基因家族分析套路

1、基因家族分析套路作者:日期:基因家族分析套路（一）近年來(lái)，測(cè)序價(jià)格的下降，導(dǎo)致越來(lái)越多的基因組完成了測(cè)序，在數(shù)據(jù)庫(kù)中形成了大量的可用資源。如何利用這些資源呢？今天小編帶你認(rèn)識(shí)一下不測(cè)序也 能發(fā)文章的思路-全基因組基因家族成員鑒定與分析（現(xiàn)在這一領(lǐng)域可是很熱 奧）;一、基本分析內(nèi)容數(shù)據(jù)庫(kù)檢索與成員鑒定進(jìn)化樹(shù)構(gòu)建保守 domain和 mo ti f分析.基因結(jié)構(gòu)分析.轉(zhuǎn)錄組或熒光定量表達(dá)分析.二、數(shù)據(jù)庫(kù)檢索與成員鑒定1、數(shù)據(jù)庫(kù)檢索1 ）首先了解數(shù)據(jù)庫(kù)用法，學(xué)會(huì)下載你要分析物種的基因組相關(guān)數(shù)據(jù)。一般也就是 下面這些數(shù)據(jù)庫(kù)了Brae hypod iumdb:TAIR:Rice Ge nome Anno

2、tation Project：.Phyto z o m e :E nsem ble:NCBI基因組數(shù)據(jù)庫(kù):2 ）已鑒定的家族成員獲取。如何獲得其他物種已發(fā)表某個(gè)基因家族的所有成員呢，最簡(jiǎn)單的就是下載該物種蛋白序列文件(可以從上述數(shù)據(jù)庫(kù)中下載)，然后按照文章中的ID,找到對(duì)應(yīng) 成員。對(duì)于沒(méi)有全基因組鑒定的，可以下列數(shù)據(jù)庫(kù)中找：a. N C B I : nucleotid e and protein db .b. EBI:.c. Un iProtKB :2、比對(duì)工具。一般使用 blast和hmm er,具體使用命令如下：Local BLASTformatdb -i d b. fas -p F/T;

3、bl a st a ll -p bl a s t p(o r else) 4 kn o wn. fas d db.fas -m 8 -b 2 (or else) e 1e-5 -o alignresu It . t xt.-b:ou tp uttw o d i ff e ren t m e m b ers in subj ec t s e que nce s ( d b ).Hmmer ( h idd e n Ma r kov Mod e 1 ) s earc h. Thesame as PS BLA ST in f u nct ion. It has a hig her se n s i t

4、ivit y , but the sp eed islower.Command: hmmbuild-infor m ataf ak now n .hmm a 1 i gnknown. fa;hmmsearchk nown.hmmdb. fas a 1 ign.out.3、過(guò)濾。Identit y :至少 50% .Co ver re g ion:也要超過(guò)50%或者蛋白結(jié)構(gòu)域的長(zhǎng)度.domain:必須要有完整的該蛋白家族的。工具p famdb ()和NCBI Batch CD- s earch .().EST支持Blast and Hmmer同時(shí)檢測(cè)到4、通過(guò)上述操作獲得某家族的所有成員基因家族

5、分析套路(二)本次主要講解在基因家族分析類(lèi)文章中，進(jìn)化部分分析的內(nèi)容。主要是進(jìn)化樹(shù)的 構(gòu)建與分析。一、構(gòu)建進(jìn)化樹(shù)的基本步驟1、多序列比對(duì). Muscl e progra m.2、Mode 1選擇.分別針對(duì)蛋白序列和核酸序列的模型選擇程序。ProtTest prog ram f o r protei n a n d ModelTe s t or Jmodetl e s t for D NA().3、算法選擇。三種. NJ, ML an d BI.4、軟件選擇ME GA (boot strap 1 ea s t 1 0 00 r e p 1 icates) , phyML and Mrbay e

6、s ().5、進(jìn)化樹(shù)修飾.M EGA: view opti o n s and s u bt r e e - d raw options. Al s o ca n b e d ecor a t e d in word ()二、具體步驟2.1 多序列比對(duì)。一般采用 mus cle。因?yàn)?MUS CLE i s on e of the be s t 一perfor m i n g m ultiple ali g n m e nt pro g rams acco rdingto pu b 1 ished ben chmar k t e s ts, wi t h acc u r a cy and sp

