收藏級(jí)資源腫瘤數(shù)據(jù)庫(kù)匯總

1、收藏級(jí)資源|腫瘤數(shù)據(jù)庫(kù)匯總現(xiàn)如今，隨著人們生活方式和環(huán)境的改變，惡性腫瘤已經(jīng)成為疾病死亡病因之一。腫瘤在全球呈現(xiàn)發(fā)病率增高，以及發(fā)病年齡年輕化的趨勢(shì)。2019年，ACancerJournalForClinicians雜志發(fā)布了最新的數(shù)據(jù)。該報(bào)告估計(jì)，2019年美國(guó)將有1,762,450例新的癌癥病例和606,888例與癌癥相關(guān)的死亡。傳統(tǒng)化療是對(duì)抗癌癥的常見方法，但它會(huì)攻擊全身，造成不必要的副作用，如脫發(fā)，惡心和疲勞。靶向治療選擇性地殺死癌細(xì)胞而不影響健康組織。靶向藥物開發(fā)將成為治療癌癥的重要手段。圖1腫瘤靶向治療高通量檢測(cè)技術(shù)迅速發(fā)展，使得與腫瘤相關(guān)的組學(xué)數(shù)據(jù)迅速積累。這些數(shù)據(jù)對(duì)于研究腫瘤的

2、發(fā)生發(fā)展機(jī)制具有重要意義。對(duì)數(shù)據(jù)的挖掘能夠確定許多與疾病有關(guān)的基因，為治療和發(fā)病機(jī)制的研究提供新的思路。如何有效利用和存儲(chǔ)這些信息就顯得尤為重要。腫瘤的生物信息學(xué)數(shù)據(jù)庫(kù)的建立提供了有效的解決方案，對(duì)腫瘤基礎(chǔ)研究的發(fā)展、臨床治療水平的提高具有極大的推動(dòng)作用。以下是一些腫瘤相關(guān)的數(shù)據(jù)庫(kù)分類和大致的信息。綜合性腫瘤數(shù)據(jù)庫(kù)腫瘤基因組數(shù)據(jù)庫(kù)腫瘤DNA甲基化數(shù)據(jù)庫(kù)腫瘤轉(zhuǎn)錄組數(shù)據(jù)庫(kù)腫瘤蛋白組數(shù)據(jù)庫(kù)腫瘤相關(guān)基因的數(shù)據(jù)庫(kù)腫瘤與藥物數(shù)據(jù)庫(kù)1.綜合性腫瘤數(shù)據(jù)庫(kù)綜合腫瘤數(shù)據(jù)庫(kù)匯總?cè)绫?所示。表1綜合性腫瘤數(shù)據(jù)庫(kù)DatebaseDescriptioncanEvolveWebportalforintegrativeonc

3、ogenomicscBioPortalcBioPortalforCancerGenomicsCGAPCancerGenomeAnatomyProjectCGHubCancerGenomicsHubCGWBCancerGenomeWorkBenchCOSMICCatalogueOfSomaticMutationsInCancerICGCInternationalCancerGenomeConsortiumTCGATheCancerGenomeAtlasUCSCGenomeBrowserUCSCCancerGenomicsBrowser以下是對(duì)數(shù)據(jù)庫(kù)的簡(jiǎn)要概述1.1canEvolvecanEvol

4、ve存儲(chǔ)的信息包括：基因、microRNA(miRNA)和蛋白質(zhì)表達(dá)譜、多種癌癥類型的拷貝數(shù)變化(CNAs)以及蛋白質(zhì)-蛋白質(zhì)相互作用信息。cBioPortalforCancerGenomics(cBioPortal)cBioPortalforCancerGenomics是一個(gè)癌癥基因組數(shù)據(jù)探索、可視化及分析平臺(tái)，可用于多個(gè)癌癥基因組學(xué)數(shù)據(jù)集的交互式探索。該數(shù)據(jù)庫(kù)可提供CNA、基因突變信息。針對(duì)每個(gè)基因，它可給出多個(gè)信息，主要包括：基因的CAN信息、基因突變?cè)跇颖局械姆植?、突變位點(diǎn)和頻率、共表達(dá)基因以及生存曲線等。對(duì)于用戶提供的基因列表，還可生成互作網(wǎng)絡(luò)并提供已知的相互作用的藥物。cBioPo

5、rtal在發(fā)現(xiàn)腫瘤相關(guān)突變、分析基因的生物學(xué)功能以及藥物選擇等方面的研究中具有重要推進(jìn)作用。cBioPoirtal&HH|伽佬n&4!lwiMDF*MMg：ClP別輯if.Sjilg伽剛工“MCISludlai問(wèn)也ZM乞如筍HCueatori:nS#R5r.：卓.河、0 x1悴巾上-冊(cè)“屮世iOrtdr*崎|員打PdfiCiKtf3d5MnrilQIvr：UKfiMVrzzWftMWJMGC.fWLWMKJEPai-Lhi|Kri7DUrs血|PadiahiErwi-uKV!lr*iMU.GHFniKriZIW：i.cdiM塾Aji韶山dhMbuM3wra*iGaanheAOfflwncw-S

