{"id":4645,"date":"2022-05-04T12:54:04","date_gmt":"2022-05-04T16:54:04","guid":{"rendered":"https:\/\/labs.icahn.mssm.edu\/minervalab\/?page_id=4645"},"modified":"2024-01-10T17:57:17","modified_gmt":"2024-01-10T22:57:17","slug":"tcga","status":"publish","type":"page","link":"https:\/\/labs.icahn.mssm.edu\/minervalab\/resources\/data-ark\/tcga\/","title":{"rendered":"TCGA"},"content":{"rendered":"

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Scientific Computing and Data<\/a> \/ Research Data Services<\/a> \/\u00a0Data Ark: Data Commons<\/a> \/ TCGA<\/p>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][\/et_pb_section][et_pb_section fb_built=”1″ admin_label=”section” _builder_version=”4.9.0″ custom_padding=”0px||||false|false”][et_pb_row _builder_version=”4.9.0″ _module_preset=”default” custom_margin=”|auto|-12px|auto||”][et_pb_column type=”4_4″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_text admin_label=”TCGA-title name” _builder_version=”4.9.0″ _module_preset=”default” header_font_size=”36px”]<\/p>\n

TCGA – The Cancer Genome Atlas Program<\/span><\/strong><\/h1>\n

[\/et_pb_text][\/et_pb_column][\/et_pb_row][et_pb_row column_structure=”1_5,3_5,1_5″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_column type=”1_5″ _builder_version=”4.9.0″ _module_preset=”default”][\/et_pb_column][et_pb_column type=”3_5″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_image src=”https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-content\/uploads\/sites\/342\/2022\/05\/tcga-png.png” alt=”tcga” title_text=”tcga-png” admin_label=”The main Image” _builder_version=”4.9.0″ _module_preset=”default” custom_margin=”-37px|||||”][\/et_pb_image][\/et_pb_column][et_pb_column type=”1_5″ _builder_version=”4.9.0″ _module_preset=”default”][\/et_pb_column][\/et_pb_row][et_pb_row _builder_version=”4.9.0″ _module_preset=”default” custom_margin=”|auto|35px|auto||” custom_padding=”28px|||||”][et_pb_column type=”4_4″ _builder_version=”4.9.0″ _module_preset=”default”][et_pb_text admin_label=”Main_content” _builder_version=”4.9.0″ _module_preset=”default” text_line_height=”1.5em” header_font=”|700|||||||” header_text_color=”#221f72″ header_2_font_size=”24px”]<\/p>\n

Overview<\/h2>\n

The Cancer Genome Atlas (TCGA)<\/a> is a landmark cancer genomics program that molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types. The program is a joint effort between National Cancer Institute and the National Human Genome Research Institute first established in 2016.<\/p>\n

Currently, two versions are hosted on the Data Ark: Version 31.0 and version 32.0. The gene model used as a reference across TCGA has been updated from GENCODE 22(GRC37\/hg19)—version 31 to GENCODE 36 (GRCh38\/hg38)–version 32. To learn more about the data sets from a different version, find the data release notes here.<\/a><\/p>\n

All the TCGA data sets belong to the \u201copen-access\u201d category and were obtained from the Genomic Data Commons Data Portal<\/a>. The TCGA folder on Minerva Supercomputer hosts all the biospecimen, clinical, RNA-seq counts, WXS -Mutation Annotation Format (MAF), and the TCGA data sets from cBioPortal<\/a>.<\/p>\n

