Richard H. Scheuermann, Ph.D. November 5, 2012 Support for Systems Biology Data in IRD/ViPR

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Richard H. Scheuermann, Ph.D.November 5, 2012

Support for Systems Biology Datain IRD/ViPR

www.viprbrc.orgwww.fludb.orgBioinformatics Resource Centers (BRCs)In addition to supporting laboratory research projects, the U.S. National Institute of Allergy and Infectious Disease supports a series of research resources.Three Genome Sequencing Centers at the University of Maryland, the J. Craig Venter Institute and the Broad Institute provide services for rapid and cost efficient production of high-quality, genome sequences and high-throughput genotyping of NIAID Category A-C priority pathogens, microorganisms responsible for emerging and re-emerging infectious diseases and their hosts, related organisms, clinical isolates, and invertebrate vectors of infectious diseases.The sequences and associated metadata are made available and integrated with related pathogen through one of five different NIAID Bioinformatics Resource Centers focused on different subsets of human pathogens.Two BRCs are focused on viral pathogens the Virus Pathogen Resource (ViPR) and the Influenza Research Database.2Genome Sequencing CentersGenomicsFunctional GenomicsProteomicsStructural GenomicsSystems Biology Other omicsPathogenFunctionalGenomicsCenterProteomicsResearchCenters StructuralGenomicsCentersClinicalProteomicsCenters SystemsBiologyCentersDatabases/Bioinformatics Resource CentersHuman Microbiome ProjectTo address key questions in microbiology and infectious diseaseTo identify new targets and develop new strategies for vaccines, diagnostics and therapeuticsNIAID Genomics ProgramHost/Pathogen Interaction SystemsBiologyOmics Data ManagementBiosamplesCells/organismsTreatedSamples PrimaryDataProcessedData MatrixBiosets1.PathogentreatmentAssay 1DataprocessingDatainterpretationProjectBiosamplesCells/organismsTreatedSamples PrimaryDataProcessedData MatrixBiosets2.Assay 2Omics Data ManagementBiosamplesCells/organismsTreatedSamples PrimaryDataProcessedData MatrixBiosets1.BiosamplesCells/organismsTreatedSamples PrimaryDataProcessedData MatrixBiosets2.PathogentreatmentAssay 1DataprocessingDatainterpretationProjectMetadataAssay 2Data Submission WorkflowsStudy metadataExperiment metadataPrimary resultsAnalysis metadataProcessed data matrixFree text metadataGEO/PRIDE/PNNL/SRA/MetaboLightsViPR/IRD/PATRICHost factor biosetpointersubmissionsubmissionpointerSystems Biology sitesHost Factor Data

8 Studies To Date

XAssociated Biosets

Bioset Example

Cross-experiment Comparison

Boolean Combinations

Search for Specific Genes

Summary of Current Omics SupportStructured metadata about study, experiments, analysis methodsSeries of derived biosetsBoolean analysis of biosets from different experimentsBiosets based on expression patternsSearch for expression patterns of specific genesAccess to complete data matrixFuture Development PlansProteomics, metabolomics and lipidomics dataIntegration of RNA expression, protein abundance and metabolite abundanceGO enrichment analysisPathway/network visualization and analysisProtein interaction networks, e.g. BioGRIDPathways, e.g. BioCyc

GOenrichmentNetworkvisualizationGOGOGOGOGOGOGOGOGOGOGOGOGOGO

AcknowledgementLynn Law, U. WashingtonRichard Green, U. WashingtonPeter Askovich, Seattle BiomedBrett Pickett, U.T. Southwestern/JCVI Jyothi Noronha, U.T. SouthwesternEva Sadat, U.T. SouthwesternEntire Systems Biology Data Dissemination Task Force, especially Jeremy ZuckerNIAID (Alison Yao and Valentina DiFrancesco)31U.T. SouthwesternRichard Scheuermann (PI)Burke SquiresJyothi NoronhaVictoria HuntEva SadatBrett PickettYun ZhangVecnaChris LarsenAl RamseyLANLCatherine MackenMira DimitrijevicU.C. DavisNicole BaumgarthUSDADavid Suarez Sage AnalyticaRobert TaylorLone SimonsenU. WashingtonMichael Gale

Northrop GrummanEd KlemMike AtassiJon DietrichPatty BergerJawwad CheemaZhiping GuSherry HeWenjie HuaWei JenSanjeev KumarXiaomei LiJason LucasBruce QuesenberryBarbara RotchfordPrabhu ShankarHongbo SuBryan WaltersSam ZarembaLiwei Zhou

U. WashingtonLynn LawRichard Green

IRD SWGGillian Air, OMRFCarol Cardona, Univ. MinnesotaAdolfo Garcia-Sastre, Mt SinaiElodie Ghedin, Univ. PittsburghMartha Nelson, FogartyDaniel Perez, Univ. MarylandGavin Smith, Duke SingaporeDave Stallknecht, Univ. GeorgiaDavid Topham, RochesterRichard Webby, St JudeViPR SWGRichard Kuhn, PurdueRaul Andino, UCSFSlobodan Paessler, UTMB GalvestonX.J. Meng, VBIColin Parrish, CornellElliot Lefkowitz, UABCarla Kuiken, LANLDavid Knipe, HarvardMatthew Henn, Broad InstituteRichard Whitley, UABJohn Young, Salk Institute

Acknowledgments N01AI40041N01AI200803831

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