6、araftflrtiitcw.PmX窗c#關(guān)uUvuiku1411n|TCGKPirem.；血pifvdEmeo記如t訕Mi單ulKiY:i：ri取山O-MifrihrhEn-TrwlEirhiEoflif*-3rUdv4CiltMia3014%-W岬H：.KMrvrITMliirq日細(xì)丹TffitiChOUiX3fCiHUllCTUtM|UEWKnil|iK&KCViCafrSMRuACiilj-ChcfMEvmmrgfrMmriCMcn3rfKn.lMfli*SIITi口C-KmdG”3112)Ow|-rnmyi|iTCs.戸押佃3曲他口UrDtiaMdawn*iTCQiii.PirniE

7、iah*4圖2cBioPortal數(shù)據(jù)庫(kù)的主頁(yè)CancerGenomeAnatomyProject(CGAP)CGAP網(wǎng)站主要提供了cDNA克隆、文庫(kù)、基因表達(dá)、SNP以及基因組變異等信息。CGAP收集的數(shù)據(jù)包括正常組織、前癌組織以及癌細(xì)胞的基因表達(dá)水平。,hlaticnalCancwInstitulB11、NUliU血1血凹MmKF|ihmU3欝rCancekGenomlCanclflGlnomeFFARACTERIZATiONINITIATiVfCGAP聞笳tOnranKE口tnirwues沖口匕albRMhlPm宙謀卒貢dmCGCICamatT輝可WflirwasPuHkxhK+耳9口m

8、ERmOiwerAikaiainyP4fieci(CMP)TbaMCrsearner&4QXTH打口他叫PiajiKEMugncuihwmriiwihvQ.adapiBiinnprsfttEaFrHrrrui.prKflnoar4ndcwkwoshiIt-rfngw*jahW3tinonaCJiamwzxianXGCjIniidhkincorpcraDimmcSharattrnEJtMn由inckmani：網(wǎng)tranaripcCTne專ustigwcorripenraoniobrt”iid-iUfriufrinvfieaik.d*urrQHit&inrnLKwadrvuiAixx才曲c:int

9、iAvandhwHivpmjKtiintingHibrartpwiwrtmcidi0vcrvthoughiaddx-araiQK4aMdcthsrngVeilCGAPOi曲CGCF圖3CGAP的主頁(yè)CancerGenomicsHub(CGHub)CGHub是美國(guó)國(guó)家癌癥研究所(NCI)測(cè)序項(xiàng)目的在線存儲(chǔ)庫(kù)，其數(shù)據(jù)來(lái)源包括癌癥基因組圖譜(TCGA)、癌癥細(xì)胞系百科全書(CCLE)和產(chǎn)生有效治療(目標(biāo))項(xiàng)目的治療應(yīng)用研究(TARGET)3個(gè)國(guó)家癌癥協(xié)會(huì)項(xiàng)目，數(shù)據(jù)來(lái)自25種不同類型的癌癥。CancerGenomeWorkBench(CGWB)CGWB提供了一系列工具來(lái)挖掘、整合以及可視化TCGA等數(shù)

10、據(jù)庫(kù)中的基因組和臨床數(shù)據(jù)，它是第一個(gè)將臨床腫瘤突變譜與參考人類基因組整合在一起的計(jì)算平臺(tái)。用戶可快速地比較患者臨床信息與基因組的變異及甲基化等。CatalogueofSomaticMutationsinCancer(COSMIC)COSMIC是世界上最大最全面的有關(guān)腫瘤的體細(xì)胞突變以及其影響的資源庫(kù)。它主要提供多種腫瘤細(xì)胞基因組中的CNA、甲基化、基因融合、SNP及基因表達(dá)等信息。這些突變信息是從科學(xué)文獻(xiàn)中手工整理的。idutliuCOSMICPrnjKfaDpmrrwrtftnnCoffSod3KWCIIPH.4IH!LHOBCtfUrmWMrtEJWKW*owmcm1uZbxuuZKilE

11、PCIEKHIjdH1蟲圖4COSMIC的主頁(yè)InternationalCancerGenomeConsortium(ICGC)ICGC的目標(biāo)是獲取包括膽道癌、膀胱癌、血癌等多達(dá)50種腫瘤及其亞型的基因組、轉(zhuǎn)錄組和表觀遺傳的全部信息。這些數(shù)據(jù)可促進(jìn)癌癥的機(jī)理和治療研究。圖5ICGC的主頁(yè)TheCancerGenomeAtlas(TCGA)8TCGA是由美國(guó)國(guó)立癌癥研究所（NCI）和國(guó)家人類基因組研究所資助,關(guān)注與癌癥的發(fā)生和發(fā)展相關(guān)的分子突變圖譜。該數(shù)據(jù)庫(kù)主要對(duì)樣本進(jìn)行外顯子組和基因組測(cè)序分析,所提供的數(shù)據(jù)包括：基UsingTCG*CoMbGt因組拷貝數(shù)變化、表觀遺傳、基因表達(dá)譜、miRNA等

12、。IOjKANCERLiwChatPubllcatiowOirtionaryAB<TCAMCERCANCERTYPESCRAHTATRAJNllGNEWSKEVENTSmrrchQHanrtAAixxiLNClxhvCiCCGRd咖rohSciyilTheCancerGenomeAtlasProgramTheCaiKflrGenomeAJtZis(TCGA).alanmarlccatKergenomicspnogrrn,molecularlycharacterizedqve*20r0DOprimaryditefarwlmatchednormalsamplesspamning33cancer

