GEO数据库的使用.docx

GEO数据库的使用（一）

1、GEO数据库介绍GEO全称GENE EXPRESSION OMNIBUS,由美国国立生物技术信息中心NCBI创建并维护的基因 表达数据库。创建于2000年，收录世界各国研究机构提交的高通量基因表达数据。
GEO上有四类数据GSM, GSE, GDS, GPLGSM是单个样本的实验数据
1. GDS是人工整理好的关于某个话题的GSM的集合，一个GDS中的GSM的平台是一样的GSE是一个实验项目中的多个芯片实验，可能使用多个平台
2. GPL 是芯片的平台,ill Affyrnetrix, Aglent 等 网址入口： http://www. ncbi. nlm. nih. gov/geo 2、GEO数据下载例如：我想找胃癌相关的疾病资料、研究文献，那么可以直接搜索gastric carcinoma
% NCBI Reeouroet® How lb©
GEO Home Documentation ■ Query & Browse ■ Email GEOGene Expression Omnibus
G€O ts a publk: functkxwi gefxxmcs data repository si4)pcrt)ng MlAME compiiamt data submiMkxu Anay- and sequence-data are oooepted. Tools are prodded to help users query and download MpermenU and curaeed gene expreeaicn profllee.

Gene Expression Omnibus
G€O ts a publk: functkxwi gefxxmcs data repository si4)pcrt)ng MlAME compiiamt data submiMkxu Anay- and sequence-data are oooepted. Tools are prodded to help users query and download MpermenU and curaeed gene expreeaicn profllee.
Getting Started
Owwww
FAQ
About GEO DawS«ts
About GEO Profiles
At)outGE02R Analyse
How to Construct a Quofy
How to Download Data
Information for Submitters
login io Submit
Tools
S«arct)for 知Oos at GEO (XataSots
Searcti for Gene Expcession at G€O ProGtes
S<ar5 GEO Docunwntaiwon
Anatyr* a Study wth GEO2R
Studies wtth Genome Dm Viewer Tracks
Programmatk: Aoooss
FTP Site
Ptatfocms：
Semples：
121450
20412
3323111
Subnwton Gugrm
Update GukMinm
SAME Standards
Citing and Unking to GEO
GuMeAnes for Reviewers
GEO Pubiicatiora

若只想关注人相关的研究，在右方选择一一如图:
"NCBI R«ourc<wl9 HowTo®
Skm in to NCBI
GEO DataSets，(gastric caranorna) AND *HcmQ sapiense(p<xgn:_txid9606)
Create «»en Advanced
SKxnfnary • 2Opor pago* Sort by Default ordor •
(Sutxrwnec &uppM)Our novel <xug magog technique revealed mac trastuzunaO. which is represeotaove anoboctx drug for breast and Qistric cancer in dinical, dstntxXod heterog«neousiy inside tuner even though 标!8fQei recepXM. HER2 (Human epWermsl growth tector receptor 2) express homo^jweously For 篇 predominant rv^ulator of trastuzumab tumor delrawy m the tumor M. trwd tumor regnn- spedne rrtcroanay analyua acoocding x> trastuzumab dWWS in peM«it dehved xenogra^ model.
S«nd to： ■ Fliurs: Mo2<» FHlm
Orvanom：Homo sap*eo«
TjpeExpressen pcofing by array
Ptomxm GPL21185 12 Sampiei
Download data: TXT
Sers ACCM5 GSE121767 O 200121787
Anirvm GEO2R
Search details
(Csgchp Fields]) AXD carcinoM(An Fields])> .\XD vH<«o sapienfi* (portn]
Off
(Subrnffier suppM) Gastric canoer b one of the meet common cancers wodchwde. Epftteirv-Bdrr vm- associeM gastric cancer accounts tor approaimatefy 10% V ell gastric cancers EBV sps* ns own protens and mRNAs |BART rn代MAs) and reguiales host gene expeession. In tib studx，we examined the effect oC EBV iniecoon on boat mRNA expeesson Dfflecentiai gene expeesson was analyzed be-Mwn EBV- noQabvo human gastric cancsr c«ll kw AGS and EBV posttrv* human gastric cancer cell line AGS-EBV. Organ^mHomo aapien*
TypeExpressen profing 5 array
PtotfOcm OR.6106 10 S>my<M
Dcmnk)ed deca： XLSX
Search
Recent activity
Q (game carcinoma) AND "Homo sapient
▼ lop Organisms fTg】
I Homo “pions 厂3：*^M<* mutcukM (15)
Ratlin norvegfcus(8) synthettc construct (7) AraNdopsis thailana ii) More .
Find related daU DatabaM

