ExpressionPlot a web-based framework for analysis of RNA-Seq and microarray gene expression data.docVIP

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ExpressionPlot a web-based framework for analysis of RNA-Seq and microarray gene expression data.doc

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ExpressionPlot a web-based framework for analysis of RNA-Seq and microarray gene expression data

ExpressionPlot:aweb-basedframeworkfor analysisofRNA-Seqandmicroarraygene expressiondata FriedmanandManiatis FriedmanandManiatisGenomeBiology2011,12:R69 /2011/12/7/R69(28July2011) FriedmanandManiatisGenomeBiology2011,12:R69 /2011/12/7/R69 SOFTWARE OpenAccess ExpressionPlot:aweb-basedframeworkfor analysisofRNA-Seqandmicroarraygene expressiondata BradAFriedman1,2,3* andTomManiatis4 Abstract RNA-Seqandmicroarrayplatformshaveemergedasimportanttoolsfordetectingchangesingeneexpressionand RNAprocessinginbiologicalsamples.WepresentExpressionPlot,asoftwarepackageconsistingofadefaultback end,whichpreparesrawsequencingorAffymetrixmicroarraydata,andaweb-basedfrontend,whichoffersa biologicallycenteredinterfacetobrowse,visualize,andcomparedifferentdatasets.Downloadandinstallation instructions,auser’smanual,discussiongroup,andaprototypeareavailableat/. Rationale ExpressionPlot can be tested as a virtual machine RNA-Seq has emerged in recent years as the eminent (runningunderVirtualBox),orinstalleddirectlyintoan platform foranalysis ofgeneexpression andRNApro- existingwebserver.InputtoExpressionPlotcanberaw cessing [1-3]. However, processing the raw sequence sequence data (FASTQ files) or Affymetrix array data datatogetuseful andaccurate information aboutgene (CELfiles),completedalignments(BAMfiles),ortables expression andRNAprocessing isstill adaunting task, of gene expression values and changes generated by even for computationally inclined researchers. High otherbackends.Oncedataarepre-processed,theweb- quality softwarepackagesnowexist toperformspecific basedfrontendallows users toeasily browsemeasures steps in the analysis pipeline [4-10], as well as web- of quality control, plot changes ingene expression and basedsystemssuchasGalaxy[11]andGenePattern[12] RNAprocessing, browse hyperlinked tables ofchanged thatenablethemanagementofdataflowthroughthese genes and splicing events, generate read plots from a tools.WepresentExpressionPlot, anopensou