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DESPRAD meeting report

DESPRAD meeting report. Patrick Kemmeren Genomics Lab, UMC Utrecht. Overview. Data deposited in ArrayExpress Current analysis pipeline Future developments. Data in ArrayExpress. Submitted through MAGE-ML documents Fully MIAME compliant Data submitted so far:

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DESPRAD meeting report

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  1. DESPRAD meeting report Patrick Kemmeren Genomics Lab, UMC Utrecht

  2. Overview Data deposited in ArrayExpress Current analysis pipeline Future developments

  3. Data in ArrayExpress • Submitted through MAGE-ML documents • Fully MIAME compliant • Data submitted so far: • 2 array designs ( 15552 and 19200 features ) • 4 experiments ( 18 hybridizations in total ) • 11 protocols

  4. MAGE-ML structure Array Designs Zones(48) BioSequences(6370) Reporters(6378) Features(15552) FeatureReporterMaps DatabasesSGDRefSeq ReporterGroupsGenesQuality ControlsNormalization Controls Array Design(A-UMCU-1) Protocol Array Manufacturers

  5. MAGE-ML structure Experiments Experimental Designself vs self, dye swap Experiment(E-UMCU-1) DescriptionNormalization Replicates Array Design(A-UMCU-1) Experimental FactorsNormalization controls Batch PhysicalBioAssay(hybridization) Lextract BioSample Extract BioAssayTreatment Hybridization protocol BioSampleTreatment Treatment protocol BioSampleTreatment Labeling protocol FeatureExtraction Image analysis protocolparameters BioSource MeasuredBioAssay(Raw data) DataTransformation QuantitationTypeMapping DerivedBioAssay(Normalized data) DataTransformation QuantitationTypeMapping BioAssayMapping DesignElementMapping DerivedBioAssay(Gene Expression Matrix)

  6. Current analysis pipeline Experiment MAGE-ML ArrayDesign MAGE-ML Scanner TIFF images Quality Control Normalization Advanced analysis Visualization Store advanced analysis and visualization GeneSpring LIMS Imagene QQCC GeNet Gene descriptions through flat files MIAME compliancy enforcement RDBMS Flat-files storage XML Database User path

  7. Future developments ArrayDesign MAGE-ML LIMS Gene descriptions through Barcode RDBMS Scanner TIFF images Quality Control Normalization Advanced analysis Visualization Raw data annotation MIAME compliancy Store advanced analysis and visualization GeneSpring Imagene QQCC BASE GeNet Store raw data in temporary table Low level analysis Filtering Normalization BioConductor R Flat-file storage RDBMS RDBMS User path Experiment MAGE-ML

  8. Future developments • Time Frame future pipeline: • BASE/BioConductor/QQCC integration => 3-6 months • LIMS integration => 2-3 months • MAGE-ML generation BASE + GeNet => 6-12 months • Upcoming submissions: • ArrayDesigns: * human oligo v2.0 * mouse oligo v3.0 * rat oligo v2.0 * yeast intergenic v1.0 • Experiments: * Copper depletion/addition time series, 4 * 12 hybs * Stationary Phase time series, 40 hybs * Deletion mutants, 20+ hybs * Head/neck cancer, 80 hybs * many, many more

  9. Genomics Lab Group leader Frank Holstege Microarray technology Joop van Helvoort Dik van Leenen Tony Miles Marian Groot-koerkamp Bioinformatics Philip Lijnzaad Harm van Bakel Transcription regulation Jeroen van de Peppel Marijana Radonjic Harm van Bakel Jean-Christophe Andrau Nynke van Berkum Theo Bijma Nienke Kettelarij Paul Roepman http://www.genomics.med.uu.nl EMBL-EBI Helen Parkinson Ele Holoway Ugis Sarkans Alvis Brazma

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