GE02R是自带在线分析工具：
* .・5・・,♦
ConChbutor($) CdMion missing Submission date updMe date Contact name E<mari(s)
MMsuMne R. Hayashi M
Hm CM study Xen所dse go to updM or noeify GfO.
Oct 25. 2018
Nov 03, 2019
Ryosuke Matsukane

OrQantzaeon name Kywhu Ur*vers<y Hospital
Department Street addreM Gty
ZlP/Postal code Country
Department of Pharmacy 3-l-lr 阮小此 H»Qdshi-ku Fukuoka
8128582
Japan

Platforms (1) GPL2118S A^itene-072M3 SurePnnt G3 Human G€ v3 8x60K Microarray
039494 (Probe Name Vision]
Samples (12)GSM3446059 Stroma poor arz in control PDX tumor. 1GSM 3446060 Stroma poor are^ in control PDX tumor 2
G5H 3446061 Strom* poor arM .n control POX tumor 3Analyze with GEO2R

Analyze with GEO2R
Download family
SOFT foEiacted family filers) MINiML formatted fdnwly Me(s) S«r»M MMnic Ftle(s)

Download family
SOFT foEiacted family filers) MINiML formatted fdnwly Me(s) S«r»M MMnic Ftle(s)
Format SOFT CD
M1ML ®
TXT 0
Supplementary fMe
GSE121787_RAW.ter
Size DownloadFlic type/resource
36.9 Mb (httpXcustom) TAR (of TXT)
定义分组：下拉分别创建两个分组：T （肿瘤组）

定义分组：下拉分别创建两个分组：T （肿瘤组）
C （对照组）

NCSl • G€O - G6O2R • CS6121787Use GE02R to compare two or more groups of Samples in order to idencry genes that are differentially expressed across expenmental condoons. Results are presented as a taMe of genes ordered t>y significance. Full UvstruBons
GEO accession
GSE121787
■ S>mpS
Group Accewoo ■ V
• Source name
■ DMne groups Enter a Qroup name
Set TUmor reqlon-specinc rmcroa
analysis dccordlng to trastuzumab diwitxjtlon In breast cancer patient derived xenopraft
• Gender scxrcc , Tissue
CoMrrw
GSMM460W
GSW5446OCO
GSM3446061
GSM3446062
GSM3446063
GSMM46064 GSM344606$
GSM3446066
GSM3446067
GSM 3446068
G5M34460W
GSMM43R

