TCGA癌癥數(shù)據(jù)庫(kù)介紹專(zhuān)題

1、TCGA數(shù)據(jù)庫(kù)介紹專(zhuān)題上海爾云上海爾云-云生信團(tuán)隊(duì)云生信團(tuán)隊(duì)2015.9.20http:/ 1. 前言前言2. 數(shù)據(jù)產(chǎn)生歷程數(shù)據(jù)產(chǎn)生歷程5. 目前已有的癌癥種類(lèi)目前已有的癌癥種類(lèi)3. barcode4. Data types and data levels6. 數(shù)據(jù)下載解讀數(shù)據(jù)下載解讀目錄前言http:/ TCGA- THE CANCER GENOME ATLAScancerGenomeTranscriptomeClinicEpigenomeProteome癌癥種類(lèi)豐富，樣本量大癌癥種類(lèi)豐富，樣本量大34 kinds of cancer325 samples on averagehttp:/c

2、/數(shù)據(jù)產(chǎn)生歷程http:/ TCGA數(shù)據(jù)的產(chǎn)生歷程：1. 組織樣本和臨床數(shù)據(jù)來(lái)源網(wǎng)站(TSS)收集的數(shù)據(jù)發(fā)送到Biospecimen核心資源(BCRs)。2. BCRs提交臨床數(shù)據(jù)和元數(shù)據(jù)到數(shù)據(jù)協(xié)調(diào)中心(DCC)和測(cè)序中心(GSCs),獲取組織變異數(shù)據(jù),然后提交給DCC。3. GSCs提交跟蹤文件,序列比對(duì)后文件到癌癥基因組學(xué)中心(CGHub)。4. 提交給DCC和CGHub的數(shù)據(jù)可供研究團(tuán)隊(duì)和基因組數(shù)據(jù)分析中心(GDACs)使用。5. 分析pipeline以及由GDACs產(chǎn)生的數(shù)據(jù)結(jié)果通過(guò)DCC保存到研究社區(qū)（community）中。http:/canc

3、/abouttcga/overviewBARCODE解讀http:/ 詳細(xì)請(qǐng)見(jiàn)：詳細(xì)請(qǐng)見(jiàn)：/display/TCGA/TCGA+barcodeDATA TYPES AND LEVELShttp:/ DATA TYPESData LevelLevel TypeDescription1RawLow-level data for single sample單個(gè)樣本的低級(jí)數(shù)據(jù)Not normalized未標(biāo)準(zhǔn)化2ProcessedNormalized single sample data標(biāo)準(zhǔn)化的單個(gè)樣本Interpreted

4、 for presence or absence of specific molecular abnormalities解釋異常的個(gè)體3Segmented/ InterpretedAggregate of processed data from single sample單個(gè)樣本整合在了一起Grouped by probed loci to form larger contiguous regions (in some cases) 根據(jù)probe的位置分組4Summary/Regions of Interest (ROI)Quantified association across class

5、es of samples量化關(guān)聯(lián)類(lèi)的樣本Associations based on two or more兩個(gè)或多個(gè)的關(guān)聯(lián)Molecular abnormalities分子水平的異常Sample characteristics樣本特性Clinical variables臨床變異DATA LEVLES注意：低水平的測(cè)序數(shù)據(jù)存儲(chǔ)在CGHub /, 申請(qǐng)下載時(shí)需要DUNS number. The Cancer Genomics Hub (CGHub) is a secure repository for storing, cataloging, and a

6、ccessing cancer genome sequences, alignments, and mutation information from the Cancer Genome Atlas (TCGA) consortium and related projects.目前已有的癌癥種類(lèi)癌癥種類(lèi)豐富，樣本量大癌癥種類(lèi)豐富，樣本量大34 kinds of cancer325 samples on average詳細(xì)見(jiàn)：詳細(xì)見(jiàn)：TCGA publication guideline, /publications/publicationguidelines數(shù)據(jù)下載及解讀http:/ 最簡(jiǎn)單的方法：最簡(jiǎn)單的方法：/tcga/tcgaHome2.jsp 第第1封郵件通知下載申請(qǐng)已經(jīng)提交封郵件通知下載申請(qǐng)已經(jīng)提交第第2封給出下載鏈接封給出下載鏈接Step4Step 4 文件內(nèi)容文件內(nèi)容File_manifest.txt，對(duì)所下載文件的說(shuō)明，對(duì)所下載文件的