TCGA Processed Data Sets<\/h4>\n

TCGA data set has been processed and uploaded to Data Ark by Dr.Deniz Demircioglu (deniz.demircioglu@mssm.edu<\/a>), who combined data from the biospecimen and clinical folder and consolidated all the RNA-seq counts files (over 11,000 patients) into 33 different outcomes. See the table below. For more information about the TCGA Study Abbreviations, click here<\/a>.<\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n\n
\u00a0Abbrev.<\/strong><\/span><\/td>\nStudy Name<\/strong><\/span><\/td>\n\u00a0Abbrev.<\/strong><\/span><\/td>\nStudy Name<\/strong><\/span><\/td>\nAbbrev.<\/strong><\/span><\/td>\nStudy Name<\/strong><\/span><\/td>\n<\/tr>\n
\u00a0ACC<\/td>\nAdrenocortical carcinoma<\/td>\nBLCA<\/td>\nBladder Urothelial carcinoma<\/td>\nBRCA<\/td>\nBreast invasive carcinoma<\/td>\n<\/tr>\n
CESC<\/td>\nCervical squamous cell carcinoma and endocervical adenocarcinoma<\/td>\nCHOL<\/td>\nCholangiocarcinoma<\/td>\nCOAD<\/td>\nColon adenocarcinoma<\/td>\n<\/tr>\n
DLBC<\/td>\nLymphoid Neoplasm Diffuse Large B-cell Lymphoma<\/td>\nESCA<\/td>\nEsophageal carcinoma<\/td>\nGBM<\/td>\nGlioblastoma multiforme<\/td>\n<\/tr>\n
HNSC<\/td>\nHead and Neck squamous cell carcinoma<\/td>\nKICH<\/td>\nKidney Chromophobe<\/td>\nKIRC<\/td>\nKidney renal clear cell carcinoma<\/td>\n<\/tr>\n
KIRP<\/td>\nKidney renal papillary cell carcinoma<\/td>\nLAML<\/td>\nAcute Myeloid Leukemia<\/td>\nLGG<\/td>\nBrain Lower Grade Glioma<\/td>\n<\/tr>\n
LIHC<\/td>\nLiver hepatocellular carcinoma<\/td>\nLUAD<\/td>\nLung adenocarcinoma<\/td>\nLUSC<\/td>\nLung squamous cell carcinoma<\/td>\n<\/tr>\n
MESO<\/td>\nMesothelioma<\/td>\nOV<\/td>\nOvarian serous cystadenocarcinoma<\/td>\nPAAD<\/td>\nPancreatic adenocarcinoma<\/td>\n<\/tr>\n
PCPG<\/td>\nPheochromocytoma and Paraganglioma<\/td>\nPRAD<\/td>\nProstate adenocarcinoma<\/td>\nREAD<\/td>\nRectum adenocarcinoma<\/td>\n<\/tr>\n
SARC<\/td>\nSarcoma<\/td>\nSKCM<\/td>\nSkin Cutaneous Melanoma<\/td>\nSTAD<\/td>\nStomach adenocarcinoma<\/td>\n<\/tr>\n
TGCT<\/td>\nTesticular Germ Cell Tumors<\/td>\nTHCA<\/td>\nThyroid carcinoma<\/td>\nTHYM<\/td>\nThymoma<\/td>\n<\/tr>\n
UCEC<\/td>\nUterine Corpus Endometrial Carcinoma<\/td>\nUCS<\/td>\nUterine Carcinosarcoma<\/td>\nUVM<\/td>\nUveal Melanoma<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

Inside each outcome folder, you will see the following files:<\/p>\n\n\n\n\n\n
aliquot.tsv<\/td>\ncount.tsv<\/td>\nfpkm.tsv<\/td>\nsample.tsv<\/td>\n<\/tr>\n
analyte.tsv<\/td>\nexposure.tsv<\/td>\nfpkm_uq.tsv<\/td>\nslide.tsv<\/td>\n<\/tr>\n
clinical.tsv<\/td>\nfamily_history.tsv<\/td>\nportion.tsv<\/td>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n

 <\/p>\n

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Access<\/h2>\n

Effective from January 22, 2024, you must read, agree and sign the Data Use Agreement <\/a>(you must be logged in through the Mount Sinai campus network or secure remote VPN). Access is granted within 24 hours, and on Minerva, you can load module $ module load dataark <\/strong>to see the path variables.<\/p>\n

By using these data, you agree to acknowledge BiNGS<\/a>\u2013the Tisch Cancer Institute Bioinformatics Core for Next-Generation Sequencing and the Data Ark team for all oral and written presentations, grand submission, awards, and publications resulting from any analyses of the data sets.<\/p>\n

Data Ark Data Sets<\/h2>\n

Please visit the Data Ark Data Set<\/a> webpage to explore other data sets.<\/p>\n

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Scientific Computing and Data \/ Research Data Services \/\u00a0Data Ark: Data Commons \/ TCGATCGA – The Cancer Genome Atlas ProgramOverview The Cancer Genome Atlas (TCGA) is a landmark cancer genomics program that molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types. The program is a joint effort between National Cancer […]<\/p>\n","protected":false},"author":415,"featured_media":0,"parent":1321,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_et_pb_use_builder":"on","_et_pb_old_content":"","_et_gb_content_width":"","footnotes":""},"class_list":["post-4645","page","type-page","status-publish","hentry"],"aioseo_notices":[],"_links":{"self":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages\/4645","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/users\/415"}],"replies":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/comments?post=4645"}],"version-history":[{"count":47,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages\/4645\/revisions"}],"predecessor-version":[{"id":7869,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages\/4645\/revisions\/7869"}],"up":[{"embeddable":true,"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/pages\/1321"}],"wp:attachment":[{"href":"https:\/\/labs.icahn.mssm.edu\/minervalab\/wp-json\/wp\/v2\/media?parent=4645"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}