简介：Thehomeobox(Hox)genesformanevolutionarilyconservedfamilyencodingtranscriptionfactorsthatplaymajorrolesinsegmentalidentityandorganspecificationacrossspecies.ThecanonicalgroupingofHoxgenespresentintheHOM-CclusterofDrosophilaorrelatedclustersinotherorganismsincludeseight"typical"genes,whicharelocalizedintheorderlabial(lab),proboscipedia(pb),Deformed(Dfd),Sexcombsreduced(Scr),Antennapedia(Antp),Ultrabithorax(Ubx),abdominalA(abdA),andAbdominalB(AbdB).ThemembersofHoxclusterareexpressedinadistinctanteriortoposteriororderintheembryo.AnalysisoftherelatednessofdifferentmembersoftheHoxgeneclustertoeachotherinfourevolutionarilydiverseinsecttaxarevealedthatthelocipb/DfdandAbdB,whicharefarthestapartinlinkage,hadahighdegreeofevolutionaryrelatedness,indicatingthatpb/DfdtypeanteriorgenesandAbdBareclosesttotheancestralanteriorandposteriorHoxgenes,respectively.ThegreaterrelatednessofotherposteriorgenesUbxandabdAtothemoreanteriorgenessuchasAntpandScrsuggestedthattheyarosebygeneduplicationsinthemoreanteriormembersratherthantheposteriorAbdB.

简介：Withthedevelopmentofgenomesequencingformanyorganisms,moreandmorerawsequencesneedtobeannotated.Genepredictionbycomputationalmethodsforfindingthelocationofproteincodingregionsisoneoftheessentialissuesinbioinformatics.Twoclassesofmethodsaregenerallyadopted:similaritybasedsearchesandabinitioprediction.Here,wereviewthedevelopmentofgenepredictionmethods,summarizethemeasuresforevaluatingpredictorquality,highlightopenproblemsinthisarea,anddiscussfutureresearchdirections.

简介：obtainaninitialoverviewofgenediversityandexpressionpatterninporcinethymus,11,712ESTs(ExpressedSequenceTags)from100-day-oldporcinethymus(FTY)weresequencedand7,071cleanedESTswereusedforgeneexpressionanalysis.ClusteredbythePHRAPprogram,959contigsand3,074singletswereobtained.Blastsearchshowedthat806contigsand1,669singlets(totally5,442ESTs)hadhomologuesinGenBankand1,629ESTswerenovel.AccordingtotheGeneOntologyclassification,36.99%ESTswerecatalogedintothegeneexpressiongroup,indicatingthatalthoughthefunctionalgene(18.78%indefensegroup)ofthymusisexpressedinacertaindegree,the100-day-oldporcinethymusstillexistsinadevelopmentalstage.Comparativeanalysisshowedthatthegeneexpressionpatternofthe100-day-oldporcinethymusissimilartothatofthehumaninfantthymus.

简介：Microarray数据基于肿瘤诊断是在生物信息学的一个很有趣的话题。关键问题之一是一个肿瘤的增进知识的基因的发现和分析。尽管解决这个问题有许多精致的途径，仅仅与microarray数据为肿瘤诊断选择增进知识的基因的一个合理集合仍然是困难的。在这份报纸，我们分类经由敏感对手惩罚了竞争学习的距离(DSRPCL)通过microarray数据表示进很多簇的基因算法然后在支持向量机器(SVM)的帮助下检测增进知识的基因簇或集合。而且，批评或强大的增进知识的基因能在获得的增进知识的基因簇上通过进一步的分类和察觉被发现。它是我们的建议DSRPCL-SVM途径为肿瘤诊断导致增进知识的基因的一种合理选择的冒号，白血病，和乳癌数据集的实验表明的井。

