收藏級資源腫瘤數(shù)據(jù)庫匯總

1、收藏級資源|腫瘤數(shù)據(jù)庫匯總現(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。2019年，ACancerJournalForClinicians雜志發(fā)布了最新的數(shù)據(jù)。該報告估計，2019年美國將有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)化療是對抗癌癥的常見方法，但它會攻擊全身，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)對于研究腫瘤的

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

3、ogenomicscBioPortalcBioPortalforCancerGenomicsCGAPCancerGenomeAnatomyProjectCGHubCancerGenomicsHubCGWBCancerGenomeWorkBenchCOSMICCatalogueOfSomaticMutationsInCancerICGCInternationalCancerGenomeConsortiumTCGATheCancerGenomeAtlasUCSCGenomeBrowserUCSCCancerGenomicsBrowser以下是對數(shù)據(jù)庫的簡要概述1.1canEvolvecanEvol

4、ve存儲的信息包括：基因、microRNA(miRNA)和蛋白質(zhì)表達譜、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是一個癌癥基因組數(shù)據(jù)探索、可視化及分析平臺，可用于多個癌癥基因組學(xué)數(shù)據(jù)集的交互式探索。該數(shù)據(jù)庫可提供CNA、基因突變信息。針對每個基因，它可給出多個信息，主要包括：基因的CAN信息、基因突變在樣本中的分布、突變位點和頻率、共表達基因以及生存曲線等。對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作用。cBioPoirtal&HH|伽佬n&4!lwiMDF*MMg：ClP別輯if.Sjilg伽剛工“MCISludlai問也ZM乞如筍HCueatori:nS#R5r.：卓.河、0 x1悴巾上-冊“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)庫的主頁CancerGenomeAnatomyProject(CGAP)CGAP網(wǎng)站主要提供了cDNA克隆、文庫、基因表達、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、前癌組織以及癌細胞的基因表達水平。,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CancerGenomicsHub(CGHub)CGHub是美國國家癌癥研究所(NCI)測序項目的在線存儲庫，其數(shù)據(jù)來源包括癌癥基因組圖譜(TCGA)、癌癥細胞系百科全書(CCLE)和產(chǎn)生有效治療(目標)項目的治療應(yīng)用研究(TARGET)3個國家癌癥協(xié)會項目，數(shù)據(jù)來自25種不同類型的癌癥。CancerGenomeWorkBench(CGWB)CGWB提供了一系列工具來挖掘、整合以及可視化TCGA等數(shù)

10、據(jù)庫中的基因組和臨床數(shù)據(jù)，它是第一個將臨床腫瘤突變譜與參考人類基因組整合在一起的計算平臺。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)腫瘤的體細胞突變以及其影響的資源庫。它主要提供多種腫瘤細胞基因組中的CNA、甲基化、基因融合、SNP及基因表達等信息。這些突變信息是從科學(xué)文獻中手工整理的。idutliuCOSMICPrnjKfaDpmrrwrtftnnCoffSod3KWCIIPH.4IH!LHOBCtfUrmWMrtEJWKW*owmcm1uZbxuuZKilE

11、PCIEKHIjdH1蟲圖4COSMIC的主頁InternationalCancerGenomeConsortium(ICGC)ICGC的目標是獲取包括膽道癌、膀胱癌、血癌等多達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)可促進癌癥的機理和治療研究。圖5ICGC的主頁TheCancerGenomeAtlas(TCGA)8TCGA是由美國國立癌癥研究所（NCI）和國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)庫主要對樣本進行外顯子組和基因組測序分析,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UCSCCancerGenomicsBrowserUCSCCancerGenomicsBrowser是一個可以對癌癥基因組學(xué)和臨床數(shù)據(jù)進行整合、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，包括基因表達水平、CNA、通路信息等。在UCSC的癌癥基因組瀏覽器中，可實現(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2.腫瘤基因組數(shù)據(jù)庫腫瘤細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?？截悢?shù)改變(CNAs)在很大程度上有助于癌癥發(fā)病機制和進展。腫瘤基因組數(shù)據(jù)庫匯總?cè)绫?所示。表2腫瘤基因組數(shù)據(jù)庫DatebaseDescriptionarrayMapReferenceresourceforgenomiccopynumberimbalancesBioMutaIntegratedsequencefeaturedatabaseCanGEMCancerGEnomeMineCasSNPCopynumberalte

