TCGA data

https://portal.gdc.cancer.gov/repository

 

TCGA 에서는 DNA와 RNA 데이터를 여러가지 형태로 제공한다.

 

다음의 순서로 원하는 데이터를 다운로드 받는다.

 

데이터 정보 ( aligned by GRCh38 )

: https://docs.gdc.cancer.gov/Encyclopedia/pages/RNA-Seq/

 

1. 데이터 선택

: [ Files ] 탭에서 데이터 분류를 선택하고, [ Cases ] 탭에서 데이터 종류를 선택한다.

2. 그래프 위쪽 부분에 [ Manifest ] 버튼을 눌러 데이터 리스트를 다운로드 받는다.

: gdc_manifest.2021-08-27.txt

 

3. 데이터 정보를 JSON 형태로 다운로드 받는다.

: files.2021-08-27.json

- Number of data list : 16843

- Data shape : [{'data_format': 'TXT', 'cases': [{'case_id': '1a93dd15-f404-484c-b67c-98169d5522c7', 'project': {'project_id': 'TCGA-LAML'}}], 'access': 'open', 'file_name': '486778af-8f8e-4000-9812-409604e274a5.FPKM.txt.gz', 'data_category': 'Transcriptome Profiling', 'annotations': [{'annotation_id': '7cf91358-0db5-5fe9-9817-6e22dbb460c6'}], 'file_size': 550816}, ... ]

 

4. GDC Data Transfer Tool 을 다운받는다.

- https://gdc.cancer.gov/access-data/gdc-data-transfer-tool

- https://github.com/NCI-GDC/gdc-client

$ wget https://gdc.cancer.gov/files/public/file/gdc-client_v1.6.1_Ubuntu_x64.zip

 

5. 원하는 폴더를 생성하여 manifest 데이터 리스트에 있는 파일들을 다운로드 받는다.

$ gdc-client download -m gdc_manifest.2021-08-27.txt --debug --log-file logfile.txt

파일들은 [ Transcript ID | FPKM ] 의 두 컬럼 데이터와 annotation.txt 데이터가 각 case_id 폴더에 있다.

 

 

Breast
- TCGA-BRCA  ( 1222 )  -  Breast invasive carcinoma

Brain
- TCGA-GBM   (  174 )  -  Glioblastoma multiforme
- TCGA-LGG   (  529 )  -  Brain Lower Grade Glioma

Endocrine
- TCGA-ACC   (   79 )  -  Adrenocortical carcinoma
- TCGA-PCPG  (  186 )  -  Pheochromocytoma and Paraganglioma
- TCGA-THCA  (  568 )  -  Thyroid carcinoma

Gastrointestinal
- TCGA-CHOL  (   45 )  -  Cholangiocarcinoma
- TCGA-COAD  (  521 )  -  Colon adenocarcinoma
- TCGA-READ  (  177 )  -  Rectum adenocarcinoma
- TCGA-ESCA  (  173 )  -  Esophageal carcinoma
- TCGA-LIHC  (  424 )  -  Liver hepatocellular carcinoma
- TCGA-PAAD  (  182 )  -  Pancreatic adenocarcinoma
- TCGA-STAD  (  407 )  -  Stomach adenocarcinoma

Gynecologic 
- TCGA-CESC  (  309 )  -  Cervical squamous cell carcinoma and endocervical adenocarcinoma
- TCGA-UCEC  (  587 )  -  Uterine Corpus Endometrial Carcinoma
- TCGA-UCS   (   56 )  -  Uterine Carcinosarcoma

HeadNeck
- TCGA-HNSC  (  546 )  -  Head and Neck squamous cell carcinoma
- TCGA-UVM   (   80 )  -  Uveal Melanoma

Hemato
- TCGA-DLBC  (   48 )  -  Lymphoid Neoplasm Diffuse Large B-cell Lymphoma
- TCGA-LAML  (  151 )  -  Acute Myeloid Leukemia
- TCGA-THYM  (  121 )  -  Thymoma

Skin
- TCGA-SKCM  (  472 )  -  Skin Cutaneous Melanoma

ST
- TCGA-SARC  (  265 )  -  Sarcoma

Thoracic
- TCGA-MESO  (   86 )  -  Mesothelioma
- TCGA-LUAD  (  594 )  -  Lung adenocarcinoma
- TCGA-LUSC  (  551 )  -  Lung squamous cell carcinoma