简介：Sincepigisanimportantlivestockspeciesworldwide,itsgeneexpressionhasbeeninvestigatedintensively,butrarelyinbrain.Inordertostudygeneexpressionprofilesinthepigcentralnervoussystem,wesequencedandanalyzed43,122highquality5′endexpressedsequencetags(ESTs)fromporcinecerebellum,cortexcerebrum,andbrainstemcDNAlibraries,involvingseveraldifferentprenatalandpostnataldevelopmentalstages.TheinitialESTswereassembledinto16,101clustersandcomparedtoproteinandnucleicaciddatabasesinGenBank.Ofthesesequences,30.6%clustersmatchedproteindatabasesandrepresentedfunctionknownsequences;75.1%hadsignificanthitstonucleicaciddatabasesandpartialrepresentedknownfunction;73.3%matchedknownporcineESTs;and21.5%hadnomatchestoanyknownsequencesinGenBank.WeusedthecategoriesdefinedbytheGeneOntologytosurveygeneexpressionintheporcinebrain.

简介：Microarraytechnologycanbeemployedtoquantitativelymeasuretheexpressionofthousandsofgenesinasingleexperiment.Ithasbecomeoneofthemaintoolsforglobalgeneexpressionanalysisinmolecularbiologyresearchinrecentyears.Thelargeamountofexpressiondatageneratedbythistechnologymakesthestudyofcertaincomplexbiologicalproblemspossible,andmachinelearningmethodsareexpectedtoplayacrucialroleintheanalysisprocess.Inthispaper,wepresentourresultsfromintegratingtheself-organizingmap(SOM)andthesupportvectormachine(SVM)fortheanalysisofthevariousfunctionsofzebrafishgenesbasedontheirexpression.Themostdistinctivecharacteristicofourzebrafishgeneexpressionisthatthenumberofsamplesofdifferentclassesisimbalanced.WediscusshowSOMcanbeusedasadata-filteringtooltoimprovetheclassificationperformanceoftheSVMonthisdataset.

简介：许多微数组研究的目的是发现在象处理类型或样品显型那样的基因表示和样品特征之间的协会。在那里，努力的巨浪为描出一直在开发不同方法协会。除了微数组数据的高维数，一很好公认的挑战是基因能复杂地被互连的事实，因此使许多统计方法不恰当在表达式数据上直接使用。Multivariate方法象主要部件分析(PCA)那样并且聚类经常被用作捕获基因关联的努力的部分，并且导出的部件或簇被用来描述在基因表示和样品显型之间的协会。我们建议一个方法因为用格言联盟者的耐心的人口dichotomization与PCA方法在联合选择了测试统计，它显示出有利结果。建议方法与一个当前认出得好的方法相比。

简介：我们从基因表示数据为肿瘤分类建议一个新方法，它主要包含三步。第一，原来的DNAmicroarray基因表达式数据被独立部件分析(集成通信适配器)建模。第二，集成通信适配器提取的大多数判别式eigenassays被顺序的漂浮的前面的选择技术选择。最后，支持向量机器被用来分类当模特儿的数据。显示出建议方法的有效性，我们使用了它分类包含各种各样的人的正常和肿瘤织物样品的三DNAmicroarray数据集。试验性的结果证明方法有效、可行。

简介：ChengandChurchalgorithmisanimportantapproachinbiclusteringalgorithms.Inthispaper,theprocessoftheextendedspaceinthesecondstageofChengandChurchalgorithmisimprovedandtheselectionsoftwoimportantparametersarediscussed.Theresultsoftheimprovedalgorithmusedinthegeneexpressionspectrumanalysisshowthat,comparedwithChengandChurchalgorithm,thequalityofclusteringresultsisenhancedobviously,theminingexpressionmodelsarebetter,andthedatapossessastrongconsistencywithfluctuationontheconditionwhilethecomputationaltimedoesnotincreasesignificantly.

