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

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

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

4. “Omics” Data Management Biosamples Cells/organisms Treated Samples Primary Data Processed Data Matrix Biosets1. Pathogen treatment Assay 1 Data processing Data interpretation Project Biosamples Cells/organisms Treated Samples Primary Data Processed Data Matrix Biosets2. Assay 2

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

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

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 Valentina DiFrancesco)

31. 31 U.T. Southwestern – Richard Scheuermann (PI) – Burke Squires – Jyothi Noronha – 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 – Jawwad Cheema – Zhiping Gu – Sherry He – Wenjie Hua – 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 IRD SWG – Gillian Air, OMRF – Carol Cardona, Univ. Minnesota – Adolfo Garcia-Sastre, Mt Sinai – Elodie Ghedin, 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 Acknowledgments N01AI40041 N01AI2008038