13、rypes.ThlsjDlmelfDrtberrieenilieNatiarilCancerInstituteandtheNsignalHumanGenomeftewarchrestitutebegenIn2006.bringmgroqetherrMearcherEfromdrverEi?disciplinesaridmultipleinstiitutiorOwrtiienes?tdozenyea勺TCiAgetfifir-atedover2庁peistrytetofgfinGmksepigenonctrsnscriptomic,BndproLeomlcdau.Hiedacawhktilias

14、制re閱丫leadwimpravemencsInour抽lliycddiagtfiose,creauandpreventcant叭will電publicforaroneIndieresearchcwwnuniiyTouw-.圖6TCGA的主頁(yè)UCSCCancerGenomicsBrowserUCSCCancerGenomicsBrowser是一個(gè)可以對(duì)癌癥基因組學(xué)和臨床數(shù)據(jù)進(jìn)行整合、可視化、分析的網(wǎng)絡(luò)分析工具。它保存癌癥基因組及臨床數(shù)據(jù)并收集了樣本的多種信息，包括基因表達(dá)水平、CNA、通路信息等。在UCSC的癌癥基因組瀏覽器中，可實(shí)現(xiàn)不同樣本以及癌癥類型之間的比較，分析基因組變異與表型之間的相

15、關(guān)性。e.NkFR=arfDFC.MJFGFHhSHNIHmiGenomeBrowserOurtoolsGenomeBrowserFnterauivgNvisualizegenDRiicdataBLATrapidly#li呂nsequencestoih?aerom&TittleBrowerdoTiloaddatafromeGe?ianieEh*databaseVariantAnnGtatiwIntegratorgetfunrtmal曲ectpredictiorsForvaiigintcallsDataIntegratorcombinedataKwrcesfromttwGerdmeBro.Yse

16、rdatabaseGerwSorterfinden凹thataresimilarbyeMpressionandothermetricsGenomeBrowserinaBox(GBiB)runlheGeromEBrwercmvdula口toporssrverIn-SilkjQPCrapidlyalfsnPCRprimerpairstoIheeTOrneLiftOvercnnvprtgenonecoordinatesbehveenessembliesTrackHubsmpwLandviewexternaldatatracks-MoreGenomeBrowserToolsMfirorsDmnload

17、sMyDitaAboutIPs圖7UCSC癌癥基因組瀏覽器主頁(yè)2.腫瘤基因組數(shù)據(jù)庫(kù)腫瘤細(xì)胞的基因組中都存在著大量的變異，主要包括染色體結(jié)構(gòu)的變異、CNA、基因融合以及SNP等。拷貝數(shù)改變(CNAs)在很大程度上有助于癌癥發(fā)病機(jī)制和進(jìn)展。腫瘤基因組數(shù)據(jù)庫(kù)匯總?cè)绫?所示。表2腫瘤基因組數(shù)據(jù)庫(kù)DatebaseDescriptionarrayMapReferenceresourceforgenomiccopynumberimbalancesBioMutaIntegratedsequencefeaturedatabaseCanGEMCancerGEnomeMineCasSNPCopynumberalte

18、rationsofcancergenomefromSNParraydataCGPCancerGenomeProjectArrayMap10ArrayMap提供預(yù)處理過(guò)的腫瘤基因組芯片數(shù)據(jù)以及CNA圖譜。在ArrayMap數(shù)據(jù)庫(kù)中，用戶可搜索自己感興趣的樣本，并在此基礎(chǔ)上分析感興趣的基因或基因組片段上的CNA；用戶還可以比較兩個(gè)樣本之間的CNA的差異。arrayMapSearchSamplEESeerthPubfiGa(i(XB:Uillviersllyof；Zurich*1Citation&LktsingusrGuick!Re叩I已卜visualizingcan匚曰genomearraydat

19、afFSMapisacuratesreferenceifetBbasem仃isbioinFarniBticsneiiaLrcE-largetingcopynimberpr-Diiing訂2詣Inhuman田n皆.lhearrMapd=it=b3pras/ide&entrypointiormelanasisarmaInnonru1lUjiIe習(xí)B0rncrikufflHrlilnm衛(wèi)M+Ff/WWWlMrW吐nhi|hHurrBhaiMm|ftibiwuffkiL*|PLiikrhi|i屮|3加|3whIcwMwimawd|CartEMTu與.*I!HllJ?WelcometoCanGEMBwo

20、a*CExHK-MfzH-iipub4-wukru-kf5iwnc4nkJirmabMi4biXii呻曲皿昭M盯穽也町町4耐pws-onw-irconpsuiMe-qetwnKnptrldtudi(aC.GHididckrijnhhqqIqhwt冊(cè)luniMHhnLili(Jf*VsM甘利bE-!-ilh*MifvTNlciorripyiDut*Mmdl|Ca-iiHMYh.komdrf*j*Cfq也Hpifhrap-W9*11j+ErcveElacwsOmvMrmiChipmfHirMKFmEfjanEf*tiLfwiiiuzpuidU”*iiiknwi筑a-iTftfartAh-4.17M

