Advanced Genomic Data Mining 英文参考文献.docVIP

Education AdvancedGenomicDataMining Xose′ M.Ferna′ndez-Sua′rez*,EwanBirney EuropeanBioinformaticsInstitute,EnsemblGroup,WellcomeTrustGenomeCampus,Hinxton,Cambridge,UnitedKingdom Introduction trieve information through different plat- formssuchasGalaxy[5]andthebiomaRt package of BioConductor [11,12]. Many ofthesetoolsalsointeractwiththeUCSC TableBrowserandhavesimilarapproach- es using the UCSC system. We also address programmatic access using Bio- Mart’s own implementation of Web ser- vices (MartService). For local deployment ofBioMart,seeTable1. pathways in the Reactome database). Click on the ‘count’ button at the top to obtainthisnumber. Asdatabanksincreasetheirsize,oneof thecurrentchallengesinbioinformaticsis tobeabletoquerytheminasensibleway. Next, we can enrich our search for enzymes in the UniProt database. This will require the ‘linked’ or secondary dataset. Follow this description, or view thetutorialsforuseofthelinkeddatabase Information is contained in different databases, with various data representa- tionsorformats,makingitverydifficultto useasinglequerytooltosearchmorethan asingledatasource. at /common/ Workshops_Online?id=117. Dataminingisvitaltobioinformaticsas it allows users to go beyond simple browsing of genome browsers, such as Ensembl [1,2] or the UCSC Genome Browser [3],toaddressquestions;forexample,the biologicalmeaningoftheresultsobtained with a microarray platform, or how to identifyashortmotifupstreamofagene, amongst others. There are a number of integrated approaches available, some of whicharedescribedbelow(Figure1). The Table Browser at UCSC [4] sup- portstext-basedbatchqueriestotheUCSC Genome Browser, limiting the output to entries meeting the selected criteria. A disadvantageofthistoolisthatusersneed tobefamiliarwiththeunderlyingdatabase schemainordertoknowwheretheirdatais stored.Similarly,performingcomplexque- riesmightrequiremultiplestepsthatcanbe burdensome with this tool. Galaxy [5] providesasetoftoolsthatcanretrievedata