7、e e d th at are consistent 1 y bett e r than C L USTALW.2. 2模型選擇。對(duì)于用蛋白序列構(gòu)建進(jìn)化樹(shù)的可以采用下面命令：java -Xmx250 m - c la s spath pat h /Pro t T e st.ja r pro t tes t .P rotTest - i a lign m .運(yùn)行結(jié)果如下圖1) ”. Phy” format. O,A- dr + + M * * * + *+* * *+ * * +* * *TrVr*M* * +M*44*+ +Beat model aGCorlinj to ftIC; 胞6福十7

8、ir * * *+* *肯b*$* +t+*+*Model如LeWKIZAICw-InL降口，。015550.510,73-7751,25儂“工犯+F2.00155fi2.510.27-?7S1.2SLG 評(píng)+.F15.611S579.120.00*7760.5ls+i+g+f30.6115581.130,00-1760.56質(zhì)1。死26.7315587.230.00-77S3.621SAG+I4G28.731558923 *門(mén)等宿 u_i Fl1 01c suin2j+F37.42L55i7.93o.oa-一 一？En ly allo w ten c h a rater s .注意名字不能重

9、復(fù)相同。2)AIC : Akaik e Inf o rmati o n Cri t erio n framework.3)Gam m a distri b u t i o n param e t er (G): gam m a sha p e.3)proport ion of inv a r ia b le s i tes : I.2 .3構(gòu)建進(jìn)化樹(shù)aMP” p，m*z 出MPK6TA1MPK6OsMPHaMPkS 一面6.PtMPK15-2 |PtMPK15-1 4Kisf。12-0 nds-wz0 3-a 4-心生信/Pliyltigcncttc analysis showed tlwt

10、the 77 MAPKs tell into four distinct gnjups (A Di with each giriGp con Wining at least hvo ZmAfPM. indjeaUng that the basal split between groupf； A. Bt (； and D was an early duplication event tkit lias been gciuMated betbre the divergence of the four species. Clado D could be divided into three sub-

11、groups, each of which contains both cucticor and monnent meniticrs U ig. indicar- nig that the diversification t)f members in group D was al ixxdy cscibiishcd bdbre 齒匕 cvolntioniiry d enjciKc of the .， -p 二彎廠 /1mwocots and cudi8K 為曲尸心 昕 型過(guò) msdy awed Xrth ?gene was lost diulng riec wolutian. l-urthcr

12、niorc, recently duplicated MARK genes (eg, ZmX/PKJ-J,辦加味/8-3, ZwM臉?！埃琎3Mp7, OkMPK& and OMPK9) in nionocotf； have an evolutionary illations hip thai is different fixim that of the related Ara bid opsis and poplar homologues (卻 FtMPKlfblr and PtMFK20-l k indicating a monocnt-spcci fie ，中 生Pl% x疣國(guó)力ampl

13、ification of these gene sets, fly contrast, the anccs*2.3.1 意義：a聚類(lèi)分析。如亞家族分類(lèi)。像MAPKKK基因家族通過(guò)進(jìn)化樹(shù)可以清楚分為MEKK , Ra f and ZIK三個(gè)亞家族.b親緣關(guān)系鑒定。在進(jìn)化樹(shù)上位于同一支的往往暗示這親緣關(guān)系很近c(diǎn)基因家族復(fù)制分析。研究基因家族復(fù)制事件 (dupli c a t i o n e vents ),兩 種復(fù)制事件類(lèi)型常采用的標(biāo)準(zhǔn)：Tan dem d u plicat ion: Ide nt i ty an d cove r re g ion more th an 70 % and tigh

14、tly 1 inked (H o lub , 2001).Ch r omosomal segment d u plicat i on: Plant Geno me Duplication Database (PGD D :)2.3.2 進(jìn)化樹(shù)。一般ML樹(shù)比較準(zhǔn)確，但應(yīng)結(jié)合方法，如NJ樹(shù)，相互驗(yàn)證。2.3.3 進(jìn)化部分分析：Ka Ks計(jì)算2. 3.3.1簡(jiǎn)單的方法.可以使用下面的網(wǎng)頁(yè) PAL2N AL ()2 .3 .3.2標(biāo)準(zhǔn)方法:.a. P araAT : Par a AT.pl h test, homolog s -n test.cds -a test, p ep -p proc f a

15、x t - k -o outputb . K aK s _C a lcula t or -m N G(or else) - i tes t .ax t - o te s t. ax t .kaksc.分歧時(shí)間計(jì)算：Diverg e nttime (T) ca 1 cu lation.T=Ks/2 卜入：mean 5. 1 -7.1 X10-9 .d . K a / Ks 意義：Ka/K s =1 .中性進(jìn)化。.K a/KsKa/Ks1. 正選擇。Po si t i v el y s elected g en e s and pro d uc e fi t n es s adv a nta g