Urologic
- TCGA-BLCA  (  433 )  -  Bladder Urothelial Carcinoma
- TCGA-PRAD  (  551 )  -  Prostate adenocarcinoma
- TCGA-TGCT  (  156 )  -  Testicular Germ Cell Tumors
- TCGA-OV    (  379 )  -  Ovarian serous cystadenocarcinoma
- TCGA-KICH  (   89 )  -  Kidney Chromophobe
- TCGA-KIRC  (  611 )  -  Kidney renal clear cell carcinoma
- TCGA-KIRP  (  321 )  -  Kidney renal papillary cell carcinoma

https://www.nature.com/articles/s42003-020-01146-2/figures/4

http://www.linkedomics.org/

Cancer Type	Cohort	ID	Samples	Death Event	Median OS (yrs)	Permission	Link	Download
Pheochromocytoma and Paraganglioma	TCGA	PCPG	179	6	NA	Y	TCGA, GDAC	Download
Prostate adenocarcinoma	TCGA	PRAD	499	10	NA	Y	TCGA, GDAC	Download
Adrenocortical carcinoma	TCGA	ACC	92	33	NA	Y	TCGA, GDAC	Download
Pancreatic adenocarcinoma	TCGA	PAAD	185	99	1.66	Y	TCGA, GDAC	Download
Ovarian serous cystadenocarcinoma	TCGA	OV	591	335	3.81	Y	TCGA, GDAC, CPTAC	Download
Lung squamous cell carcinoma	TCGA	LUSC	504	203	4.64	Y	TCGA, GDAC	Download
Mesothelioma	TCGA	MESO	87	72	1.54	Y	TCGA, GDAC	Download
Skin Cutaneous Melanoma	TCGA	SKCM	470	221	6.58	Y	TCGA, GDAC	Download
Stomach and Esophageal carcinoma	TCGA	STES	628	236	2.58	Y	TCGA, GDAC	Download
Uterine Corpus Endometrial Carcinoma	TCGA	UCEC	548	91	NA	Y	TCGA, GDAC	Download
Uterine Carcinosarcoma	TCGA	UCS	57	34	2.22	Y	TCGA, GDAC	Download
Uveal Melanoma	TCGA	UVM	80	23	3.82	Y	TCGA, GDAC	Download
Thymoma	TCGA	THYM	124	9	NA	Y	TCGA, GDAC	Download
Thyroid carcinoma	TCGA	THCA	503	16	NA	Y	TCGA, GDAC	Download
Lung adenocarcinoma	TCGA	LUAD	522	179	4.11	Y	TCGA, GDAC	Download
Testicular Germ Cell Tumors	TCGA	TGCT	134	3	NA	Y	TCGA, GDAC	Download
Stomach adenocarcinoma	TCGA	STAD	443	162	2.86	Y	TCGA, GDAC	Download
Sarcoma	TCGA	SARC	261	97	5.45	Y	TCGA, GDAC	Download
Colorectal adenocarcinoma	TCGA	COADREAD	629	124	6.94	Y	GDAC, CPTAC	Download
Lymphoid Neoplasm Diffuse Large B-cell Lymphoma	TCGA	DLBC	48	9	17.60	Y	TCGA, GDAC	Download
Esophageal carcinoma	TCGA	ESCA	185	74	2.19	Y	TCGA, GDAC	Download
Cholangiocarcinoma	TCGA	CHOL	45	19	3.84	Y	TCGA, GDAC	Download
Cervical and endocervical cancers	TCGA	CESC	307	71	8.48	Y	TCGA, GDAC	Download
Bladder urothelial carcinoma	TCGA	BLCA	412	178	2.84	Y	TCGA, GDAC	Download
Liver hepatocellular carcinoma	TCGA	LIHC	377	125	4.91	Y	TCGA, GDAC	Download
Glioblastoma multiforme	TCGA	GBM	595	472	1.21	Y	TCGA, GDAC	Download
Breast invasive carcinoma	TCGA	BRCA	1097	151	10.81	Y	TCGA, GDAC, CPTAC	Download
Kidney renal papillary cell carcinoma	TCGA	KIRP	291	44	NA	Y	TCGA, GDAC	Download
Brain Lower Grade Glioma	TCGA	LGG	515	123	7.29	Y	TCGA, GDAC	Download
Glioma	TCGA	GBMLGG	1110	595	2.05	Y	TCGA, GDAC	Download
Kidney renal clear cell carcinoma	TCGA	KIRC	537	175	7.57	Y	TCGA, GDAC	Download
Acute Myeloid Leukemia	TCGA	LAML	200	109	1.34	Y	TCGA, GDAC	Download
Pan-kidney cohort	TCGA	KIPAN	941	230	NA	Y	TCGA, GDAC	Download
Head and Neck squamous cell carcinoma	TCGA	HNSC	528	218	4.75	Y	TCGA, GDAC	Download
Kidney Chromophobe	TCGA	KICH	113	11	NA	Y	TCGA, GDAC	Download

 

 

Reference

- Systematic pan-cancer analysis of tumour purity (2015), https://www.nature.com/articles/ncomms9971

- https://rnbeads.org/methylomes.html