Human genome u133a 2.0 array hg u133a 2

The CAD and CAD&RA datasets GSE110008 were downloaded from the National Center for Biotechnology Information (NCBI) Gene Expression Omnibus (GEO) (https://www.ncbi.nlm.nih.gov/geo/). The datasets included eight CAD&RA and eight control CAD samples according to the analysis of biopsies of the ascending aorta, and the platform was Affymetrix Human Genome U133A 2.0 Array (HG-U133A_2). The primary data was annotated to form an expression matrix, each probe was matched to their homologous gene symbols, and the repeated gene symbols in the matrix were excluded.
Differentially expressed genes (DEGs) between CAD&RA and CAD patients were identified using R (version 4.1.1) limma package. Genes with a false discovery rate (FDR) adjusted to p < 0.05 were considered as DEGs. Then, the DEGs were compared with the CAD-related and RA-related genes. To obtain CAD-related and RA-related genes, data were retrieved using the key words “coronary artery disease” and “rheumatoid arthritis” in the HPO (https://hpo.jax.org/app/), OMIM (https://omim.org/) and dbSNP (https://www.ncbi.nlm.nih.gov/snp/) databases during October, 2021.

We acquired gene expression profiles from the Gene Expression Omnibus (GEO) database through the keyword “DKD” or “DN” (Barrett et al., 2013 (link)). The inclusion criteria were as follows: 1) dataset from the same sequencing platform that covered the maximum sample sizes and 2) the studied objects should come from the microdissected kidneys of Homo sapiens. We downloaded and analyzed the gene expression profiles of GDKD (GSE30528) and TDKD (GSE30529) from the GPL571 platform [Affymetrix Human Genome U133A 2.0 Array (HG-U133A_2)]. GSE30528 and GSE30529 are the subseries of GSE30122. The glomerular samples of GSE30528 included nine DKD and 13 controls, while the tubulointerstitial samples of GSE30122 included 10 DKD and 12 controls. The diagnosis of DKD patients was based on the presence of diabetes, decreased eGFR (<60 ml/min), increased blood urea nitrogen (BUN), and serum creatinine, as well as proteinuria. Control samples were acquired from nephrectomies, living donors, and healthy people (Woroniecka et al., 2011 (link)). To evaluate the quality of GSE30528 and GSE30529, we used the R software to test the intragroup data repeatability via the principal component analysis (PCA).