GSMM460W
GSW5446OCO
GSM3446061
GSM3446062
GSM3446063
GSMM46064 GSM344606$
GSM3446066
GSM3446067
GSM 3446068
G5M34460W
GSMM43R
Worn® poor area s contra PDX lu«w_1
Sawia poor area «i control PDX tumor 2
S»c*na poo a<M s corwoi PDX lumo<_3
S^oma nch am r control POX tumcr_1
Sawa nch area r oortroi POX turner_2
Svcrne nch r» corlrol POX Uxnor_3
S»orna poor area <i tra»tu2umab adnwaJTaoed POX Vrxx 1 Saxma poor area s vastuajmab MlnwMVMd POX krux_2 Svonw poor afM s trstfuzumtb adnwMMed POX krxx_3 S»oma nch area r trasajAnab *dnwtstrato3 PDX tumor ,1 Svong rtch wm m trMAMnab aonccM睥led POX iumor.2 S^oma nch arw r» traeftxAjmab adnwMstfaled PDX tumor ,3
Stroma poor vea m cor*oi POX Mw
Strom* poor area m cortKH POX 5or
Stroma poor area m com«i POX vtmx
Stromi ncf» area s control PDX tumor
Stroma ntf» area s control PDX tumor
Stroma neft stm s control PDX tumor
Strom* poor a-oa m Twtuzunub »»nn5tratod POX ttjrnor S&oma poor aroa m VMhaurrub Mnnsfutod POX ttxnor Sdoma poor area m r«MuzumM) •dnmtralod POX vner Stroma ntf» area s trastuzumo admnsTaMd POX Vnx Stroma 2 arx o HMfuzumab ada«n«»inM POX xrax $Hocna rxt» area r tfostuzucnab admn^rsted POX Krxx
NCC-BCP69 pebect Oenved neoogrtA (1>0X| Vtkm NCC BCPG9 cobent denved xenograt (PDX) Unor NCC-OCP69 denvM Keno^M (POX) VW NCC ®CP09 pobent denvM xencvS (POX) Vnor NCC-BCP69 falMfM <knv«d xtno/at(PDX| Vnor NCC<BCA69 a(F Oerwtd EO7・t (POX> Mnor
NCC-BCPC9 pobent derved xeix^at (PDX» lumof rv»r/<
NCC-8CF69 cotKct derwed xtnoQrat (PDX| Mnor invMM NCC-80^9 pobenf devw«d ntnofrM (POX) tumor nvMM NCC BCP69 pabent derw« xtno^ot(TOX| tumor fivum NCGeOSQatmtSvMxtntvmtMOXlSor ESM NCC-8CPC9 CQbert devwM neoocF^ (K>X? Vnor nvsm

Use GE02R to compare two or more groups of Samples In order to identify Qenes that are diffefentially expressed across experimental conditions. Results are presented as a tatMe or gnes ordered t>y slgnmcance. Fu・ instructfons
CEO accession GSE121787Set Tumor region-speclOc mlcroarray anal^s according to trastuzurrmb distribution In breast cancer(>atient derived xenograftGroup Aa*MK>n
. GSUM460W
・ GSMM46060
- GSMM400ei
- GSMM460W
・ GSMM46063
・ GSMM460M
- GSMM46065
. G$MM46Oie

Group Aa*MK>n
. GSUM460W
・ GSMM46060
- GSMM400ei
- GSMM460W
・ GSMM46063
・ GSMM460M
- GSMM46065
. G$MM46Oie
SVom» ncfi area m cocM POX tumor_2
Sl»oma ncti m c<x*crt POX wnor_3
Stroma poor atm r trastuzumab adnwtstraiod POX kmx_1
Stroma dock area n trasturunub adnwintraled POX fcrwx 2
S<XM(* neme.
Stoma poor n cctW POX turner
Stoma poor area n oortroi POX tumcf
S>om> poof aroe r oortrol POX tumor
Swom* — MM s conrot POX tumor
Stomi nc» area m corm PDX tumor
Stoma w erM m conrd PDX Uxnor
Stroma poor area n trasWumab adnwatratod POX Kmx
Stana ooo< area n traskaumib adnwntrated POX Krxx
三三三
AMcted Oout of 12 tampltv
、，.・• ♦
NCC-8CPeO denvM X«rogran (POXj mtmx NCC^CPW paoom dtnvtd xcrogran(PDX| 5<x NCC-BCPW p*>en! denved w^ograH (POX| Mrxx NCC-BCP6® patent —ogrS (POX) 5<x NCC-BCPS9 panerrt denved xtrogran (PDX| Kmoc NCC-BCPW P«en! denvM xtrogrart (POX) Vrxx NCC-BCP69 paMrfl denv*3 Mrcgian (PDX) Vtxx NCC BCPW CMOcnt «5enved xerooran 1PDX1 Mw