简介：Microarraydataareoftenextremelyasymmetricindimensionality,suchasthousandsoreventensofthousandsofgenesbutonlyafewhundredsofsamplesorless.Suchextremeasymmetrybetweenthedimensionalityofgenesandsamplescanleadtoinaccuratediagnosisofdiseaseinclinic.Therefore,ithasbeenshownthatselectingasmallsetofmarkergenescanleadtoimprovedclassificationaccuracy.Inthispaper,asimplemodifiedantcolonyoptimization(ACO)algorithmisproposedtoselecttumor-relatedmarkergenes,andsupportvectormachine(SVM)isusedasclassifiertoevaluatetheperformanceoftheextractedgenesubset.Experimentalresultsonseveralbenchmarktumormicroarraydatasetsshowedthattheproposedapproachproducesbetterrecognitionwithfewermarkergenesthanmanyothermethods.IthasbeendemonstratedthatthemodifiedACOisausefultoolforselectingmarkergenesandmininghighdimensiondata.

简介：微数组技术是的模仿的微严肃(SMG)生物反应器和DNA识别“玩的空间基因”的强大的工具在对微严肃的细胞的反应给角色调音。我们使用了这些生物工学工具由用生物反应器在正常严肃为15，50，和60d由恢复culturing跟随了的高方面比率容器为3，4，9，和10d暴露房间到SMG在人的表皮的keratinocytes上调查SMG和post-SMG恢复效果。作为结果，我们鉴别162差别表示了基因，其32是“最一致地在路线试验的时间被影响的中心基因”。十一中心基因从综合压力反应小径并且是并列地下面调整的。七个中心基因，都是金属硫蛋白MT-I和MT-IIisoforms，是并列地起来调整的。另外，HLA-G，在细胞的有免疫力的反应抑制的关键基因，被发现在恢复阶段期间显著地起来调整。总的来说，超过80%差别从更短的暴露表示了基因(/=9d)暴露，超过50d被需要恢复到更短的暴露的影响水平。数据显示那更短的SMG暴露持续时间将从微严肃效果导致更快、更完全的恢复。

简介：AhybridGA(geneticalgorithm)-basedclustering(HGACLUS)schema,combiningmeritsoftheSimulatedAnnealing,wasdescribedforfindinganoptimalornear-optimalsetofmedoids.Thisschemamaximizedtheclusteringsuccessbyachievinginternalclustercohesionandexternalclusterisolation.TheperformanceofHGACLUSandothermethodswascomparedbyusingsimulateddataandopenmicroarraygene-expressiondatasets.HGACLUSwasgenerallyfoundtobemoreaccurateandrobustthanothermethodsdiscussedinthispaperbytheexactvalidationstrategyandtheexplicitclusternumber.

简介：Microarrayhasbecomeapopularbiotechnologyinbiologicalandmedicalresearch.However,systematicandstochasticvariabilitiesinmicroarraydataareexpectedandunavoidable,resultingintheproblemthattherawmeasurementshaveinherent"noise"withinmicroarrayexperiments.Currently,logarithmicratiosareusuallyanalyzedbyvariousclusteringmethodsdirectly,whichmayintroducebiasinterpretationinidentifyinggroupsofgenesorsamples.Inthispaper,astatisticalmethodbasedonmixedmodelapproacheswasproposedformicroarraydataclusteranalysis.TheunderlyingrationaleofthismethodistopartitiontheobservedtotalgeneexpressionlevelintovariousvariationscausedbydifferentfactorsusinganANOVAmodel,andtopredictthedifferentialeffectsofGV(genebyvariety)interactionusingtheadjustedunbiasedprediction(AUP)method.ThepredictedGVinteractioneffectscanthenbeusedastheinputsofclusteranalysis.Weillustratedtheapplicationofourmethodwithageneexpressiondatasetandelucidatedtheutilityofourapproachusinganexternalvalidation.