18、rationsofcancergenomefromSNParraydataCGPCancerGenomeProjectArrayMap10ArrayMap提供預(yù)處理過的腫瘤基因組芯片數(shù)據(jù)以及CNA圖譜。在ArrayMap數(shù)據(jù)庫中，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CancerGenomeProject(CGP)14CGP提供了腫瘤中的CNA及基因型信息，該數(shù)據(jù)庫的主要目標是利用人類基因組序列和高通量的突變檢測技術(shù)識別體細胞突變，進而發(fā)現(xiàn)人類腫瘤發(fā)生過程中重要的基因。該數(shù)據(jù)庫還提供了一些識別突變、CNA的軟件，如BioView、Home-fioenreGRAFT等。Anchrsofi-Group仙抄忙!&OfmfetumMIOrtindl”myGroupsFacultyGroupsgi8W*CTi$(MFMMIjrini)他辭爲玲切野蘢曲郵h1嵌|巾圉護套腳聞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3.腫瘤DNA甲基化數(shù)據(jù)庫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，對維持細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)庫匯總?cè)绫?所示。站(4機年Kte問咖討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DatebaseDescriptionDiseaseMethHumandiseasemethylationdatabaseMENTMethylationandexpressiond

25、atabaseofnormalandtumortissuesMethDBCommonresourceforepigeneticphenomenonMethHCDNAmethylationandgeneexpressioninhumancancerMethyCancerHumanDNAMethylationandCancerNGSmethDBNext-generationsequencingsingle-cytosine-resolutionDNAmethylatio31DiseaseMeth15DiseaseMeth是一個人類疾病甲基化數(shù)據(jù)庫，其重點是對各種疾病的DNA甲基化數(shù)據(jù)集進行有效的存

26、儲和統(tǒng)計分析。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MethHCMethHC是一個集成數(shù)據(jù)庫，包含大量DNA甲基化數(shù)據(jù)和mRNA/microRNA在人類癌癥中的表達譜。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陽叨廉.aidihikludclomEdiwlixm阿呦pK-diiw*Klag.IniKiirwikmMCvMfl

33、kuI,piIWie0pThSHdSBIFEiKKHSFdfinphcaWfilHFN*Gffr團的丼如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啦皿誠聽RdfiiihgiiJAincarionMmwh號iburwnlaiirdttK-iYir）alrwE|眄40也=LaAjpwld-ltMJiiqtEp3

34、|nnTiic3Praj*d&CfelmMrtljCwvrilariHhkijijiattarrbywtctiwmhJJIfc#Id!-criaaidarotieallaudrEhamlkusrrH-號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的主頁除了上述針對癌癥基因組甲基化的數(shù)據(jù)庫外，還有一些數(shù)據(jù)庫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，主要集中于環(huán)境因子對甲基化的影響；NGSmethDB叫基于高通量測序數(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)庫腫瘤細胞具有較強的生長和繁殖能力，生命活動旺盛，因此與正常細胞相比基因的轉(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DatebaseDescriptionArrayExpressMicroarraygeneexpressiondataChiTaRSChimerictranscriptsa

36、ndRNA-sequencingdataGEOGeneExpressionOmnibusmiRCancerMicroRNAcancerassociationdatabaseOncomineCancermicroarraydatabaseOncomiRDBExperimentallyverifiedoncogenicandtumor-suppressivemicroRNAsSomamiRSomaticmutationsimpactingmicroRNAfunctionincancerArrayExpressArrayExpress是基于微陣列和高通量測序(HTS)的功能基因組實驗的主要知識庫之一

