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

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

2. Bioinformatics Resource Centers (BRCs) www.viprbrc.org www.fludb.org

3. NIAID Genomics Program Functional Genomics Systems Biology Other “omics” Structural Genomics Genomics Proteomics Genome Sequencing Centers Pathogen Functional Genomics Center Proteomics Research Centers Structural Genomics Centers Systems Biology Centers Human Microbiome Project Clinical Proteomics Centers Host/Pathogen Interaction Systems Biology Databases/Bioinformatics Resource Centers To identify new targets and develop new strategies for vaccines, diagnostics and therapeutics To address key questions in microbiology and infectious disease

4. “Omics” Data Management Project Pathogen treatment Data processing Data interpretation Assay 1 Biosamples Cells/organisms Treated Samples Primary Data Processed Data Matrix 1. Biosets Assay 2 Biosamples Cells/organisms Treated Samples Primary Data Processed Data Matrix 2. Biosets

5. “Omics” Data Management Project Metadata Pathogen treatment Data processing Data interpretation Assay 1 Biosamples Cells/organisms Treated Samples Primary Data Processed Data Matrix 1. Biosets Assay 2 Biosamples Cells/organisms Treated Samples Primary Data Processed Data Matrix 2. Biosets

6. Data Submission Workflows Free text metadata GEO/PRIDE/PNNL/SRA/MetaboLights Primary results submission Study metadata pointer submission Experiment metadata ViPR/IRD/PATRIC Analysis metadata Processed data matrix pointer Host factor bioset Systems Biology sites

7. Host Factor Data

8. 8 Studies To Date

11. X

12. Associated Biosets

13. Bioset Example

14. Cross-experiment Comparison

15. Boolean Combinations

20. Search for Specific Genes

26. Summary of Current “Omics” Support • Structured metadata about study, experiments, analysis methods • Series of derived biosets • Boolean analysis of biosets from different experiments • Biosets based on expression patterns • Search for expression patterns of specific genes • Access to complete data matrix

27. Future Development Plans • Proteomics, metabolomics and lipidomics data • Integration of RNA expression, protein abundance and metabolite abundance • GO enrichment analysis • Pathway/network visualization and analysis • Protein interaction networks, e.g. BioGRID • Pathways, e.g. BioCyc

28. GO enrichment Network visualization GO GO GO GO GO GO GO GO GO GO GO GO GO GO

30. Acknowledgement • Lynn Law, U. Washington • Richard Green, U. Washington • Peter Askovich, Seattle Biomed • Brett Pickett, U.T. Southwestern/JCVI • Jyothi Noronha, U.T. Southwestern • Eva Sadat, U.T. Southwestern • Entire Systems Biology Data Dissemination Task Force, especially Jeremy Zucker • NIAID (Alison Yao and ValentinaDiFrancesco)

31. U.T. Southwestern Richard Scheuermann (PI) Burke Squires JyothiNoronha Victoria Hunt Eva Sadat Brett Pickett Yun Zhang Vecna Chris Larsen Al Ramsey LANL Catherine Macken Mira Dimitrijevic U.C. Davis Nicole Baumgarth USDA David Suarez Sage Analytica Robert Taylor Lone Simonsen U. Washington Michael Gale Northrop Grumman Ed Klem Mike Atassi Jon Dietrich Patty Berger JawwadCheema ZhipingGu Sherry He WenjieHua Wei Jen Sanjeev Kumar Xiaomei Li Jason Lucas Bruce Quesenberry Barbara Rotchford Prabhu Shankar Hongbo Su Bryan Walters Sam Zaremba Liwei Zhou U. Washington Lynn Law Richard Green Acknowledgments • IRD SWG • Gillian Air, OMRF • Carol Cardona, Univ. Minnesota • Adolfo Garcia-Sastre, Mt Sinai • ElodieGhedin, Univ. Pittsburgh • Martha Nelson, Fogarty • Daniel Perez, Univ. Maryland • Gavin Smith, Duke Singapore • Dave Stallknecht, Univ. Georgia • David Topham, Rochester • Richard Webby, St Jude • ViPR SWG • Richard Kuhn, Purdue • Raul Andino, UCSF • Slobodan Paessler, UTMB Galveston • X.J. Meng, VBI • Colin Parrish, Cornell • Elliot Lefkowitz, UAB • Carla Kuiken, LANL • David Knipe, Harvard • Matthew Henn, Broad Institute • Richard Whitley, UAB • John Young, Salk Institute N01AI40041 N01AI2008038