The Cancer Genome Atlas Pan-Cancer analysis project
Cite
Weinstein, J.N., Collisson, E.A., Mills, G.B., Shaw, K.R., Ozenberger, B.A., Ellrott, K., Shmulevich, I., Sander, C. and Stuart, J.M., 2013. The cancer genome atlas pan-cancer analysis project. Nature genetics, 45(10), pp.1113-1120.
https://doi.org/10.1038/ng.2764
Abstract
The Cancer Genome Atlas (TCGA) Research Network has profiled and analyzed large numbers of human tumors to discover molecular aberrations at the DNA, RNA, protein and epigenetic levels. The resulting rich data provide a major opportunity to develop an integrated picture of commonalities, differences and emergent themes across tumor lineages. The Pan-Cancer initiative compares the first 12 tumor types profiled by TCGA. Analysis of the molecular aberrations and their functional roles across tumor types will teach us how to extend therapies effective in one cancer type to others with a similar genomic profile.
Datasets
Tissue
Leiden clustering
Project ID
Age
Ethnicity
Sex
Race
Vital status
Year of birth
Year of death
Stage - AJCC clinical - M
Stage - AJCC clinical - N
Stage - AJCC clinical stage
Stage - AJCC clinical - T
Stage - AJCC pathologic - M
Stage - AJCC pathologic - N
Stage - AJCC pathologic stage
Stage - AJCC pathologic - T
Stage - AJCC staging system edition
Ann Arbor - B symptoms
Ann Arbor - Clinical stage
Ann Arbor - Extranodal involvement
Stage - FIGO stage
ICD-10 code
Stage - IGCCCG stage
Stage - Masaoka stage
Morphology
Disease
Gleason grade (primary)
Prior malignancy
Prior treatment
Gleason grade (secondary)
Tissue (sampling site)
Synchronous malignancy
Year of diagnosis
Age group
Reference genome
Assay
Upper lobe, lung582 cells Lower lobe, lung352 cells Adrenal gland, NOS149 cells Head of pancreas130 cells Lower third of esophagus122 cells Cortex of adrenal gland80 cells Rectosigmoid junction76 cells Lateral wall of bladder63 cells Posterior wall of bladder52 cells Fundus of stomach48 cells Middle third of esophagus44 cells Middle lobe, lung37 cells Intrahepatic bile duct31 cells Trigone of bladder23 cells Anterior wall of bladder20 cells Lymph nodes of head, face and neck16 cells Overlapping lesion of lung12 cells Hepatic flexure of colon12 cells Overlapping lesion of eye and adnexa8 cells Upper third of esophagus5 cells Splenic flexure of colon5 cells Lymph nodes of inguinal region or leg4 cells Intra-abdominal lymph nodes4 cells Lymph nodes of axilla or arm4 cells Upper-outer quadrant of breast3 cells Lower-inner quadrant of breast3 cells Upper-inner quadrant of breast2 cells Small intestine, NOS2 cells Overlapping lesion of pancreas2 cells Thoracic esophagus2 cells Overlapping lesion of breast2 cells Medulla of adrenal gland1 cells Intrathoracic lymph nodes1 cells Lesser curvature of stomach, NOS1 cells Lower-outer quadrant of breast1 cells not hispanic or latino7,140 cells hispanic or latino344 cells black or african american880 cells american indian or alaska native25 cells native hawaiian or other pacific islander13 cells Intermediate Prognosis9 cells Adenocarcinoma, NOS1,630 cells Infiltrating duct carcinoma, NOS946 cells Squamous cell carcinoma, NOS866 cells Papillary adenocarcinoma, NOS686 cells Serous cystadenocarcinoma, NOS563 cells Clear cell adenocarcinoma, NOS532 cells Malignant melanoma, NOS422 cells Endometrioid adenocarcinoma, NOS407 cells Hepatocellular carcinoma, NOS358 cells Transitional cell carcinoma344 cells Lobular carcinoma, NOS205 cells Mucinous adenocarcinoma144 cells Astrocytoma, anaplastic131 cells Oligodendroglioma, NOS119 cells Adenocarcinoma with mixed subtypes118 cells Pheochromocytoma, NOS110 cells Papillary carcinoma, follicular variant105 cells Oligodendroglioma, anaplastic82 cells Tubular adenocarcinoma80 cells Adrenal cortical carcinoma79 cells Adenocarcinoma, intestinal type77 cells Renal cell carcinoma, chromophobe type66 cells Carcinoma, diffuse type66 cells Papillary transitional cell carcinoma65 cells Squamous cell carcinoma, large cell, nonkeratinizing, NOS61 cells Squamous cell carcinoma, keratinizing, NOS59 cells Mullerian mixed tumor45 cells Malignant lymphoma, large B-cell, diffuse, NOS42 cells Pheochromocytoma, malignant40 cells Mixed epithelioid and spindle cell melanoma40 cells Papillary carcinoma, columnar cell37 cells Leiomyosarcoma, NOS33 cells Cholangiocarcinoma32 cells Mixed germ cell tumor30 cells Infiltrating duct and lobular carcinoma28 cells Embryonal carcinoma, NOS26 cells Thymoma, type AB, malignant23 cells Acinar cell carcinoma22 cells Spindle cell melanoma, NOS22 cells Adenocarcinoma, endocervical type21 cells Basaloid squamous cell carcinoma21 cells Epithelioid cell melanoma20 cells Bronchiolo-alveolar