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SUMMERTutorial07-29-2020SalkIGC
Systeminformationbox:Usedforinstructionsandwarningmessages.
Datauploadpanel
Dataanalysistabs
OverviewofSUMMERwebserver
downloadsampledataset
Torunatestdataset:
1. Checkthisbox(ontopleftcorner)
2.Clickthisbutton(bottomleftcorner)
Torunanewanalysis:
1.choosetousetranscriptomeorproteomedata.Note:ifyoudon’thaveeither,leavetheselectionasis,skiptheuploadoftranscriptomicsdata,click“Runanalyses”.
3.uploadthemetabolomicsdata(must).Chooseiftheinputtablehasaheaderlineandwhetherthetableisdelimitedbycomma,semicolon,ortab.
4.uploadthetranscriptomicsorproteomicsdata(optional).
Apaneltouploadproteomicsdatawillappearif“Proteome”isselectedinstep1.
5.Don’tforgettocheckthisboxformicroarraydata.Datawillbequantile-normalizeduponthisselection.
2.choosespecies.
Torunanewanalysis(continued):
6.setupexperimentdesignformetabolomicsdata.First,choosethecolumnheadersfromdrop-downmenuthatcontainKEGGmetaboliteIDs.Then,choosethecolumnheadersthatcontainreplicatesforeachcondition
7.setupexperimentdesignfortranscriptomics/proteomicsdata.
8.click“Runanalyses”tostarttheanalysis.
Runanalyses
Afterclicking“Runanalyses”,gototheinformationbox.Itwillshowhowmanymetabolites,transcripts/proteinsaremappedandfiltered.Replicatenumbersareallowedtobedifferentformetabolomicsandtranscriptomics/proteomicsfornow.
Nowitisreadytoactuallyruntheanalyses.Note:Pathwayanalysisandnetworkgraphcanonlyberunafterdifferentialexpressionanalysisisperformed.
PrincipleComponentAnalysis(PCA)
Thisbuttonwillappeariftheuploadeddatalooksgood.ClicktorunPCA.
ClickPCAtab.
PrincipleComponentAnalysis(PCA)
Afterclickingthe“RunPCA”button,thePCAplotswillbegeneratedtovisualizesampleseparations.Detailswillbeshownuponmousehovering.
Ittakesabouthalfaminutetorendertheplots,pleasebepatient.
PCApanelswillbedisplayedintheorderofmetabolite(top),gene(middle),andprotein(bottom).
Plotscanbedownloaded
DifferentialExpression(DE)Analysis
ClickDifferentialExpressiontab.
Thisbuttonwillappeariftheuploadeddatalooksgood.Note:bootstraptakesabout2-5minstorundependingondatasize.
DifferentialExpression(DE)Analysis
DownloadbuttontodownloadtheDEresults.
• ThedefaultDEcutoffisabsolutelogFC>0.5andadjustedp-val <0.05formetabolites,absolutelogFC>0.5andrankingscore<0.05forreactions.
• ThedefaultDEcutoffisusedforthisbarplot,andthepathwayenrichmentanalysisonthenextslide.
• ThedefaultDEcutoffisnotadjustableatthismoment.
PathwayAnalysisClickPathwayAnalysistab.
ThisbuttonwillappeariftheDEanalysisisperformed.
Currently,onlyOver-representationAnalysisissupported.ChooseDEcutoffforthepathwayenrichmentresult.
PathwayAnalysis
Downloadbuttontodownloadthepathwayresults.
Barplots ofsignificantlyenrichedKEGGmetabolicpathwaytermsforDEmetabolitesandDEreactions.
PathwayAnalysis
ChooseKEGGmetabolicpathwaysfromdrop-downmenustogenerateanetworkgraphforthatpathway.Allmeasuredmetaboliteswillbeshownregardlessofitsstatisticalsignificance.
Downloadbuttontodownloadthepathwaynetworkgraphindifferentformats.
PathwayviewofNetworkGraph
NetworkGraph
ClickNetworkGraphtab.
ThisbuttonwillappearaftertheDEanalysisisperformed.
ChoosethestatisticalsignificancecutofftoconstructanetworkofDEmetabolitesandDEreactionsplustheirassociatedpartners.
NetworkGraph
GlobalviewofNetworkGraph
Canbemagnifiedbymousescrolling.
Choosefromdrop-downmenuthemetabolite/reactionneedstobehighlighted.
Downloadbuttontodownloadthenetworkgraphindifferentformats.
Square=reaction,circle=metabolite.red=up-regulation,blue=down-regulation.Networknodesizerepresentsitsrelativeconnectivitywithothers.Soonemetabolitenodecanbetinyifitonlyconnectswithonereaction.