virus pathogen resource ( vipr )
DESCRIPTION
Virus Pathogen Resource ( ViPR ). 26 September 2011 Richard H. Scheuermann, Ph.D. Department of Pathology U.T. Southwestern Medical Center. ViPR Overview. www.viprbrc.org. Virus Taxonomy Browser. ViPR Usage. ViPR Overview. www.viprbrc.org. Database Search. Virus-specific Details. - PowerPoint PPT PresentationTRANSCRIPT
www.viprbrc.org
Virus Pathogen Resource(ViPR)
26 September 2011
Richard H. Scheuermann, Ph.D.Department of Pathology
U.T. Southwestern Medical Center
www.viprbrc.orgViPR Overview
www.viprbrc.org
www.viprbrc.orgVirus Taxonomy Browser
www.viprbrc.orgViPR Usage
www.viprbrc.orgViPR Overview
www.viprbrc.org
www.viprbrc.orgDatabase Search
www.viprbrc.orgVirus-specific Details
www.viprbrc.orgSearch Page
www.viprbrc.orgSearch Results
www.viprbrc.orgStrain Information
www.viprbrc.orgClinical Metadata
www.viprbrc.orgGenome Data
www.viprbrc.orgGene/Protein Data
www.viprbrc.orgDomain/Motif Annotation
www.viprbrc.orgViPR Overview
www.viprbrc.org
www.viprbrc.orgAnalysis Tools
www.viprbrc.orgGenome Annotator
www.viprbrc.orgViPR Overview
www.viprbrc.org
www.viprbrc.orgWorkbench
www.viprbrc.orgSequence => Tools
www.viprbrc.orgMeta-CATS
www.viprbrc.orgGroup Assignment
www.viprbrc.orgMeta-CATS Result
www.viprbrc.orgWorkbench Updated
www.viprbrc.orgViPR Challenges
• Diverse research communities• Diverse genome structures• Variable quality of gene/protein annotations• Deviation from the one gene – one functional protein
paradigm (polyproteins)• Growing complexity and inconsistency of metadata• Driving Biological Projects taking us in a new
direction that focuses on host genes
www.viprbrc.org
DIVERSE GENOME STRUCTURES
www.viprbrc.orgLarge DNA Virus Genome
www.viprbrc.org
Genome Browser for DNA Viruses
www.viprbrc.org
Single Strand RNA Virus Genome
www.viprbrc.org
INCOMPLETE/INCONSISTENTGENE/PROTEIN ANNOTATIONS
www.viprbrc.orgDomain/Motif Annotation
www.viprbrc.orgIncomplete Annotation
www.viprbrc.orgIncomplete Annotation
www.viprbrc.orgGene/Protein Data
www.viprbrc.orgScaling Manual Curation
www.viprbrc.org
POLYPROTEINS
www.viprbrc.orgGene/Protein Data
www.viprbrc.org
COMPLEXITY OF CLINICAL METADATA
www.viprbrc.orgGrowing Clinical Metadata
www.viprbrc.orgComplex Query Pages
www.viprbrc.org
DBP AND HOST GENE DATA
www.viprbrc.orgViPR Driving Biological Projects
• Abraham Brass, Mass. General Hospital– Creation of a Dengue virus-host interaction database using
functional genomics and bioinformatics • Lynn Enquist / Moriah Szpara, Princeton University– Deep Sequencing and Neuronal Microarrays for Functional
Genomic Analysis of Herpes Simplex Virus
www.viprbrc.org
Brass (DENV) DBP – Lab Component
• Carry out whole-genome screens with multiple siRNA libraries
• Validate DENV host factor “hits” w/ RT-PCR• Perform viral lifecycle and primary cell experiments
on candidate genes
www.viprbrc.org
Brass (DENV) DBP – ViPR Component
• Providing Data storage– Save “high-scoring” hits from the siRNA screens
• Associate virus life cycle data with the respective hits
• Developing Analytical Capability– Assist in assessing validity of lower confidence hits from
screens– Over-representation of hits in biological pathways/networks
• Enhancing Resource Usability– Developing visualization strategy to interpret siRNA data
(Interesting Gene Lists)
www.viprbrc.org
Enquist/Szpara (HSV-1) DBP – Lab Component
• Obtain and assemble NGS data– Oral and encephalitic HSV-1 isolates
• Use gene expression microarrays to observe differences in human neuronal cells during a time course of infection
• Temporally dissect results by blocking infection at several phases– Entry, viral gene expression, and genome replication