21、UG應(yīng)1990西刖ITS莊材屮1釀旳討a-i鈕ftwLihit-f-d-jUnrtvl1vlVud*MAnr.hvt卜呻.人NrII打tl-HilTtnldlKn+1jrpi呻&nnjiwcewAsft.mijridMrfMd窗亡嗣qKfTi期憑*EtfGu卻目貳111LlirJM：liwdjlJllilWILI-曲士UKgicEINPJDUEQCLL倔S.iOAh8TtAtMbGomoamw*tml*DrwriM-rrtWTpefKIbIVCJbflhllrDf-IlHJutfXreikmCh11GDieIjjiLhwHmujbt,-Fji4Hhd7-.#i_4ilml圖10CanGEM的主

22、頁(yè)CancerGenomeProject(CGP)14CGP提供了腫瘤中的CNA及基因型信息，該數(shù)據(jù)庫(kù)的主要目標(biāo)是利用人類基因組序列和高通量的突變檢測(cè)技術(shù)識(shí)別體細(xì)胞突變，進(jìn)而發(fā)現(xiàn)人類腫瘤發(fā)生過(guò)程中重要的基因。該數(shù)據(jù)庫(kù)還提供了一些識(shí)別突變、CNA的軟件，如BioView、Home-fioenreGRAFT等。Anchrsofi-Group仙抄忙!&OfmfetumMIOrtindl”myGroupsFacultyGroupsgi8W*CTi$(MFMMIjrini)他辭爲(wèi)玲切野蘢曲郵h1嵌|巾圉護(hù)套腳聞IW吋訓(xùn)rf蝕*1叩門亦牌科1曲.蚌也呻M紳詢Wirrpinarnti:JjlFouEandA

23、smkIbccFacuiymwiberalud由ormwigroups已pascdKiDraii創(chuàng)幻?,PNDmlefiis!suppanseiIT.AAiWClfiWFftCWOfnup&AarwfinG*DU(iMhnKGr(MBjnxHOETGUpBjpTDKsirGroupBcjrjsuErcupCm#網(wǎng)刪為戲謝Wiiifiiiffii|&ri5nifctBemmanimpBrad即肓mupCancerGenomePmcctCw審GwriCi&曲zmic*DcinwEinMpEmitEnujpFvnokrdlB#fonldlWTGem?EdrufflMDfAfdMQdtfiDnWJSi

24、nwliTim衛(wèi)diicnZCanmonarnicaQuanciuiiKmod日&ofganadipiGrsskfi圖11CGP主頁(yè)3.腫瘤DNA甲基化數(shù)據(jù)庫(kù)DNA甲基化修飾是表觀遺傳學(xué)的一種重要形式，它調(diào)節(jié)基因的轉(zhuǎn)錄水平，對(duì)維持細(xì)胞的正常功能起著重要作用。DNA甲基化模式的改變可能導(dǎo)致癌癥腫瘤DNA甲基化數(shù)據(jù)庫(kù)匯總?cè)绫?所示。站(4機(jī)年Kte問(wèn)咖討iMecnzDi卿囲臼就】恨血畑餉罠悵1辭表3腫瘤DNA甲基化數(shù)據(jù)庫(kù)DatebaseDescriptionDiseaseMethHumandiseasemethylationdatabaseMENTMethylationandexpressiond

25、atabaseofnormalandtumortissuesMethDBCommonresourceforepigeneticphenomenonMethHCDNAmethylationandgeneexpressioninhumancancerMethyCancerHumanDNAMethylationandCancerNGSmethDBNext-generationsequencingsingle-cytosine-resolutionDNAmethylatio31DiseaseMeth15DiseaseMeth是一個(gè)人類疾病甲基化數(shù)據(jù)庫(kù)，其重點(diǎn)是對(duì)各種疾病的DNA甲基化數(shù)據(jù)集進(jìn)行有效的存

26、儲(chǔ)和統(tǒng)計(jì)分析。它涉及的疾病包括癌癥、神經(jīng)發(fā)育和退行性疾病、自身免疫疾病等。在DiseaseMeth中可以比較疾病與疾病之間、基因與基因之間以及疾病與基因之間的甲基化關(guān)系。Di$ea$eMethversion2.0hehumandiseasemethyllationdatabaseDnwnOtKadHomeSearchAri-alfzeDIsHethBrowserHelp柚型沁ins*Mar211a&1&,ThcSGarchEngirwiwxradfisqnsdntathracquan*entrance:Garw&ajriti,DiEQasaSajirdiiandAdvjnEflSidrili.

27、IntirwIUCtlQniDIseaseMethverslQn2.0dettasummaryThehundisesemethyiadond3t9basrDi&easeMeth湘舊on2.0is呂別曲冏泗Hr&soircefocusedanthbarrntmathylaiYifiofhumanUntilwsrit曲bulesoflarqa-ECJiladatsarc：JivabtaandarertizreasinglYgmwn,fnornwhictirnETCinfirmatKincmnbamnG?JtogjinfurtharntarmtKintQarctehumncksEascs.SkinC

28、utaneouHMdancrnatSCMJ-267呂色airetiVl5U9llzeAnalyzeDataDiseaseMthVersionKlchevrfinalpapllajiceil&arckicKlRP-311AcixeMioidLLfcemiab!uyiL:787LbwhxacelLlartart6ioLD-360BidderUrahelial匚artinoma0LCAJ-2511ijiiob!acni3muftiionnefGeHJ-507BranLowerSr-ideGhamaLGG:IL口ElBrnastInvasivecarcinoniaBft匚M1274Sidnevrena