对样本进行分组：选择后点击T或C即可GEO accession GSE121787Set TUmof region-specific mkroarray analysis dccorOn^ to trastuzumab dlstrtxiUon in breast cancer patient dertved xenograft
Tine
SV(xn«pa
Stroma poc
■ OeAne groups Ertef 4 grg name Ust
■ C^noHwIeclE
CJ0whx*»»
T (6
Stroma poc, —.・■・・.■.
Stroma nch area m control POX tumor」
Stroma nch area m control POX tumor_2
Svocni nch wet m control POX lumor_3
Stroma poor ar«a tn orastuAjmab »Or*natfaiod POX kirwj Stroma poor area m vastuzunab a^nstnMod POX fcmor 2
♦ Source name•
Stroma poor a-ea m cootrol POX luw
Sirorna poor Me* m comroi POX iu?nor
Stroma poor aroa m contnM POX tunw
Stroma nch area s oortroi PDX tumor
SVocna 的 area r cortrol PDX tumor
Stroma hch vm o ccrtroi PDX turrx*
Stroma poor m trnsturu^rub Adnwtslratixl POX tumor
Stroma poor area m trastuxmub admnslratcd POX tumor
SVoma poor area m Csturumab
xlPOXhmor 3
Stroma poor area m trattuximab adnvnntratod POX tumor
二二二二三二
二二三

这里我们只保存了前250个基因
GE02RVMjM 皿SonOpS P 心“aph R&cr*
▼ Quick start
• Sp«c#y a GEO accnslon and a Platform rf pcompsod
• Cldc 'Defne ^oups, and onto* njmw foe the groups o< Sampics you pUn io cocr^re e g . lest sd controlAssign Samples to wch gro^ Height Sanv*« »ows thee ckfc the group name to rh»e Semplw to the gr^p Us« Z metadata (title source and characiecWs) wlumns io Mp determine which Samptes belong to which group
• Cicfc Top 2S0* Io porform tw cakuiation wth dd*uft stings
• ReMjfts are p<eMa(ed as a table o< ^enw ordered by signikince The top 250 9ene^ are preMc«ted and may be viewed as profie graphs AltenMtiveV Z cocnpMe resufes table may be Mved
• You may change ag)s h Op0<m ub

GEO2R
Vaiua dhtnbution
Opoons Profta gr*
R script
I 24 I NIH | Email GEO ； QlKUIm*( Acs迎曲cy
前250个基因如下，点击保存Selected 12 out of 12 samples

• Quick sunLog-transionnadon hai be«n appted to the data. You can change this In the Option* tab.
RacakulMfi It you cfiangwi arr/ o(2tton& I Savo al results I S^tacf aMumns•IT

•IT
•<2<P336092* ,A-23.P3626X. ,幻 2为 ”492，- •J33.P32I2Y69. •A-35.M2127W 久 33.P3280M5, •七33.P3280X5. •A-2LMO13SW ,K-33.P3336038* •A_33-M25IT2T- ,3m6i”r •A.23-P26024* •A-2LM00653T- •A_24.M0309r •农23.P210465' XH.W776T3- ,A_2】.PMl“T9' •A_2LPtXn"T尸 •七 23.P8I898. ,A-33_mJS3089・ ,心 3.P333308T 优33.P32601“・ 'A-，M2601"・ .虹 21.PC004052. •七22.的00192" •A.22_PDOOi92«r ,农 23.P266W *0.03314* - •七22■的 0005555' •A.22.Pt»0l<T8r •七 2?・-
rar •p.vaue*ef
板-lorfr tB.MT
•SKUEKr *-3.853W4* •-5.425T565- *-2.959SHS* •・2.
*2.502IS1K
*0.002成 •0.002成 *0.0141- ,0.023DT •0.0230T
-5.86«-0B- •7.39，・08. •?.2?e-0V •|.28«-06, •?. I5e-O6-
•-9.W36I!!* •-T.12226侦 •T.G78008r
•7.41753*
,7.2OMT v6.618«2r -4.T16»7-
Y.65g・
0 023询
*2. 38e-06-
•-T.O2O78W
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-・2. 65<»79'
•0.033U-
•<.eie-or
•-6.a??2T-
y. owwr
F 00M10T
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«16«-O6*
•-6.M74383-
•3.9JBS79-
•・2. M6CTW
•0.033T4-
.& 356・
•6. 53^6305-
•3.5)^6-
*2.6932M 矿
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r.mwr
,・2. 7841124’
•0.033T4*
•9.956.
,•6.N6W
•3.3917戚
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0 0331(
n.we-oy
,-C.0003922-
9"：',
*-2.6M(nr
•0.033TV
•|.96«-05-
•-5.粉84292.
-2. 82WS6*
*-2.432154r
•0.033T4-
•2.06e-0T
•5.<7tewr
•2. W174-
•2.5915W6-
*0.033Tr
•2.09e-05-
•YW232W
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F.99T»«'
S0331T
•2. Me-05-