简介：Genomicresearchhasmadealargenumberofsequencesofnovelgenesorexpressedsequencetagsavailable.Toinvestigatefunctionsofthesegenes,asystemforconditionalcontrolofgeneexpressionwouldbeausefultool.Inducibletransgeneexpressionthatusesgreenfluorescentproteingene(gfp)asareportergenehasbeeninvestigatedintransgeniccelllinesofcotton(COT;GossypiumhirsutumL.),Fraserfir[FRA;Abiesfraseri(Pursh)Poir],Nordmannfir(NOR;AbiesnordmannianaLk.),andrice(RIC;OryzasativaL.Cv.Radon).Transgeniccelllineswereusedtotestthefunctionofthechemicalinducerdexamethasone.Inducibletransgeneexpressionwasobservedwithfluorescenceandconfocalmicroscopy,andwasconfirmedbynorthernblotanalyses.Dexamethasoneat5mg/Linducedgfpexpressiontothenearlyhighestlevel48haftertreatmentinCOT,FRA,NOR,andRIC.Dexamethasoneat10mg/LinhibitedthegrowthoftransgeniccellsinFRAandNOR,butnotCOTandRIC.Theseresultsdemonstratedthatconcentrationsofinducerforoptimuminduciblegeneexpressionsystemvariedamongtransgeniccelllines.Theinduciblegeneexpressionsystemdescribedherewasveryeffectiveandcouldbevaluableinevaluatingthefunctionofnovelgene.

简介：Transcriptionfactor(TF)bindingtoitsDNAtargetsiteplaysanessentialroleingeneregulation.Thelocation,orientationandspacingoftranscriptionfactorbindingsites(TFBSs)alsoaffectregulatoryfunctionoftheTF.However,hownucleosomalcontextofTFBSsinfluencesTFbindingandsubsequentgeneregulationremainstobeelucidated.Usinggenome-widenucleosomepositioningandTFbindingdatainbuddingyeast,wefoundthatbindingaffinitiesofTFstoDNAtendtodecreasewithincreasingnucleosomeoccupancyoftheassociatedbindingsites.WefurtherdemonstratedthatnucleosomalcontextofbindingsitesiscorrelatedwithgeneregulationofthecorrespondingTF.Nucleosome-depletedTFBSsarelinkedtohighgeneactivityandlowexpressionnoise,whereasnucleosome-coveredTFBSsareassociatedwithlowgeneactivityandhighexpressionnoise.Moreover,nucleosome-coveredTFBSstendtodisruptcoexpressionofthecorrespondingTFtargetgenes.WeconcludethatnucleosomalcontextofbindingsitesinfluencesTFbindingaffinity,subsequentlyaffectingtheregulationofTFsontheirtargetgenes.ThisemphasizestheneedtoincludenucleosomalcontextofTFBSsinmodelinggeneregulation.

简介：Hox基因，为沿着在embryogenesis的anteroposterior轴的地区性的说明负责，在迄今为止定序的大多数eumetazoan染色体作为簇被发现。无脊椎动物与第二等的簇破裂的一些例外拥有单个Hox基因簇，当时osteichthyans(多骨的脊椎动物)有多重Hox簇。在tetrapods，四Hox聚类，源于所谓的二回合的整个染色体复制(2R-WGDs)，被观察。总的来说，Hox基因簇的数字在动物染色体被认为是ploidy层次的一个可靠标记。事实上，这个计划也在经历了另外的WGD的teleost鱼适合状况。在这评论，我作为将充满在无脊椎动物和osteichthyans之间的差距的系集中于圆口动物和软骨的鱼。最近的研究在galeomorph鲨鱼系加亮HoxC簇的可能的损失，当软骨的鱼Hox簇的另外的方面通常标记他们的保存性质时。相反，存在资源建议圆口动物展出Hox的一个不同模式簇组织。为这组种类，其染色体能不同地从jawed脊椎动物对2R-WGDs作出回应，因此，Hox簇的数字不能用作他们的ploidy水平的好指示物。

简介：Microarrayanalysesofgeneexpressionarewidelyused,butreportsofthesameanalysesbydifferentgroupsgivewidelydivergentresults,andraisequestionsregardingreproducibilityandreliability.Wetakeasanexamplerecentpublishedreportsonmicroarrayexperimentsthatweredesignedtoidentifyretinoicacidresponsivegenes.Thesereportsshowsubstantialdifferencesintheirresults.Inthisarticle,wereviewthemethodology,results,andpotentialcausesofdifferencesintheseapplicationsofmicroarrays.Finally,wesuggestpracticestoimprovethereliabilityandreproducibilityofmicroarrayexperiments.

