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

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

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Support for Systems Biology Data in IRD/ ViPR. Richard H. Scheuermann, Ph.D. November 5 , 2012. Bioinformatics Resource Centers (BRCs). www.viprbrc.org. www.fludb.org. NIAID Genomics Program. Functional Genomics. Systems Biology Other “ omics ”. Structural Genomics. Genomics. - PowerPoint PPT Presentation

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Page 1: Richard H. Scheuermann, Ph.D. November  5 , 2012

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

Support for Systems Biology Datain IRD/ViPR

Page 2: Richard H. Scheuermann, Ph.D. November  5 , 2012

www.viprbrc.org www.fludb.org

Bioinformatics Resource Centers (BRCs)

Page 3: Richard H. Scheuermann, Ph.D. November  5 , 2012

Genome Sequencing

Centers

GenomicsFunctional Genomics Proteomics

Structural Genomics

Systems Biology Other

“omics”PathogenFunctionalGenomics

Center

ProteomicsResearchCenters

StructuralGenomicsCenters

ClinicalProteomics

Centers

SystemsBiologyCenters

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

SystemsBiology

Page 4: Richard H. Scheuermann, Ph.D. November  5 , 2012

“Omics” Data Management

BiosamplesCells/organisms

TreatedSamples

PrimaryData

ProcessedData Matrix Biosets1.

Pathogentreatment Assay 1 Data

processingData

interpretation

Project

BiosamplesCells/organisms

TreatedSamples

PrimaryData

ProcessedData Matrix Biosets2.

Assay 2

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

“Omics” Data Management

BiosamplesCells/organisms

TreatedSamples

PrimaryData

ProcessedData Matrix Biosets1.

BiosamplesCells/organisms

TreatedSamples

PrimaryData

ProcessedData Matrix Biosets2.

Pathogentreatment Assay 1 Data

processingData

interpretation

Project

Metadata

Assay 2

Page 6: Richard H. Scheuermann, Ph.D. November  5 , 2012

Data Submission Workflows

Study metadata

Experiment metadata

Primary results

Analysis metadata

Processed data matrix

Free text metadataGEO/PRIDE/PNNL/SRA/MetaboLights

ViPR/IRD/PATRIC

Host factor bioset

pointer

submission

submission

pointer

Systems Biology sites

Page 7: Richard H. Scheuermann, Ph.D. November  5 , 2012

Host Factor Data

Page 8: Richard H. Scheuermann, Ph.D. November  5 , 2012

8 Studies To Date

Page 9: Richard H. Scheuermann, Ph.D. November  5 , 2012
Page 10: Richard H. Scheuermann, Ph.D. November  5 , 2012
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X

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Associated Biosets

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Bioset Example

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Cross-experiment Comparison

Page 15: Richard H. Scheuermann, Ph.D. November  5 , 2012

Boolean Combinations

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Search for Specific Genes

Page 21: Richard H. Scheuermann, Ph.D. November  5 , 2012
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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

Page 27: Richard H. Scheuermann, Ph.D. November  5 , 2012

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

Page 28: Richard H. Scheuermann, Ph.D. November  5 , 2012

GOenrichment

Networkvisualization

GOGOGOGOGOGOGOGOGOGOGOGOGOGO

Page 29: Richard H. Scheuermann, Ph.D. November  5 , 2012
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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)

Page 31: Richard H. Scheuermann, Ph.D. November  5 , 2012

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

N01AI40041N01AI2008038