Screening of potential gene markers for predicting carotid atheroma plaque formation using bioinformatics approaches

Abstract

The present study aimed to investigate potential gene markers for predicting the formation of carotid atheroma plaques using high-throughput bioinformatics methods. The GSE43292 gene expression profile was downloaded from the Gene Expression Omnibus database. Following data processing, differentially expressed genes (DEGs) were screened using a paired t-test in the Linear Models for Microarray Data package with the criteria of a false discovery rate of P<0.05 and |log2 fold-change| ≥0.58, followed by functional enrichment, protein-protein interaction (PPI) network construction, key node and module analysis, and prediction of transcription factors (TFs) targeting genes in the significant modules. The results revealed that the gene expression profiles from 32 paired samples of carotid atheroma plaque tissue and macroscopically intact tissue were obtained, based on which 886 DEGs, including 513 upregulated genes and 373 downregulated genes, were identified. The upregulated and downregulated gene sets were enriched in 24 and 13 pathways, respectively. The PPI network constructed with these DEGs comprised 35 key nodes with degrees ≥20, among which spleen tyrosine kinase (SYK), LYN and phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit γ (PIK3CG) were the three highest. A significant module was mined in the PPI network, which consisted of 29 DEGs targeted by 11 TFs. The DEGs between the carotid atheroma plaque and macroscopically intact tissue samples may be involved in carotid atherogenesis. Key nodes in the PPI network constructed from these DEGs and the genes involved in the significant module, including SYK, LYN and PIK3CG, are promising for the prediction of carotid plaque formation.

Comprehensive analysis identifies crucial genes associated with immune cells mediating progression of carotid atherosclerotic plaque

“…Guiming Wang et al screened 513 upregulated genes and 373 downregulated genes. The PPI network constructed with these DEGs included 35 key nodes with degrees≥20, among which SYK, LYN and PIK3CG were the three highest [ 29 ]. Julong Guo et al analyzed GSE41571, GSE120521, E-MTAB-2055 and one non-coding RNA dataset (GSE111794) to discover genetic molecules linked to histologically unstable carotid atherosclerotic plaques and found 10 hub genes.…”

Bioinformatic Analysis Revealed the Essential Regulatory Genes and Pathways of Early and Advanced Atherosclerotic Plaque in Humans

“…Previous studies have used the microarray datasets of GSE43292 and GSE28829 to screen DEGs, key genes, and pathways in a single atherosclerotic plaque stage [ 17 , 18 , 31 , 32 , 33 ]. In comparison, the current study comprehensively investigated the gene expression profiles of atherosclerotic plaque in the stages of non-plaque to plaque as well as early to advanced.…”

IGFBP6 Is Downregulated in Unstable Carotid Atherosclerotic Plaques According to an Integrated Bioinformatics Analysis and Experimental Verification

“…Stroke is the third leading cause of mortality and the major cause of crippling in developed countries 1 ) . Carotid atherosclerotic plaques are one of the leading causes of ischemic cerebral stroke 2 ) .…”