The table below summarises TCGA expression data available for 33 cancer types.
Additionally, for Bladder Urothelial Carcinoma, Pancreatic Adenocarcinoma and Lung Adenocarcinoma cohorts extended sets are available (see Extended datasets table), including neuroendocrine tumours (NETs), intraductal papillary mucinous neoplasm (IPMNs), acinar cell carcinoma (ACC) samples and large-cell neuroendocrine carcinoma (LCNEC).
Finally, 10 samples from each of the 33 datasets were combined to create Pan-Cancer dataset.
The dataset of interest can be specified by using one of the TCGA project IDs (Project column) for the --dataset argument in RNAseq_report.R script (see Arguments section).
To readuce the data processing time and the size of the final html-based Patient Transcriptome Summary report the following datasets were restricted to inlcude expression data from 300 patients: BRCA, THCA, HNSC,
LGG, KIRC, LUSC, LUAD, PRAD, STAD and LIHC.
| No | Project | Name | Tissue code* | Samples no.** |
|---|---|---|---|---|
| 1 | BRCA |
Breast Invasive Carcinoma | 1 | 300 |
| 2 | THCA |
Thyroid Carcinoma | 1 | 300 |
| 3 | HNSC |
Head and Neck Squamous Cell Carcinoma | 1 | 300 |
| 4 | LGG |
Brain Lower Grade Glioma | 1 | 300 |
| 5 | KIRC |
Kidney Renal Clear Cell Carcinoma | 1 | 300 |
| 6 | LUSC |
Lung Squamous Cell Carcinoma | 1 | 300 |
| 7 | LUAD |
Lung Adenocarcinoma | 1 | 300 |
| 8 | PRAD |
Prostate Adenocarcinoma | 1 | 300 |
| 9 | STAD |
Stomach Adenocarcinoma | 1 | 300 |
| 10 | LIHC |
Liver Hepatocellular Carcinoma | 1 | 300 |
| 11 | COAD |
Colon Adenocarcinoma | 1 | 257 |
| 12 | KIRP |
Kidney Renal Papillary Cell Carcinoma | 1 | 252 |
| 13 | BLCA |
Bladder Urothelial Carcinoma | 1 | 246 |
| 14 | OV |
Ovarian Serous Cystadenocarcinoma | 1 | 220 |
| 15 | SARC |
Sarcoma | 1 | 214 |
| 16 | PCPG |
Pheochromocytoma and Paraganglioma | 1 | 177 |
| 17 | CESC |
Cervical Squamous Cell Carcinoma and Endocervical Adenocarcinoma | 1 | 171 |
| 18 | UCEC |
Uterine Corpus Endometrial Carcinoma | 1 | 168 |
| 19 | PAAD |
Pancreatic Adenocarcinoma | 1 | 150 |
| 20 | TGCT |
Testicular Germ Cell Tumours | 1 | 149 |
| 21 | LAML |
Acute Myeloid Leukaemia | 3 | 145 |
| 22 | ESCA |
Esophageal Carcinoma | 1 | 142 |
| 23 | GBM |
Glioblastoma Multiforme | 1 | 141 |
| 24 | THYM |
Thymoma | 1 | 118 |
| 25 | SKCM |
Skin Cutaneous Melanoma | 1 | 100 |
| 26 | READ |
Rectum Adenocarcinoma | 1 | 87 |
| 27 | UVM |
Uveal Melanoma | 1 | 80 |
| 28 | ACC |
Adrenocortical Carcinoma | 1 | 78 |
| 29 | MESO |
Mesothelioma | 1 | 77 |
| 30 | KICH |
Kidney Chromophobe | 1 | 59 |
| 31 | UCS |
Uterine Carcinosarcoma | 1 | 56 |
| 32 | DLBC |
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma | 1 | 47 |
| 33 | CHOL |
Cholangiocarcinoma | 1 | 34 |
| No | Project | Name | Tissue code* | Samples no.** |
|---|---|---|---|---|
| 1 | LUAD-LCNEC |
Lung Adenocarcinoma dataset including large-cell neuroendocrine carcinoma (LCNEC, n=14) | 1 | 314 |
| 2 | BLCA-NET |
Bladder Urothelial Carcinoma dataset including neuroendocrine tumours (NETs, n=2) | 1 | 248 |
| 3 | PAAD-IPMN |
Pancreatic Adenocarcinoma dataset including intraductal papillary mucinous neoplasm (IPMNs, n=2) | 1 | 152 |
| 4 | PAAD-NET |
Pancreatic Adenocarcinoma dataset including neuroendocrine tumours (NETs, n=8) | 1 | 158 |
| 5 | PAAD-ACC |
Pancreatic Adenocarcinoma dataset including acinar cell carcinoma (ACCs, n=1) | 1 | 151 |
| No | Project | Name | Tissue code* | Samples no.** |
|---|---|---|---|---|
| 1 | PANCAN |
Samples from all 33 cancer types, 10 samples from each | 1 and 3 (LAML samples only) |
330 |
* Tissue codes:
| Tissue code | Letter code | Definition |
|---|---|---|
| 1 | TP | Primary solid Tumour |
| 3 | TB | Primary Blood Derived Cancer - Peripheral Blood |
** Each dataset was cleaned based on the quality metrics provided in the Merged Sample Quality Annotations file merged_sample_quality_annotations.tsv from TCGA PanCanAtlas initiative webpage (see TCGA-data-harmonization repository for more details).