29、lclearcdlc-arciicm3KJRC:75Lun-g*j&ioc-arcirioniai_ijD-51AO-arianserouscvataffenoc-ar-dnomaCO-1622UterirwCtrpu3GrdofltnalCardnomaliXiE匚:2173LltiqsuamouflcellJlunDirrdIbsiksThDianlixmiisldad4rT5tnmsqIqeIik!dahrramtiiCECiGcnb曰pr0ianEhmrsusijrtdTOGAHhftCanbariZwiomaAl曲IGeneSearch-Cwal-CsnoawNormal-Suttj

30、ipG：-CcmiisiwOverview-lnlja3jdi3&spOHK4dix.OBST111Zwahanana叩口叩勺口口a4jBanKaraTEL*32-+2-BGn1l4FAXKB2-J2-afll-1T5aCapTight2D11苗KaraRfepartFiingttJgMEidecwnMm3日KbachrnulDEffK=dE日；4lrlgnisrts&had.圖13MENT的主頁(yè)MethHCMethHC是一個(gè)集成數(shù)據(jù)庫(kù)，包含大量DNA甲基化數(shù)據(jù)和mRNA/microRNA在人類癌癥中的表達(dá)譜。這些數(shù)據(jù)可以幫助研究人員確定表觀遺傳模式。DauProcessAnnotationU

31、CSGenomeSrowMirOB$rvFxpffWEiQnd4lt(RNAScq)nnicroRPJAEipre-uiandma4mlRf4A5ehvLailMiuidChiterUftlhyCiihMi1Ifil/diieiibil5gsiIsr-s*ei-h（i!itm網(wǎng)1巧hgi|州呦雖鴉H閒WbM4伽昭“閆曲日mUWWJtalOflKVMrtw*曲lutwvKjEdDrchrK）wnniUibuviaiaMzLiiMrafFirDd【i*山mdEiLa-laoii扌canuiird*4-MW；EtrS4RdEiiWIEinj卻dYOtAMtHICUDi綿Crickladwrmlhfa

32、iLMnrlmin#1*ranAvaxciiiiKr9n*n-am*Thtradr1r0mEicAUHEPtUaitriL3iasituldTnaTMTh?jijlugtMhWTMfiHU.MfffkjilMiiMil沖芮HEli,奸if4g?T旳:!ti助!nhwtfai,rlftJAHBih-Nirngtmi|9!ilon3fdcviceiIluriiHIH抽dtla疳DH.*.wiiliiwcK-r-iEkM的e.mlalcviandcwairionii#nlhxnpt射t陽(yáng)叨廉.aidihikludclomEdiwlixm阿呦pK-diiw*Klag.IniKiirwikmMCvMfl

33、kuI,piIWie0pThSHdSBIFEiKKHSFdfinphcaWfilHFN*Gffr團(tuán)的丼如IIHlp垃田吊aiUUOUtfdOU33$dillttVilYaMrtiUiliiCMArl.eI金曲打lid由Wj*MCanoai汕diiKinqasmitimirkwYraiwnKut4別auri日crtonr-torEuhrlCGIdsivbuKfi祈加科qalMiaiiuihiiii4BvaiCdh皿13“ilrMcaiu啦皿誠(chéng)聽RdfiiihgiiJAincarionMmwh號(hào)iburwnlaiirdttK-iYir）alrwE|眄40也=LaAjpwld-ltMJiiqtEp3

34、|nnTiic3Praj*d&CfelmMrtljCwvrilariHhkijijiattarrbywtctiwmhJJIfc#Id!-criaaidarotieallaudrEhamlkusrrH-號(hào)G.mHth豈、事Ityujriki*TrliUnheifiiiiBbnjsFf!1咤*/Cl弊*農(nóng)iEuwIsiltirpswnwrtaglitihurTwik4il.C,EM眄IflrpiflJJ.Zhpr.q：dpBp.rtpilli|.JZEKWefT/CpicijrHi?71kmsiCT4Arwhj/twiiandCHK*r如沁匕曲知.35DffM理1尸世刊曲圖15MethyCance

35、r的主頁(yè)除了上述針對(duì)癌癥基因組甲基化的數(shù)據(jù)庫(kù)外，還有一些數(shù)據(jù)庫(kù)搜集和整理更為廣泛的甲基化數(shù)據(jù)，如MethDB和NGSmethDB。MethDB是較早的DNA甲基化數(shù)據(jù)庫(kù)，主要集中于環(huán)境因子對(duì)甲基化的影響；NGSmethDB叫基于高通量測(cè)序數(shù)據(jù)，最近更新中還包含了SNP信息，以便后續(xù)分析。腫瘤轉(zhuǎn)錄組數(shù)據(jù)庫(kù)腫瘤細(xì)胞具有較強(qiáng)的生長(zhǎng)和繁殖能力，生命活動(dòng)旺盛，因此與正常細(xì)胞相比基因的轉(zhuǎn)錄水平和模式也存在較大的差異。表4腫瘤轉(zhuǎn)錄組數(shù)據(jù)庫(kù)DatebaseDescriptionArrayExpressMicroarraygeneexpressiondataChiTaRSChimerictranscriptsa

36、ndRNA-sequencingdataGEOGeneExpressionOmnibusmiRCancerMicroRNAcancerassociationdatabaseOncomineCancermicroarraydatabaseOncomiRDBExperimentallyverifiedoncogenicandtumor-suppressivemicroRNAsSomamiRSomaticmutationsimpactingmicroRNAfunctionincancerArrayExpressArrayExpress是基于微陣列和高通量測(cè)序(HTS)的功能基因組實(shí)驗(yàn)的主要知識(shí)庫(kù)之一