carcinoma, non-mucinous19 cells Infiltrating duct mixed with other types of carcinoma19 cells Thymoma, type B2, malignant18 cells Mucinous adenocarcinoma, endocervical type17 cells Metaplastic carcinoma, NOS16 cells Signet ring cell carcinoma14 cells Renal cell carcinoma, NOS14 cells Carcinosarcoma, NOS11 cells Thymoma, type B3, malignant10 cells Thymoma, type A, malignant10 cells Spindle cell melanoma, type B9 cells Thymoma, type B1, malignant9 cells Thymic carcinoma, NOS9 cells Papillary serous cystadenocarcinoma8 cells Neuroendocrine carcinoma, NOS8 cells Adenocarcinoma in tubolovillous adenoma8 cells Amelanotic melanoma7 cells Combined hepatocellular carcinoma and cholangiocarcinoma7 cells Adenosquamous carcinoma6 cells Medullary carcinoma, NOS6 cells Infiltrating lobular mixed with other types of carcinoma6 cells Solid carcinoma, NOS6 cells Intraductal papillary adenocarcinoma with invasion6 cells Papillary squamous cell carcinoma5 cells Bronchio-alveolar carcinoma, mucinous5 cells Superficial spreading melanoma4 cells Thymoma, type AB, NOS4 cells Thymoma, type B2, NOS4 cells Hepatocellular carcinoma, clear cell type4 cells Intraductal micropapillary carcinoma4 cells Nonencapsulated sclerosing carcinoma4 cells Hepatocellular carcinoma, fibrolamellar3 cells Pleomorphic carcinoma3 cells Paget disease and infiltrating duct carcinoma of breast3 cells Teratoma, malignant, NOS3 cells Micropapillary carcinoma, NOS3 cells Carcinoma, undifferentiated, NOS3 cells Acral lentiginous melanoma, malignant3 cells Bronchiolo-alveolar adenocarcinoma, NOS3 cells Thymoma, type A, NOS2 cells Dedifferentiated liposarcoma2 cells Endometrioid adenocarcinoma, secretory variant2 cells Papillary carcinoma, NOS2 cells Lentigo maligna melanoma2 cells Myxoid leiomyosarcoma2 cells Phyllodes tumor, malignant1 cells Paraganglioma, malignant1 cells Secretory carcinoma of breast1 cells Thymoma, type B1, NOS1 cells Squamous cell carcinoma, small cell, nonkeratinizing1 cells Synovial sarcoma, spindle cell1 cells Oxyphilic adenocarcinoma1 cells Serous surface papillary carcinoma1 cells Follicular adenocarcinoma, NOS1 cells Follicular carcinoma, minimally invasive1 cells Hepatocellular carcinoma, spindle cell variant1 cells Large cell neuroendocrine carcinoma1 cells Mesodermal mixed tumor1 cells Epithelioid mesothelioma, malignant1 cells Giant cell sarcoma1 cells Cribriform carcinoma, NOS1 cells Desmoplastic melanoma, malignant1 cells Cystadenocarcinoma, NOS1 cells Basal cell carcinoma, NOS1 cells Apocrine adenocarcinoma1 cells Adenoid cystic carcinoma1 cells Adenocarcinoma with neuroendocrine differentiation1 cells Upper lobe, lung585 cells Lower lobe, lung356 cells Adrenal gland, NOS152 cells Head of pancreas130 cells Lower third of esophagus122 cells Lymph nodes of axilla or arm96 cells Cortex of adrenal gland79 cells Rectosigmoid junction76 cells Lateral wall of bladder63 cells Lymph nodes of inguinal region or leg54 cells Posterior wall of bladder52 cells Fundus of stomach48 cells Middle third of esophagus44 cells Middle lobe, lung37 cells Lymph nodes of head, face and neck35 cells Intrahepatic bile duct31 cells Trigone of bladder23 cells Skin of upper limb and shoulder23 cells Skin of lower limb and hip21 cells Anterior wall of bladder20 cells Hepatic flexure of colon15 cells Connective, subcutaneous and other soft tissues of lower limb and hip13 cells Connective, subcutaneous and other soft tissues, NOS13 cells Overlapping lesion of lung12 cells Connective, subcutaneous and other soft tissues of trunk, NOS12 cells Connective, subcutaneous and other soft tissues of thorax11 cells Connective, subcutaneous and other soft tissues of upper limb and shoulder11 cells Small intestine, NOS10 cells Skin of scalp and neck8 cells Pelvic lymph nodes8 cells Overlapping lesion of eye and adnexa8 cells Specified parts of peritoneum6 cells Intra-abdominal lymph nodes6 cells Upper third of esophagus5 cells Splenic flexure of colon5 cells Connective, subcutaneous and other soft tissues of head, face, and neck5 cells Connective, subcutaneous and other soft tissues of pelvis5 cells Upper-outer quadrant of breast3 cells Lower-inner quadrant of breast3 cells Thoracic esophagus2 cells Upper-inner quadrant of breast2 cells Connective, subcutaneous and other soft tissues of abdomen2 cells Overlapping lesion of breast2 cells Overlapping lesion of pancreas2 cells Skin of other and unspecified parts of face1 cells Overlapping lesion of rectum, anus and anal canal1 cells Lower-outer quadrant of breast1 cells Lesser curvature of stomach, NOS1 cells Intrathoracic lymph nodes1 cells Bones of skull and face and associated joints1 cells Illumina TruSeq9,638 cells 