简介：Horizontalgenetransfer(HGT)haslongbeenconsideredasaprincipalforceforanorganismtogainnovelgenesingenomeevolution.Homologysearch,phylogeneticanalysisandnucleotidecompositionanalysisarethreemajorobjectiveapproachestoarguablydeterminetheoccurrenceanddirectionalityofHGT.Here,21genesthatpossessthepotentialtohorizontaltransferwereacquiredfromthewholegenomeofMagnaporthegriseaaccordingtoannotation,amongwhichthreecandidategenes(correspondingproteinaccessionnumbersareEAA55123,EAA47200andEAA52136)wereselectedforfurtheranalysis.AccordingtoBLASThomologyresults,wesubsequentlyconductedphylogeneticanalysisofthethreecandidateHGTgenes.Moreover,nucleotidecompositionanalysiswasconductedtofurthervalidatetheseHGTs.Inaddition,thefunctionsofthethreecandidategenesweresearchedinCOGdatabase.Consequently,weconcludethatthegeneencodingproteinEAA55123istransferredfromClostridiumperfringens.AnotherHGTeventisbetweenEAA52136andacertainmetazoan'scorrespondinggene,butthedirectionremainsuncertain.Yet,EAA47200isnotatransferredgene.

简介：Brassinosteroid(BR)andgibberellin(GA)aretwogroupsofplantgrowthregulatorsessentialfornormalplantgrowthanddevelopment.TogaininsightintothemolecularmechanismbywhichBRandGAregulatethegrowthanddevelopmentofplants,especiallythemonocotplantrice,itisnecessarytoidentifyandanalyzemoregenesandproteinsthatareregulatedbythem.Withtheavailabilityofdraftsequencesoftwomajortypes,japonicaandindicarice,ithasbecomepossibletoanalyzeexpressionchangesofgenesandproteinsatgenomescale.Inthisreview,wesummarizericefunctionalgenomicresearchbyusingmicroarrayandproteomicapproachesandourrecentresearchresultsfocusingonthecomparisonofcDNAmicroarrayandproteomicanalysesofBR-andGA-regulatedgeneandproteinexpressioninrice.WebelieveourfindingshaveimportantimplicationsforunderstandingthemechanismbywhichBRandGAregulatethegrowthanddevelopmentofrice.

简介：Predictingprotein-codinggenesstillremainsasignificantchallenge.Althoughavarietyofcomputationalprogramsthatusecommonlymachinelearningmethodshaveemerged,theaccuracyofpredictionsremainsalowlevelwhenimplementinginlargegenomicsequences.Moreover,computationalgenefindinginnewlyse-quencedgenomesisespeciallyadifficulttaskduetotheabsenceofatrainingsetofabundantvalidatedgenes.Herewepresentanewgene-findingprogram,SCGPred,toimprovetheaccuracyofpredictionbycombiningmultiplesourcesofevidence.SCGPredcanperformbothsupervisedmethodinpreviouslywell-studiedgenomesandunsupervisedoneinnovelgenomes.BytestingwithdatasetscomposedoflargeDNAsequencesfromhumanandanovelgenomeofUstilagomaydi,SCG-Predgainsasignificantimprovementincomparisontothepopularabinitiogenepredictors.WealsodemonstratethatSCGPredcansignificantlyimprovepredic-tioninnovelgenomesbycombiningseveralforeigngenefinderswithsimilarityalignments,whichissuperiortootherunsupervisedmethods.Therefore,SCG-Predcanserveasanalternativegene-findingtoolfornewlysequencedeukaryoticgenomes.Theprogramisfreelyavailableathttp://bio.scu.edu.cn/SCGPred/.