37、。ArrayExpress中的所有數(shù)據(jù)都以MAGE-TAB格式提供。4韶rvHceaisResesncn總Tr*ninfloAiwuiuaEMBL-EBI:：；:HustonEM9L-EHIArrayExpressr-HnDj-iJdhWCAdwardiCihiIbciuaHomeSutmm|m|pI*loginiiilDataContentUpdaladlodayal03:0072012eKp&nrnents23&54Qiassays-M41T&ofarchived-data&Links%ToolsandAccess冽RelatedProjectsArrayExpressfunctionlg

38、enomicsdataAiFgyExpressAndhi*erfFundionalGenomicsDabaslDnssdatafromhagh-itiraughputfunclionai9mc*nic5experirngnte,andprovidesItiesa：刪曲furreiEfl1otheresi&ancticonwnuniiy.rowseArrayExpress需LatestNews11February2tl19-AfvayExp/s；&-.p起b葩訊常rpublishe-d!An旳pubicsUDH雖洌binglhedewlDpnienlEndfature-planstorlii&A

39、rray&cpressariHWmanddalahaseservicerecenllxbeenpublrshednNucleicAodsR&ssarcJi:AjrayEkpresaMpdaba-IhmMuistogJmle-cal出甲勵(lì)刖斷daia_Rtadil.dodrsccwrUhebreadlhoilh&dalacorrtariedwilTinthearchiveandhoMrilhssdevelopsaverIheyears粘ren&alh&lal&stlecPinol旳wenhjedkx詒IoenDfinlcs.inpfliljculersinglecellsequeuKlna.自血

40、!tolearnaboiltheimprowdfuiKtonginfescaitslinkedsubmissonLool.Annfflare.pleaseatsthispapermyourpublkticvucsiMhemirerferenangArrayExpress圖16ArrayExpress的主頁(yè)ChiTaRS20ChiTaRS數(shù)據(jù)庫(kù)包含嵌合轉(zhuǎn)錄本和RNA-Seq數(shù)據(jù)。ChiTaRS嵌合轉(zhuǎn)錄本和RNA-Seq數(shù)據(jù)數(shù)據(jù)庫(kù)是由GenBank、ChimerDB、dbCRID、TICdb和其他用于人類、小鼠和蒼蠅的數(shù)據(jù)庫(kù)的表達(dá)序列標(biāo)記(ESTs)和mRNA識(shí)別的嵌合轉(zhuǎn)錄本集合。THEIMPRO

41、VEDDATABASEOFCHIMERICTRANSCRIPTSANDRNASEQDATA*沁.vJ-aciana1血InvEssticiisriesV-viEVDncoldgcisEUMnati直RRflAiCKMin駁射帕期1AMD4砒AZtJUICHOMMNK$HUBTHEIMPROVEDDATABASEOFCHIMERICTRANSCRIPTSANDRNASEQDATA,CH-ITARS-2/1沖蝕旳也補(bǔ)伽mcwaimESBi譽(yù)巾mRjjAsEniGer&riktipwEitenusedtotetanychrnencrima弓orwoormoreQ啊怙瑞gengs旳宦ousantfeo

42、rthrnsncESBby附屮sequencingwefoLTdIhaflIhtEiprE55nlevelncNmertESTSisgeneralkiwandIhehghtyEesuespeciDcinnormalcel&HerewepeewrtWevmcnenn任曲創(chuàng)aaeMdence&i空Inis旳呂ns弓叩peofTie昶氏曰國(guó)eniniaiLiraniunpbdinesa帕證邊eonfirriwd申阿Imenl曰忖byFTT-PCR|PCR.PHAcwerlnand斤曲弘艸咖1畑$feneddion.#eccNfetedgbouM.JOOcanciixetwinlBwiffilheei

43、prKxcfilereterrchmencRFlAscomUnwedhyIhtpared-endRr4A.-sequericingeipenmentaindnenailbssuesrthLm;an&metaidtillfliesGriaiMi*作附口Ciinw3ftghnPUBLISHEDUHiT廨月鳥事日郵由燈竄麻*事riumtsm鬥匕卑仃；jh盅切柯吃欝1肝力曰耳1并口內(nèi)心代心嘩魚口“哥勺。尸勺日即和口燈停注直日0甘網(wǎng)欝昌晝丑倨N*1口idgpTBi”dc;|QdQ紬陽(yáng)門舊|*1Q41PuaMtHIbfl.mOhiTM雷aatstfmPfaWiiridivCQii.Diioni?？苾?nèi)“口麗

44、勺rq占爭(zhēng)UpHOriedbyCMjvbgiiti喘用帆.COtH則盼KSNC&DC踐*皿飢圖17ChiTaRS的主頁(yè)GeneExpressionOmnibus(GEO)21GEO是由美國(guó)國(guó)家生物技術(shù)信息中心(NCBI)建立的，其最初的目標(biāo)是作為一個(gè)公共存儲(chǔ)庫(kù)，存儲(chǔ)主要由微陣列技術(shù)生成的高通量基因表達(dá)數(shù)據(jù)。此外，該數(shù)據(jù)庫(kù)還包括比較基因組分析、描述基因組蛋白相互作用的染色質(zhì)免疫沉淀分析非編碼RNA分析、SNP基因分型和基因組甲基化狀態(tài)分析。NCBIRuiuca&MH謝Rj回CEQHomeDocLmencaanQuery苗曰!鮎疋唧笨。GereExpressionOmnibusWr*liqprwu