16、emutatio ns to evolve new functions.基因家族分析套路(三)本節(jié)主要講基因結(jié)構(gòu)分析套路1、Motif 分析Sitpplv*ii-c Hint t iyurc S?_ I )l r ihttl ion nt :uld il ioikiI ktnicrv c nnti 1 identi tic J hv l| - Mb-、4fTh J* (EHt之生信r -T1. t m.臼使用軟件MEME ,命令如下：m e me s a mp 1 e. f a - d na - r evcom p - nmotifs 10 - mod zoops min w 6 m axw

17、5 0mem e _ht m l F ormat. h t ml2、基因結(jié)構(gòu)分布圖可以使用在線網(wǎng)站 GSDS2.0:webs i t e :用法如下：用一 GSDS2.0 Gene Structure DisplaServerHome I Help | About | Unks: PlantRegMapL Gene FcitlLiresamat hlqrr jiiijtjl itiInput lIcjIj.AYT?7 .7 .二.70* 7 37 YOTT57 avuTTj? AYrrTTiT :.TOV/T 加普， 上行工如G iY5：dr：3 .殖r- 7 I ; t i r- L J -

18、h- 5 b 5 n J nr 2 15 9- J- T 9 3 7 s 1 4 IT 1 I I ? 2 I- Il、可以杵費(fèi)方仲相入女件怖寸“匕JhgjiJ 可口注石用成的式?、當(dāng)?shù)仙璅A5TR琴式是*由/集給主瞅5與基 國(guó)摩利1。一段*i . mwi rfltt Ahhwi - winrtflBV tfesn t一 rfvun 一NKTMVM 。1 J r3、基因結(jié)構(gòu)常見(jiàn)統(tǒng)計(jì)信息：自己e x cel或?qū)懗绦蚪y(tǒng)計(jì)a . The num b e r of intro n an d exon.b . The splicing i ntronpa t te r n in c ulding 0 ,

19、1, 2 phas e .c. Th e mark e d r e gion. Fo r example kinase domaid . seque n ce lengt h .e. UTR .4、啟動(dòng)子分析。網(wǎng)站:主要做植物的：Search for CARESequim nee I ubial 1as eav DMA sequence： or a -iSequence nameDale of submission*B- 、f-1I - -ita| Search : RtgoiFflmi | | gg |MIE PCCCCG Ti：XCA7Ch?T I 工 G 巧 TAAT TTTTCC7陸

20、TSH TCCAIC7(iC TTAA T-JLLllrJA： IC r I1J1IIA1WL二 JmLALSGi；匚匚TEG 里 hAATG 匚匚 lif&UJJLI A GKbG I GOGACTiJ QTG T ?TT二 4TGGG TTustQrs39.207 genes in clustersSlrawbeny33納9.S9518.170人神求助關(guān)干基因家族聚類(lèi)分析的venn圖376A基因家族分析套路（四）、轉(zhuǎn)錄組及芯片原始數(shù)據(jù)下載網(wǎng)站用法見(jiàn)下圖GPL: platorleries.iles.on the data le concentatebeled GDS can banalyze

21、dorne geneoGPLusedrimenSoft rd 內(nèi) NtaWt 加加 rSand* ： !imahng的 階 理酬力槽9* A4 弓工位 E二21 ：/t qI 匚e sNMNHM auim imE- GSMgtrmnabng yatn. Pluttl icects prt?pw tar 期 rrwHion 4mg th Mtd tUvtfiiMtt* ftavitlfinqigM nt a th* Mayrgonw wiJinsnipt 蜩 nuturjiiDn 護(hù) mnthm DTMitM他Hkif Mio compare inexpl匚。，遭2博之蛭3hjf4尊tauf.3

22、 Efk_電Uek 3 2獨(dú)寸土二上后GDS GSEGSE: m ulThe dl i nei 1 yG EO數(shù)據(jù)ID命名規(guī)則：GPL - GT he d i f fer e nn b eGEO da t e s ets / p r o )口由E QP|t i s si m n le anda i n the samG SM: m u ltipIO 2T22m內(nèi)中”店口對(duì)第甥Organism for searchExperimentDetail informatio下面是在線分析轉(zhuǎn)錄組數(shù)據(jù)的用法：E Online Anatysis(GDS)DMLftMt Ibh 1sOt3dliVs，npw

