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ICGC數據庫如何下載癌癥數據

時間:2019-07-30 11:35來源:生信自學網 作者:樂偉 點擊:
ICGC網址:

ICGC網址:https://icgc.org/
幾年前,國際癌癥基因組協會(ICGC)在著名的《Nature Communications》雜志,發表了一篇令人瞠目的文章,它為即將到來的癌癥基因組學研究時代,奠定了基礎。該項目,是由Centro Nacional de Analisis Genómico (CNAG-CRG)和German Cancer Research Center (DKFZ)帶領完成的,是一項旨在為體細胞突變檢測產生可靠標準的研究,這些體細胞突變是癌癥基因組的一個標志。體細胞突變是一個細胞自發獲得的遺傳改變,可以在細胞分裂和腫瘤生長過程中傳遞給突變細胞的后代。體細胞突變不同于從父母傳遞給兒童的種系變異。

今天給大家介紹如何從ICGC數據庫下載數據,首先我們看下ICGC數據庫有哪些數據:

[ALL-US] Acute Lymphoblastic Leukemia - TARGET, US
[AML-US] Acute Myeloid Leukemia - TARGET, US
[BLCA-CN] Bladder Cancer - CN
[BLCA-US] Bladder Urothelial Cancer - TCGA, US
[BOCA-FR] Soft Tissue cancer - Ewing sarcoma - FR
[BOCA-UK] Bone Cancer - UK
[BPLL-FR] B-Cell Prolymphocytic Leukemia
[BRCA-EU] Breast ER+ and HER2- Cancer - EU/UK
[BRCA-FR] Breast Cancer - FR
[BRCA-KR] Breast Cancer - Very young women
[BRCA-UK] Breast Triple Negative/Lobular Cancer - UK
[BRCA-US] Breast Cancer - TCGA, US
[BTCA-JP] Biliary Tract Cancer - JP
[BTCA-SG] Biliary Tract Cancer - SG
[CCSK-US] Clear Cell Sarcomas of the Kidney - TARGET, US
[CESC-US] Cervical Squamous Cell Carcinoma - TCGA, US
[CLLE-ES] Chronic Lymphocytic Leukemia - ES
[CMDI-UK] Chronic Myeloid Disorders - UK
[COAD-US] Colon Adenocarcinoma - TCGA, US
[COCA-CN] Colorectal Cancer - CN
[DLBC-US] Lymphoid Neoplasm Diffuse Large B-cell Lymphoma - TCGA, US
[EOPC-DE] Early Onset Prostate Cancer - DE
[ESAD-UK] Esophageal Adenocarcinoma - UK
[ESCA-CN] Esophageal Cancer - CN
[GACA-CN] Gastric Cancer - CN
[GACA-JP] Gastric Cancer - JP
[GBM-CN] Brain Cancer - CN
[GBM-US] Brain Glioblastoma Multiforme - TCGA, US
[HNSC-US] Head and Neck Squamous Cell Carcinoma - TCGA, US
[KICH-US] Kidney Chromophobe - TCGA, US
[KIRC-US] Kidney Renal Clear Cell Carcinoma - TCGA, US
[KIRP-US] Kidney Renal Papillary Cell Carcinoma - TCGA, US
[LAML-CN] Leukemia - CN
[LAML-KR] Acute Myeloid Leukemia - KR
[LAML-US] Acute Myeloid Leukemia - TCGA, US
[LGG-US] Brain Lower Grade Glioma - TCGA, US
[LIAD-FR] Benign Liver Tumour - FR
[LICA-CN] Liver Cancer - CN
[LICA-FR] Liver Cancer - FR
[LIHC-US] Liver Hepatocellular carcinoma - TCGA, US
[LIHM-FR] Liver Cancer - Hepatocellular macronodules
[LINC-JP] Liver Cancer - NCC, JP
[LIRI-JP] Liver Cancer - RIKEN, JP
[LMS-FR] Soft tissue cancer - Leiomyosarcoma
[LUAD-US] Lung Adenocarcinoma - TCGA, US
[LUSC-CN] Lung Cancer - CN
[LUSC-KR] Lung Cancer - KR
[LUSC-US] Lung Squamous Cell Carcinoma - TCGA, US
[MALY-DE] Malignant Lymphoma - DE
[MELA-AU] Skin Cancer - AU
[NACA-CN] Nasopharyngeal cancer - CN
[NBL-US] Neuroblastoma - TARGET, US
[NKTL-SG] Blood Cancer - T-cell and NK-cell lymphoma - SG
[ORCA-IN] Oral Cancer - IN
[OS-US] Osteosarcoma - TARGET, US
[OV-AU] Ovarian Cancer - AU
[OV-CN] Ovarian Cancer - CN
[OV-US] Ovarian Serous Cystadenocarcinoma - TCGA, US
[PAAD-US] Pancreatic Cancer - TCGA, US
[PACA-AU] Pancreatic Cancer - AU
[PACA-CA] Pancreatic Cancer - CA
[PACA-CN] Pancreatic Cancer - CN
[PAEN-AU] Pancreatic Cancer Endocrine neoplasms - AU
[PAEN-IT] Pancreatic Endocrine Neoplasms - IT
[PBCA-DE] Pediatric Brain Cancer - DE
[PBCA-US] Pediatric Brain Tumor - Multiple subtypes
[PEME-CA] Pediatric Medulloblastoma - CA
[PRAD-CA] Prostate Adenocarcinoma - CA
[PRAD-CN] Prostate Cancer - CN
[PRAD-FR] Prostate Cancer - Adenocarcinoma
[PRAD-UK] Prostate Adenocarcinoma - UK
[PRAD-US] Prostate Adenocarcinoma - TCGA, US
[READ-US] Rectum Adenocarcinoma - TCGA, US
[RECA-CN] Renal Cancer - CN
[RECA-EU] Renal Cell Cancer - EU/FR
[RT-US] Rhabdoid Tumors - TARGET, US
[SARC-US] Sarcoma - TCGA, US
[SKCA-BR] Skin Adenocarcinoma - BR
[SKCM-US] Skin Cutaneous melanoma - TCGA, US
[STAD-US] Gastric Adenocarcinoma - TCGA, US
[THCA-CN] Thyroid Cancer - CN
[THCA-SA] Thyroid Cancer - SA
[THCA-US] Head and Neck Thyroid Carcinoma - TCGA, US
[UCEC-US] Uterine Corpus Endometrial Carcinoma- TCGA, US
[UTCA-FR] Uterine Cancer - Carcinosarcoma
[WT-US] Wilms Tumor - TARGET, US
1、進入ICGC官網:
https://icgc.org/
進入
官網之后,往下拉,在左下方,我們就可以看到ICGC的數據類型,比如中國的膀胱癌數據:

2、在網站最上方導航欄進入數據界面:Data Portal
也可以直接點擊進入網址:
https://dcc.icgc.org/

進入Data Portal之后,我們選擇DCC Data Releases進入數據版本

進入數據版本只有,我們可以看到很多數據版本,那么我們選擇最新更新的數據
點擊current進入數據選擇界面


進入到數據界面,點擊Projects

然后就到達選擇下載界面,在這里我們可以看到也有TCGA、TARGET的數據,如果大家需要分析TCGA或者TARGET的數據庫,那么直接進入TCGA和TARGET官網下載和分析就可以了,沒有必要在這里選擇。生信自學網也有專門的課程講解TCGA和TARGET數據庫挖掘。
3、選擇我們感興趣的研究,比如我們這里選擇LIRI-JP


3、選擇LIRI-JP進入數據下載頁面,我們可以看到LIRI-JP所有的數據,我們可以把所有的這些數據下載下來,下載很簡單,直接右鍵“另存為”

接下來,我們給大家解釋一下這些數據:

donor.LIRI-JP.tsv.gz   病人的數據(臨床數據)
exp_seq.LIRI-JP.tsv.gz  表達數據(測序數據)
sample.LIRI-JP.tsv.gz  樣品信息

simple_somatic_mutation.open.LIRI-JP.tsv.gz  突變數據
specimen.LIRI-JP.tsv.gz  實驗處理數據(可以區分正常和癌癥)
structural_somatic_mutation.LIRI-JP.tsv.gz 結構變異數據

在這里需要提醒大家的是,ICGC每個項目的數據是不同的,大家需要根據自己研究找到合適的癌癥,然后找到所有的這些數據。
當然也可以購買生信自學網給大家準備的《ICGC數據庫挖掘視頻課程》


責任編輯:樂偉
作者申明:本文版權屬于生信自學網(微信號:18520221056)未經授權,一律禁止轉載!
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