45、iQnOnrltLiiS44rchGettingStartedOwi申FMfttwinGEOOsliSfflB赳xmGEO尸町AbouIGEDJRyUiaJySitsMowtaConslrurt3AeryHwMDmwikKadDLalaToolsSsHirhterStudiesaftGEODataSetsSaardiforGerri訶啦iiJiSDPraffaiSoldiGEODwxriFrt3liCTiAfiBiyze-a5i曲hGEQ2RSoidrinihEuuYriWtifTficPragiair-alKArcFTPSif包row空eContent口帝血聽E*wwr口at昭gSffifl

46、SG)PUitowia:如E1122251dDM1IU9DGEOisapjbikfundiDnaigprwmwschfcarepafcarysupfwrijngMME-ccnipfiarittihlaEubmhsianiAiray-andBfquwce-tHseddataarenceptedIndsarapridedIphelpu生hiquerfanddmfflkHdwpimTfc!amcuratedgnAKpf5diOlplfithAInrorrnAtiontorSubmittersLtjCfinra-Submh9jbnniw0sGudlnd!&UpdateGuKtainmMLCJJEEta

47、ida-daCling3rilCkimauidCu陽(yáng)Bnikratruri*Z3D4wthIhrtLEb4dii|YWHOfl號(hào)til/EdrhrpaiLir圧斗=-inf4cL:n-MlHijirich,oxtansi曲ii/id芒nnrrolfidonidn劈afehiu-SevritfdistdAhiala一卯ihcanndonjichai:.assuredvjradoaid&EiitInErprLJtlonGofrasulibd|.4uknowll*Mbpyu匸irKhid*ttivImfarDncmtirRHanchErainEdhannU5MdrpartifpbEflbxih7Qr

48、ticLml:-rnsnrrtreibM.iontorrent岡lnwmpHw$WlkVlHk-MrMwa*ECM-hBdacEImSLnL土nwrnc-Hiiwrwi(hOr*cflto*MRri#irciiPTtmii詔I麗eyounb*EEAftxMirfiAiiu.Ansvwrrktaqua5donfwith伽orMppr1niani3,MlaciEhHK&tprarridn號(hào)gigorcvlIlnA,jridcase忡hpfichasis.eventsxRUwrit、Elram.IrmMt-afoundationforprund-brvaMnEdKowieswithuniquefMt

49、um-Hi-Stindud-Designbetterexpenments.Gainmoreinsights.PreparetopublishfastenOrK&minaResaarcliEdition:715datasetssnd86,733sannplMRASMDUe圖20Oncomine的主頁(yè)OncomiRDB24OncomiRDB主要收集和注釋通過(guò)實(shí)驗(yàn)驗(yàn)證的對(duì)癌癥具有促進(jìn)或抑制作用的miRNA信息。該數(shù)據(jù)庫(kù)的所有數(shù)據(jù)是通過(guò)人工收集和整理。47SomamiR25SomamiR數(shù)據(jù)庫(kù)集成了多種類型的數(shù)據(jù)，用于研究體細(xì)胞和種系突變對(duì)癌癥中miRNA功能的影響。該數(shù)據(jù)庫(kù)主要收集miRNA及其靶序

50、列上的突變。另外，數(shù)據(jù)庫(kù)還提供了存在miRNA靶序列體細(xì)胞突變且腫瘤相關(guān)的基因及其參與的通路。SomamiRDB2.0SomaticmutationsalteringmicrnRNA-ceRNAinteractionsmu祐titansinxpeimErHialliHEntifiecIrniR何曲Unset錄聆；fLASH虧口EmticEuZtianmknExp色rimwnt古II*iciEntifiEijEiRN匹trgietmit毛耳；PAR-LIEHITHUPnwoci白tEdat亡ne舌thatfomtaiinnrhiRKIA帕陽(yáng)m吐i右mutationsBiol陰icalpathwa

51、ysimwctectbysomaticmutatioTK舒l匕占anSueeI征nulitiginFinprMctedFrtiRW丸tar君Et占巴5圖21SomamiR的主頁(yè)腫瘤蛋白組數(shù)據(jù)庫(kù)蛋白是生命活動(dòng)的主要承擔(dān)者，蛋白結(jié)構(gòu)變異、蛋白修飾的改變以及蛋白含量的變化等導(dǎo)致細(xì)胞的生長(zhǎng)和代謝變化是腫瘤發(fā)生的重要因素。表5腫瘤蛋白組數(shù)據(jù)庫(kù)DatebaseDescriptionCancer3DCancermutationsandproteinstructuresCancerPPDAnticancerpeptidesandproteinsCanProVarCancerProteomeVariationD

