虽然TCGA数据库有33种癌症

我们一直提到过下载TCGA的33种癌症的全部数据，尤其是表达量矩阵和临床表型信息啦，这里我们推荐在ucsc的xena里面下载：https://xenabrowser.net/datapages/

GDC TCGA Acute Myeloid Leukemia (LAML) (15 datasets)
GDC TCGA Adrenocortical Cancer (ACC) (14 datasets)
GDC TCGA Bile Duct Cancer (CHOL) (14 datasets)
GDC TCGA Bladder Cancer (BLCA) (14 datasets)
GDC TCGA Breast Cancer (BRCA) (20 datasets)
GDC TCGA Cervical Cancer (CESC) (14 datasets)
GDC TCGA Colon Cancer (COAD) (15 datasets)
GDC TCGA Endometrioid Cancer (UCEC) (15 datasets)
GDC TCGA Esophageal Cancer (ESCA) (14 datasets)
GDC TCGA Glioblastoma (GBM) (15 datasets)
GDC TCGA Head and Neck Cancer (HNSC) (14 datasets)
GDC TCGA Kidney Chromophobe (KICH) (14 datasets)
GDC TCGA Kidney Clear Cell Carcinoma (KIRC) (15 datasets)
GDC TCGA Kidney Papillary Cell Carcinoma (KIRP) (15 datasets)
GDC TCGA Large B-cell Lymphoma (DLBC) (14 datasets)
GDC TCGA Liver Cancer (LIHC) (14 datasets)
GDC TCGA Lower Grade Glioma (LGG) (14 datasets)
GDC TCGA Lung Adenocarcinoma (LUAD) (15 datasets)
GDC TCGA Lung Squamous Cell Carcinoma (LUSC) (15 datasets)
GDC TCGA Melanoma (SKCM) (14 datasets)
GDC TCGA Mesothelioma (MESO) (14 datasets)
GDC TCGA Ocular melanomas (UVM) (14 datasets)
GDC TCGA Ovarian Cancer (OV) (15 datasets)
GDC TCGA Pancreatic Cancer (PAAD) (14 datasets)
GDC TCGA Pheochromocytoma & Paraganglioma (PCPG) (14 datasets)
GDC TCGA Prostate Cancer (PRAD) (14 datasets)
GDC TCGA Rectal Cancer (READ) (15 datasets)
GDC TCGA Sarcoma (SARC) (14 datasets)
GDC TCGA Stomach Cancer (STAD) (15 datasets)
GDC TCGA Testicular Cancer (TGCT) (14 datasets)
GDC TCGA Thymoma (THYM) (14 datasets)
GDC TCGA Thyroid Cancer (THCA) (14 datasets)
GDC TCGA Uterine Carcinosarcoma (UCS) (14 datasets)

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其实并不是每个癌症都有很好的数据，如果使用一个简单的标准，比如大于150个样品的癌症，过滤一下就剩下了22种癌症。参考文献：《Complex impact of DNA methylation on transcriptional dysregulation across 22 human cancer types》，如下所示：

22种癌症

这22种癌症可以划分为9个类别：

• lung (lung adenocarcinoma, LUAD; lung squamous cell carcinoma, LUSC),
• digestive system (colon adenocarcinoma, COAD; esophageal carcinoma, ESCA; liver hepatocellular carcinoma, LIHC; pancre- atic adenocarcinoma, PAAD; stomach adenocarcinoma, STAD),
• endocrine system (pheochromocytoma and para- ganglioma, PCPG; thyroid carcinoma, THCA),
• skin (skin cutaneous melanoma, SKCM),
• brain (brain lower grade glioma, LGG),
• reproductive system (breast invasive carci- noma, BRCA; cervical squamous cell carcinoma and endo- cervical adenocarcinoma, CESC; ovarian serous cystade- nocarcinoma, OV; prostate adenocarcinoma, PRAD; tes- ticular germ cell tumors, TGCT; uterine corpus endome- trial carcinoma, UCEC),
• urinary system (bladder urothe- lial carcinoma, BLCA; kidney renal clear cell carcinoma, KIRC; kidney renal papillary cell carcinoma, KIRP),
• head and neck (head and neck squamous carcinoma, HNSC)
• soft tissue (sarcoma, SARC).

这样的话，就方便大家分门别类的讨论，消化道和生殖系统癌症肯定是差异很大，混起来讨论后也需要拆开对比说明。