• Test phenotype of loci predicted to contribute to neurovirulence – Swapping candidate gene(s)
www.viprbrc.org
Enquist/Szpara (HSV-1) DBP – ViPR Component
• Providing Data storage– Import whole genome (consensus) sequences from GenBank– Import microarray results from GEO
• Associate virus life cycle data with respective genes
• Enhancing Resource Usability– Microarray data
• Make results searchable and cross reference with other related studies
– Incorporate genome browser into resource• Integrate genotype-phenotype data
– Developing visualization strategy• Interpret microarray results (Interesting Gene Lists)
www.viprbrc.orgViPR Summary
• Funded by U.S. National Institute of Allergy and Infectious Diseases (NIAID)
• Free and open access with no use restrictions• Developed by a team of research scientists, bioinformaticians
and professional software developers• Comprehensive collection of public data• Novel derived data, novel analytical tools, unique functions
• Integration – Integration – Integration• www.viprbrc.org
www.viprbrc.orgViPR Challenges
• Diverse research communities• Diverse genome structures• Variable quality of gene/protein annotations• Deviation from the one gene – one functional protein
paradigm (polyproteins)• Growing complexity and inconsistency of metadata• Driving Biological Projects taking us in a new
direction that focuses on host genes
www.viprbrc.orgViPR Acknowledgements
• Univ. 0f Texas Southwestern– Richard Scheuermann PhD (PI)– Brett Pickett, PhD– Eva Sadat, PhD– Yun Zhang, MS
• Vecna Technologies– Chris Larsen, Ph.D.– Al Ramsey, Ph.D.
• Northrop Grumman– Mike Atassi, Program Manager– Ed Klem, Ph.D., Project Manager– Patty Berger– Jawwad Cheema– Jon Dietrich– Zhiping Gu, Ph.D.– Sherry He– Wenjie Hua– Wei Jen– Sanjeev Kumar– Xiaomei Li, Ph.D.– Jason Lucas– Bruce Quesenberry– Barbara Rotchford– Prabhu Shankar– Hongbo Su, Ph.D.– Bryan Walters– Sam Zaremba, Ph.D.– Liwei Zhou, Ph.D.
• NIAID / NIH– Andrei Gabrielian, Ph.D., Bioinformatics Program Officer
• Co-PI’s– Michael Gale, Ph.D. (University of Washington)– Jingming Ma, Ph.D. (University of Rochester Medical Center)
• Scientific Working Group– Richard Kuhn ( Purdue University)– Raul Andino ( University of California, San Francisco)– Slobodan Paessler ( University of Texas Medical Branch at Galveston)– X.J. Meng ( Virginia Polytechnic Institute and State University)– Colin Parrish ( Cornell University)– Elliot Lefkowitz ( University of Alabama, Birmingham)– Carla Kuiken ( Los Alamos National Laboratory)– David Knipe ( Harvard University)– Matthew Henn ( Broad Institute)– Richard Whitley ( University of Alabama, Birmingham)– John Young ( Salk Institute for Biological Studies)
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• U.T. Southwestern– Richard Scheuermann (PI)– Burke Squires– Jyothi Noronha– Victoria Hunt– Shubhada Godbole– Brett Pickett– Yun Zhang
• MSSM– Adolfo Garcia-Sastre– Eric Bortz– Gina Conenello– Peter Palese
• Vecna– Chris Larsen– Al Ramsey
• LANL– Catherine Macken– Mira Dimitrijevic
• U.C. Davis– Nicole Baumgarth
• Northrop Grumman– Ed Klem– Mike Atassi– Kevin Biersack– Jon Dietrich– Wenjie Hua– Wei Jen– Sanjeev Kumar– Xiaomei Li– Zaigang Liu– Jason Lucas– Michelle Lu– Bruce Quesenberry– Barbara Rotchford– Hongbo Su– Bryan Walters– Jianjun Wang– Sam Zaremba– Liwei Zhou
• 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– David Spiro, JCVI– Dave Stallknecht, Univ. Georgia– David Topham, Rochester– Richard Webby, St Jude
• USDA– David Suarez
• Sage Analytica– Robert Taylor– Lone Simonsen
• CEIRS Centers
Acknowledgments
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