Supplementary Figure 11: Abundance of HLA-II gene expression in various tumors.
From: Predicting HLA class II antigen presentation through integrated deep learning
Bulk RNA-Seq values of (a) HLA-DRA, (b) HLA-DQA1, and (c) HLA-DPA of 5077 TCGA tumor samples and 6 MCL tumor samples plotted as box plots. All tumor types have higher than 100 median TPM for HLA-DRA and HLA-DPA1. Most of tumors have lower HLA-II gene expressions compared to diffuse large B-cell lymphoma (DLBC, ~1000 median TPM). Few tumor samples have lower than 10 TPM (grey dash line) for HLA-DRA and HLA-DPA1. Top and bottom lines indicate 95% confidence interval, and the box indicates the first and third quartiles. MCL: mantle cell lymphoma, n=8; PRAD: prostate adenocarcinoma, n=558; HNSC: head and neck squamous cell carcinoma, n=566; OV: ovarian serous cystadenocarcinoma, n=430; SKCM: skin cutaneous melanoma, n=473; SARC: sarcoma, n=265; BRCA: breast invasive carcinoma, n=1256; MESO: mesothelioma, n=87; GBM: glioblastoma multiforme, n=175; KIRC: kidney renal clear cell carcinoma, n=618; LUAD: lung adenocarcinoma, n=601; DLBC: diffuse large B-cell lymphoma, n=48.