,2.UWW
•・3・920初.
*0.033ir
•2.3!e-05*
,5.810391r
*2. 68*2?.
•2.616G&T
•0.033H-
•2.4U-05-
•5. 7906W2-
•2.650676-
.2.4686?2S，
-0.033TC
•2.53«-05*
-5.7SW038*
•2. 609X3'
-2.5I00WT

•0-033T4"
•2.S?e-05*
•5. T57U6P
•2.5"?
y W .2.9"05.
•-5.72082Z
•5.e?976?T-
*2. S49IST •2 .姒叶
•SPOT.W
•ai.ooojsr 5299V ,ML00ITW *HI_00ITl(r •BCW08W
*HI_0062Br
•»_00l035-
,CAGJUGCCATCJ^CCATarj^JlCJ^UTATCCJ^AGATTCTTTaCCATCCTGOXACC*
•GKJUrCATAMOCWTCA^TCAUTTC/JLATTCAW^TTCCTTCAAGAATCUAAT-
•aCTTCCT^AMTAGAGTTKATCAT^^TTCKCTWTCATACATnGTWTCKAC* •MCCJUXiTCTACArCJUCUTCCGCATAACJLUGCCliXTCTCJIG^ACATGCTCAAnr •TTCTTTTK^TCTCATTTatfXATCTCCTCTTWA^AAACCCATTCACAAJATCTCA*
* TUTGCCATCTCATTCJfcXJUZJLUCAAAACTCCKAATUJUCCA^XCTCTGCAATCTC*
A24.P3360 疗 •七23.P36264. •幻 23_P2492.
,W«tr
,GCATTT^iC^TCCCA^XCAGTTCAW^CAATTTCXUTAA^TOGTTCTCAUTTC- A2501 f •JL3LP333G0W ,ATTTTCKAATTtXC^^TTCTCWTTTTCTWA^TCCAAXTCTCTTTOXMCA-
,CATCCJbXTA^TTCTTTCAnTCTCOCATTCCTTOWATCAACAUnTGCTMraXCC-
,BI.0324ir •ACTCTGC'XAUTGCTTCTCCTjlCATTTnACGCnTCTCTACATTTTTTCCCCTCTCCA- •JL23.P2602V
,• •imCTCTTOXCTCCATnCCCCaTTOOCAAOX^nCAAAXACTCKAAAYMAr •A_2LP000653?" •ML0Q1665'
•—002638* •M.003MT-
•DCMW
•M_0063f»r
WT2的成
•W_00llP5«r
•2.090402-
,•2. 3864S740 •3.3536*
,GTCJWGCCATAATTGTTCTTAGnTGCAJnACKTAA^GTGMXMTCAWTCAlX- • TOCTCCCCCAnANTTGJlTaXCTCOXCAKTKAATOCCCCTAACCCCTCCTTCJUU' •CMWTAC2 耕CCATMEN"FYMMgag>gCTT«aXr .OCina 心 UCTCTTCMIGTCTCTGnnGWAAlXCmM：心 XiATAAAA^CA'
•ATTTWTWAT^T^AWAJ^TATAWCCCAACTCTAWTTTCTTWATTCTAA* •g/HAT 心耕 OCGKCCT 心 gJMKTGTACK心 ATCSUATGAKCCMOr
,A^^TWAOW^^TWTCAGWAAlXCTTCCOC/CTCACTWiyXAWWTTTTC*
•A_24.P30309r ,农23.肋。“5° •颂.「2?顺3.
.A_23.P81898.
•CAnATTGTTCaTTTTCCCJUXTAMZTaCCKiiaCTCKTTTATCTCJCTOJTCTCC* X^LPOOMOSr ・.-TTKAT WTO^ WA^ATTAG^A^AWCA^ATWCGT^ WATAAATOJTWA-
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-L9«0?2r
•0.033TC
•AST
・5・6O«836・
•2.如心
2262260T

