, WAS), chemokine signalling pathway (LYN, PTK2B, HCK, GRK6, GRK3, RAF1, CXCR2, JAK3, FOXO3, WAS), endocytosis (CHMP2A, CHMP1B, RAB5C, VPS45, TGFBR2, GRK6, GRK3, CXCR2) and natural killer cell-mediated cytotoxicity (TNFRSF10C, PTK2B, ICAM2, RAF1, FCGR3B, SH3BP2). The hub genes such as RAF1, GRK3 and CXCR2, might be potential genetic biomarkers of hyperlipidemia. Discussion: This study identified the critical pathways and hub genes associated with hyperlipidemia. In particular, these critical pathways may help clarify the pathogenesis of hyperlipidemia, and the hub genes may become new biomarkers and therapeutic target for hyperlipidemia.
Keywords: Hyperlipidemia, Specific modules, Hub genes, weighted gene co-expression network analysis, RAF1, GRK3, CXCR2
Received: 14 Apr 2025; Accepted: 05 Nov 2025.
Copyright: © 2025 Zhao, Cao, Gu and Yao. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
* Correspondence: Hanxin Yao, yhx05401@126.com
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