In recent years, intense research has been conducted to explore the diagnostic value of mRNA expression differences in atherosclerosis (AS). Nevertheless, because various technology platforms are applied and sample sizes are small, the results are inconsistent among the studies. We conducted a comprehensive analysis of a total of 161 tissue samples from 4 published studies after evaluating 230 datasets from the Gene Expression Omnibus and ArrayExpress. Adopting the newly published robust rank aggregation approach, combined with Kyoto Encyclopedia of Genes and Genomes pathway analysis, Gene Ontology functional enrichment analysis, and protein-protein interaction network construction, we identified four significantly upregulated genes (CCL4, CCL18, MMP9 and SPP1) for diagnosing AS, even in the advanced stage. Then, we performed gene set enrichment analysis to identify the pathways that were most affected by altered mRNA expression in atherosclerotic plaques. We found that four hub genes cooperatively targeted lipid metabolism and inflammatory immune-related pathways and validated their high expression levels in ruptured plaques by qRT-PCR, western blot analysis and immunohistochemical staining. In summary, our study showed that these genes can be used as interventional targets for plaque progression, and the results suggested we should focus on small changes in these key indicators in the clinical setting.