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ChiTaRS20ChiTaRS數(shù)據(jù)庫包含嵌合轉(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)庫是由GenBank、ChimerDB、dbCRID、TICdb和其他用于人類、小鼠和蒼蠅的數(shù)據(jù)庫的表達序列標記(ESTs)和mRNA識別的嵌合轉(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沖蝕旳也補伽mcwaimESBi譽巾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紬陽門舊|*1Q41PuaMtHIbfl.mOhiTM雷aatstfmPfaWiiridivCQii.Diioni祝科內(nèi)“口麗

44、勺rq占爭UpHOriedbyCMjvbgiiti喘用帆.COtH則盼KSNC&DC踐*皿飢圖17ChiTaRS的主頁GeneExpressionOmnibus(GEO)21GEO是由美國國家生物技術(shù)信息中心(NCBI)建立的，其最初的目標是作為一個公共存儲庫，存儲主要由微陣列技術(shù)生成的高通量基因表達數(shù)據(jù)。此外，該數(shù)據(jù)庫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Bnikratruri*Z3D4wthIhrtLEb4dii|YWHOfl號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gigorcvlIlnA,jridcase忡hpfichasis.eventsxRUwrit、Elram.IrmMt-afoundationforprund-brvaMnEdKowieswithuniquefMt

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

50、列上的突變。另外，數(shù)據(jù)庫還提供了存在miRNA靶序列體細胞突變且腫瘤相關(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的主頁腫瘤蛋白組數(shù)據(jù)庫蛋白是生命活動的主要承擔者，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)致細胞的生長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DatebaseDescriptionCancer3DCancermutationsandproteinstructuresCancerPPDAnticancerpeptidesandproteinsCanProVarCancerProteomeVariationD

52、atabaseCPTACClinicalProteomicTumorAnalysisConsortiumdbDEPCDifferentiallyexpressedproteinsinhumancancersCancer3D26Cancer3D數(shù)據(jù)庫整合了來自TCGA和CCLE的體細胞錯義突變信息，在蛋白結(jié)構(gòu)水平上分析其對蛋白功能的影響。該數(shù)據(jù)庫通過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是一個抗癌肽(ACPs)和抗癌蛋白的儲存庫，在設(shè)計基于肽的抗癌療法中非常有用。在CancerPPD中，針對每個條目，都

53、有其詳細的注釋信息，如肽的來源、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CancerProteomeVariationDatabase(CanProVar)28CanProVar數(shù)據(jù)庫整合了來自各種公共資源的蛋白質(zhì)序列變異信息，重點是癌癥相關(guān)的變異，CanProVar中的數(shù)據(jù)主要來源于TCGA、COSMIC、OMIM、HPI等數(shù)據(jù)庫以及一些文獻研究。在該數(shù)據(jù)庫中，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)果頁面會給出蛋白的基本信息、GO注釋以及相關(guān)的研究文獻。ClinicalProteomicTumorAnalysisConsortium(CPTAC)29CPTAC整合了基因組和蛋白組的數(shù)據(jù)，旨在識別和描述腫瘤組織

60、和正常組織中的全部蛋白，發(fā)掘可作為腫瘤生物標記的候選蛋白。DbDEPC30DbDEPC是一個專門收集腫瘤樣本中出現(xiàn)的差異表達蛋白的數(shù)據(jù)庫。在該數(shù)據(jù)庫中，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)庫表6腫瘤相關(guān)基因的數(shù)據(jù)庫DatebaseDescriptionDriverDBExomesequencingdatabaseforcancerdrivergeneNCGNetworkofCancerGenesTP53MULTLoadTP53mutationdatabaseUMDTP53TP53database6.1DriverDBDriverDB收集了來自TCGA、IC