52、atabaseCPTACClinicalProteomicTumorAnalysisConsortiumdbDEPCDifferentiallyexpressedproteinsinhumancancersCancer3D26Cancer3D數(shù)據(jù)庫(kù)整合了來(lái)自TCGA和CCLE的體細(xì)胞錯(cuò)義突變信息，在蛋白結(jié)構(gòu)水平上分析其對(duì)蛋白功能的影響。該數(shù)據(jù)庫(kù)通過(guò)e-Driver和e-Drug兩種算法，幫助用戶分析突變的分布模式及其與藥物活性變化的關(guān)系。CancerPPD27CancerPPD是一個(gè)抗癌肽(ACPs)和抗癌蛋白的儲(chǔ)存庫(kù)，在設(shè)計(jì)基于肽的抗癌療法中非常有用。在CancerPPD中，針對(duì)每個(gè)條目，都

53、有其詳細(xì)的注釋信息，如肽的來(lái)源、肽的性質(zhì)、抗癌活性、N-和C-末端修飾、構(gòu)象等。除了天然肽，CancerPPD還含有非天然的、經(jīng)過(guò)化學(xué)修飾的殘基肽和D-氨基酸。CancerPPD還整合了一些基于web的工具，包括關(guān)鍵字搜索、數(shù)據(jù)瀏覽、序列和結(jié)構(gòu)相似性搜索。CcautllixialrtiDHLeltifuimatiiHLBalaSu.biiiiDinDevdcipersContactAEistaDJC6RelatedDatabasesji巧孔各ielaLj2015CancerPPD:adhtabiis匕otantiDaoeerpeptidesandproteins-XucLAcids斗TCanc

54、erPPDisauniqueresoiiDceofliskind,whleliprovidesdeisiledinformationrelated10sperimentalbipTCrifiedanticancerpeptides(ACPa)andproteins.Dataw曲curatedmanuallytroinbothpabJishediritid/BS?.patentsas砧asfromohecrpoEitones.Since-Etiuetoresplayunportantrulesintheanticancera.ctLiithavepredictEditcTtiniystructu

55、res(auticancerp亡pbd-c-2usingitiLc-oiaitmethodJEPstrandsecon-danfsmicturesiatesareassignedusingDSSPTheLtnportanli伽Imreofcan-cfrPPDIsthattlalsoprovidesinformationrelatedtovm-au3tJiemicaJmodificationslikenjon-natural,D-amirwacids,modified-amin-oacidlikeoinitliine.Hiedatabaseiscross-linked-withvariousot

56、herrelatedrfsourcesinordertopimideoaniprehenisivePt=pciikBrmrseTotalPeptideEntries:3491TolalCellLines:249TotalTissueTypes:21PtolninwinSMILESTiiiUAhtseCdlLineuisaEJJiSTSlidih-lVcteJILiEMeinbiaiiiolyucnwdc口1用輛百仇StromireAlig.nzniuitibnjiimlviicmedeoifji-cticbTiMippinfKejrFeaturesDownloadS&Quena-(1)Data

57、Retrieval:Toolsfordatafetchinglikeslmplehandachancedsearchintegrated!.Inaddidon,iosearchpeptides,peptidesearchandSMILESsearchopiwnsarealsoprovided,二)DataAttahsit:BLAST3Smjtli-waterniali.sequEiceandstmcluiemappingtoolsareLnotporated!.whichfaciJjtatethesamiLaTiti1?,-ba3edseBrch.StracturpReflateAckrKxi

58、fciEdg.EmsntBrowsing:Variauisbrows-ingfieldshavebeenpraded,wtuchfacLlitalrethedatabrowHiRRina+巳ryconnienwa”SMILESmidStructures:AnimportantfeatiLftofCancerPPDisthatitcontainsinformationofACPsinSMILESforniatinaddidoriipriietedterttarv*structuresofaUACPsawavailablexvhi-chmakesit&smpreliensiveresource.圖

59、22CancerPPD的主頁(yè)CancerProteomeVariationDatabase(CanProVar)28CanProVar數(shù)據(jù)庫(kù)整合了來(lái)自各種公共資源的蛋白質(zhì)序列變異信息，重點(diǎn)是癌癥相關(guān)的變異，CanProVar中的數(shù)據(jù)主要來(lái)源于TCGA、COSMIC、OMIM、HPI等數(shù)據(jù)庫(kù)以及一些文獻(xiàn)研究。在該數(shù)據(jù)庫(kù)中，用戶可在網(wǎng)站中搜索特定蛋白或者某種腫瘤，獲取蛋白的突變情況，在結(jié)果頁(yè)面會(huì)給出蛋白的基本信息、GO注釋以及相關(guān)的研究文獻(xiàn)。ClinicalProteomicTumorAnalysisConsortium(CPTAC)29CPTAC整合了基因組和蛋白組的數(shù)據(jù)，旨在識(shí)別和描述腫瘤組織

60、和正常組織中的全部蛋白，發(fā)掘可作為腫瘤生物標(biāo)記的候選蛋白。DbDEPC30DbDEPC是一個(gè)專門收集腫瘤樣本中出現(xiàn)的差異表達(dá)蛋白的數(shù)據(jù)庫(kù)。在該數(shù)據(jù)庫(kù)中，你可以了解你所感興趣的蛋白質(zhì)是否在某些癌癥中發(fā)生了變化。腫瘤相關(guān)基因的數(shù)據(jù)庫(kù)表6腫瘤相關(guān)基因的數(shù)據(jù)庫(kù)DatebaseDescriptionDriverDBExomesequencingdatabaseforcancerdrivergeneNCGNetworkofCancerGenesTP53MULTLoadTP53mutationdatabaseUMDTP53TP53database6.1DriverDBDriverDB收集了來(lái)自TCGA、IC