ArrayAnalysis

1. ArrayAnalysis.org Introduction Lars Eijssen l.eijssen@maastrichtuniversity.nl

2. Arrayanalysis.org • Workflowsforanalysing high throughputdata • Modularsetup • Public site: Qualitycontrol and normalisation module for Affymetrix chips • Other modules • www.arrayanalysis.org/dev • restrictedaccess • use ‘ebicourse’ and‘bioinformatics’ • soontransferredtopublic site

4. QC andnormalisationmoduleflow chart

5. QC andnormalisationmoduledetailedoverview

6. Affymetrix gene expressionworkflow CEL files Normalised data Statisticalresults Biologicalpathwayresults AffymetrixQC and normalisation module Statistics module Pathway analysis module

7. Gene expression workflow Raw data files Normalised data Statisticalresults Biologicalpathwayresults QC and normalisation module Statistics module Pathway analysis module

9. Arrayanalysis.org • Publiclyavailable module • Qualitycontrol and preprocessing for Affymetrix chips • Other modules • Statisticalanalysisfor gene expression • Pathwayanalysis (calling PathVisio – xml.rpc interface) • Illumina gene expressionanalysis (developedby TNO) • NimbleGenenrichmentanalysis (methylation, TF binding, histonemodification) • Soon to beadded: QC and normalisation of spotted (Agilent, customspotted) arrays

11. Modularuse Affymetrix gene expression QC and pre-processing Statisticalanalysis Pathwayanalysis Illumina gene expression QC and pre-processing Dashedarrowsindicate input and output from and to othersources Overrepresentation QC and pre-processing Statisticaloverrepresentationanalysis • Input maybe even from different sourcesthan the onescurrentlyoffered in the workflow • (e.g. normalised data fromother types of gene expressionexpressionarraysfor the statisticalanalysis module) • Input mayalsobefromother data sourcesbesidesmicroarrays, e.g. nextgenerationsequencingfor • the pathwayanalysis module • New modules caneasilybeadded • Support integrativeanalysis of multiple data types and incorporation of publiclyavailable data

12. Use cases • Arrayanalysis is useful to process any new data set that you generate • But it is also very useful to process existingdata sets from repositories such asArrayExpress and Gene Expression Omnibus • Perform QC on (older) studies that you want to compare to or integrate with yours • Systematically analyse a set of studies using the same protocol • Recall that some of the modules can also be used on other data types beyond microarrays • For example the (soon to be released) pathway module to analyse processed results from High Throughput Sequencing experiments

13. Web data flow local machine web server calculation server

14. Web andlocalusea- run through web b- run locally * download main script,connect to functions in repository * download all files

15. Acknowledgements part 1Maastricht University • Michiel AdriaensAffy QC & norm. module; Nimblegenenrichment module • WibowoArindrartoNimblegenenrichment module • Maarten CoonenSpottedarrayworkflow • AnweshaDuttaStatistics module; pathwayanalysismodule, PathVisio RPC • Stan GajSpottedarrayworkflow; Affy QC & norm. module • MagaliJaillardAffy QC & norm. module; statistics module, pathwayanalysismodule • Martina KutmonPathwayanalysis module • NunoNunesIT management of the servers and processes • Chris EveloFacilitating the Arrayanalysis.org and PathVisio projects

16. Acknowledgements part 2Externalcollaborators • Wageningen UR: • Philip de Groot Affy QC & norm. module • TNO:Illumina gene expression module • VarshnaGoelela • Thomas Kelder • MarijanaRadonjić • Minke Informatics Ltd., UK: • Tony TravisIT support and adviceforArrayanalysis