•OCTCTATTCATTCACTTCTUnCCAGTGTCTCCTTCATCCCTCCAACnCJtfCCTCACA- .农 23.P266641 •<WAW^AAATO：ACTTATATCTCACTTT^ATTT，ZCAJXTGCTTTTAnTTTATTTOGr
'BIIM650*
• ^XCTCTTaTCAGWTCCJICACCACJlWCTTCCCTCTTUnTJIGCTCTCjUCTTCCAC*
•TCnGCCATCUTCTCMKTCATTATCTTCTCCTACATCACACTGAACTnTATCAATCA*
.SXTHTCgMmWAJXAAA故ATC 心"ATWmeenrCTATHg.

•0.033T4-
•X5l»-05-
•5.W9672V
.2. 3W743-
•2.2893535-
•■I.I53M0*
•J23g?6|・
•0.033TV
•X?5e-05-
••5 .渤 250K
•2. 21M5，
••2."戚仃
•MC002<23.
-
*0.03374*
•4.06e-05*
•-5.52?680f
•2・ 20700T
*-l.8412M3*
,S«_00632r

,as o«wccrwee«
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HITTCC-
•4 X—CL
icoc^«y
,AOLAATCTCMTCJUtfAAATTATGCTCACTAnCGATOXGTTTTCTCAnTMaCTCT* • TTWTATWACATTWKTOAraTMWCAGWAWTAfCCAKCTATWAAATOCA- •GCCJUM：CCTCCClGTA^：TACnTGCTTTnCCCT/OCAGAGAjiaC：ArGrA^JLU*
•/■n-rTrrr/*vvv^r*rw**-TTVTrvvrrTT*T*a*44Tra«rT<-V4rrr avrT^Tr-
优 23J»2H26r .J23.P52?61.
,妃 2；_P131BO5,
将以上结果粘贴保存在TXT中，然后用EXCEL打开，如下
ID
Ad^P.Val
P.ValM
t
B
logFC
G8.ACC
SEQUENCE
SPOTJD
♦ Q5 炒 2
OOW15
5Me<»
•9为
7418
•3M
NM_00»31
CAGAAGCGATCAG
A_24_P3W0tt
，3J>3«W4
08215
7 39^<A
-911
7249
-543
NM_1W997
OTCACGATAAACCT
A_23_PM26W
►A-23-P24W
00141
727X7
•77
5515
•2笛
NM.001734
OCCnOCTAGAOGT
W2492
,3.P15W87
0 0?309

•712
4 716
•277
NM.001710
MOOAOOTCTACAT

■ A-J3.P32127W
0 02309
215^05
7 08
4 653
25
BCQ2C34
TTCTTTTACOCCTO

0 02309
2 38^05
-7«
4 57
•255
NV_0Ck6288
HATOGCATCTCATT

► A_21_P0013865
0 01374
4612
-666
4 031
•301

OCATTTGCACACTT

► A_13_P333W3S
0 01374
516^05

3939
•2S5

CATCCACCTAAGTT
A_33_P3136038

0 01