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

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Support for Systems Biology Data in IRD/ ViPR - Proteomics. Richard H. Scheuermann, Ph.D. November 5 , 2012. Projects with Host Factor Data. Four s ystems biology groups funded by NIAID, including: Systems Virology (Michael Katze group, Univ. Washington) - PowerPoint PPT Presentation


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

Support for Systems Biology Datain IRD/ViPR - Proteomics

Projects with Host Factor DataFour systems biology groups funded by NIAID, including:Systems Virology (Michael Katze group, Univ. Washington)Influenza H1N1 and H5N1 and SARS Coronavirusstatistical models, algorithms and software, raw and processed gene expression data, and proteomics dataSystems Influenza (Alan Aderem group, Institute for Systems Biology/Seattle Biomed)Various influenza virusesmicroarray, mass spectrometry, and lipidomics dataViPR Driving Biological ProjectsAbraham Brass, Mass. General HospitalDengue virus host factor database from RNAi screen Lynn Enquist / Moriah Szpara, Princeton UniversityDeep sequencing and neuronal microarrays for functional genomic analysis of Herpes Simplex VirusRichard Kuhn, Purdue UniversityMetabolomics data of Dengue virus infection of human cells and mosquitosMike Diamond, Washington UniversityIdentification of inhibitory interferon-stimulated genes against flaviviruses and noroviruses using shRNA knockdownDetermine the mechanism of action of individual inhibitory ISGsOmics data management (MIBBI vs MIBBI-DB)Project metadata (1 template)Title, PI, abstract, publicationsExperiment metadata (~6 templates)Biosamples, treatments, reagents, protocols, subjectsPrimary results dataRaw expression valuesData processing metadata (1 template)Normalization and summarization methodsProcessed dataData matrix of fold changes and p-valuesData interpretation metadata (1 template)Fold change and p-value cutoffs usedInterpreted results (Host factor biosets)Interesting gene, protein and metabolite listsVisualize biosets in context of biological pathways and networksStatistical analysis of pathway/sub-network overrepresentationStrategy for Handling Omics DataData Submission WorkflowsStudy metadataExperiment metadataPrimary resultsAnalysis metadataProcessed data matrixFree text metadataGEO/PRIDE/PNNL/SRA/MetaboLightsViPR/IRD/PATRICHost factor biosetpointersubmissionsubmissionpointerSystems Biology sitesMetadata Submission Template Examples

Host Factor Data

8 Studies To Date

Host Factor Bioset

Transcriptomics => ProteomicsMetadata fields are largely re-usable, with some exceptionsExp_sample_template (protein).xlsResults data differencesPeptide-level and protein-levelIM005_Peptide_normalization_matrix.V2.xlsxIM005_Protein Normalization matrix.xlsxStatistical measuresResults_matrix_ IM005_sig Protein_RM.xlsxMetadata Field ChangesGEO GSM ID => Primary Data Archive + Primary Data Archive IDSemi-structured Experiment Variable to Structured Experiment VariableFree text (1 day) => value unit pairs in separate fields (1/day; 10^4/plaque forming units)Multiple processed data matrix filesConcatenated IDs separated by (; |)Reagents and protocols are different but should not require submission template changesNormalized DataArchive at BRC (standard format?)Peptide normalized dataProtein normalized dataResults matrix of significant proteinsBRCs derive bioset lists from results matrixHandling different significance measurest-test flag, t-test p-value, g-test flag, g-test p-value, log10 ratioHost Factor Bioset

On DeckMetabolomics and lipidomics dataIntegration of RNA expression, protein abundance and metabolite abundancePathway/network visualization and analysisAcknowledgementLynn 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)

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