DEG identification

The DEGs between the T1D patients and controls were analyzed with procedures including data preparation (data normalization and summarization) and DEG analysis (DEG selection and annotation). The affy package in R Software was used for data normalization, and limma package was applied for the remaining processes. The progression of DEG selection included model design, linear model fitness, contrast matrix generation, Bayesian model building and gene filtering, all of which were conducted by the functions in the limma package. Genes with the P<0.05 and |log Fc| (fold change) >1 were considered as DEGs.