Identification and validation of three diagnostic autophagy-related genes associated with advanced plaques and immune cell infiltration in carotid atherosclerosis based on integrated bioinformatics analyses

We acquired 222 autophagy-related genes (ATGs) from the human autophagy database (http://www.autophagy.lu/index.html). Two CAS mRNA expression profiles (GSE100927 and GSE28829) were downloaded from the GEO database (http://www.ncbi.nlm.nih.gov/geo/). The GSE100927 dataset was based on the GPL17077 platform (Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381) and consisted of 35 early plaques and 69 advanced plaques. We chose 12 early CAS plaques and 29 advanced CAS plaques from the GSE100927 dataset for our analysis (Steenman et al. 2018). The GSE28829 dataset was based on the GPL570 platform (Affymetrix Human Genome U133 Plus 2.0 Array) and consisted of 13 early CAS plaques and 16 advanced CAS plaques. The probe IDs in the expression matrix were processed into gene symbols using the annotation file in the gene chip.