23、ihImi F0iffc j .011- *Hyiilfc *liij11httrIndMCHTMimd M4rtt hacbirn H drihurig ZArmtng i#t4iMmuf*MhH Mg fM 幡IM/* 凱d V *4 E *W4 / uml Mpt j* )厘“ W 9*wwuJ;wfl廿*1ngi g U 叫M.5 惴w %HMb 第學(xué)Zr mjhl EIM 快KuhMMU 中壯r *舊臚護(hù)*M4 y押8 g 上叩加M4KOfHdAttnlP vWf-tfrrtatfonH白孔 IM;“rirr ll Alhmcni Uhn Jwnt 5 力rMSmnwnAiH U44

24、E Wnta A MM V* Mrr r*Aritanm* wMMtoft BlAlMhHfMv*fWMrwhMrtMbifttMUl Hmm HtMiHnKllnBlHhHNiy lit也 I UI *.1IHMI*44erMe WtIml 0119X3BMvb cmmA0Hiw*cwtMta4 iMilirW/umRefe/exe for ctornftg gene2、E BI ArrayExpr e s s ()該數(shù)據(jù)庫(kù)下載數(shù)據(jù)用法如下AccK.wnnotTff*Crg/mor依“化Eh asri 心1 業(yè)1d 總M 到姐gbbd *& ne業(yè)xnA：將 MM flit BHtf 叫j4

25、gH 岫l的 wi時(shí)A聆中4附蚪呱加.qdW C&Udlm伸腳口網(wǎng)13豆工七出訃的里工 g*cc al 產(chǎn)業(yè)g r uxjgd mF：蟲(chóng) urHter com stsss rtweas 紂edt dev3nd也時(shí)林 r WaGmAjEW-H4drwKWpodin dMtlcfi*b. LA 2(313上、E玷監(jiān)蠅植加對(duì)dcodm皆掙用Mm dcbdTw甥T/M8., det y / -i-j-j 甘m乎酹說(shuō)口 bffliflf sstiEgg (nBoclp抬皿)的燈31 p小西t am c-加心中汨昕reins* h wastd#電覽 wp# 通” r s *i 學(xué)2u,fi -E獲田四臚柏

26、：513T鼻WM000111H010Y11001010lOVG100001C11101硼f磔醐跳淅腳部貓桶SW胸怖21 2,.F| ； U TOeno expressloii resources for plarts md punt pathogensFind Your Gene Publications - Tools 10g ID:Password:( LOfl1n Log in needed to continue.The page you attempted to access is only available to registered users. If you have and

27、 password.Why Log in?S PathOQQcs & Symbiionts View your pnvate expenments and group protected experiments Create and modfy groups Update your personal informationf or downloddin。Public D空“ Sot午 you may use the following Login ID/PW:plexdbdownioad/downoadpLogin io： ptexdbdownload-O Search Ents田 T。B Y

28、our AccountorganismSubmission Helpassword:downloadpwPLEXdb Current Working Policy for Data SubmiPLEXdb 話 committed 2 makng expression frori pl wide. Data submissions candesignateo 不，丫於后 前河)、 access) ensures that data is password proie-&d for 6 rnQnths7dDownload for PLEXdbDownload CenterorganismAvjbi

29、IaKIc* SxpcrimGrt*。for Triic&arti nocz上ACCMBKX) NoTASName M WTwvcRNA 9 UyGEOngArrV。9lfor ft2 co mTAX USVJaazt：EL fites( gz)16.00 MTAI CEL.tar.cSoft file(expression ftestgz)930 00 KXAl_MA$_RMA.0rRRMA treatment means for all pfobesets (.txt TA1 RMA 5：means txt MAS treatment means for all probesets (.t

30、xt TAl MAS tmt mans.txtHMA tratmntfor prbeatTA1 M li b rary(affy ); 1 i b rary (ma k ec d fe n v);lib r a ry bar ley G e n ome = make.cdf.e n v ( b arleyGen o m e.c d f)myd a ta ese t wr i te.ex p rs(e s et, fil e = m ydata.tx t ) design v-m ode 1 .m a trix(-1 + fact o r (c(1 , 1,2, 2,3 ,3) # Create s appropriate d e sig n m atrix . co 1 nam e s(de s ign) fi t c on tras t. m atrix fit2 f i t2 t o pTable(f i t2, coe f = 1 ,adj u s t = fdr, sor t .by=B , number= 10) # G e ne r ate s list oft op 10 (/ numb e r= 1 0) di f f e r e n tia 1 l y e x pr e s s e d genes s orted by B -