Combining the results of the PPI network and GO/KEGG enrichment analysis above and reviewing the literature on the association between DEPs and myasthenia gravis, the key proteins that may be related to the prognosis of thymoma with myasthenia gravis were finally identified: SELL was downregulated, and C5 and HLA-A were upregulated. This evidence concerns the gene HLA-A and thymoma.