ViPR 26 September 2011 Richard H Scheuermann PhD Department of Pathology UT Southwestern Medical Center ViPR Overview wwwviprbrcorg Virus Taxonomy Browser ViPR Usage ViPR Overview ID: 932051
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Slide1
Virus Pathogen Resource(ViPR)
26 September 2011Richard H. Scheuermann, Ph.D.Department of PathologyU.T. Southwestern Medical Center
Slide2ViPR Overview
www.viprbrc.org
Slide3Virus Taxonomy Browser
Slide4ViPR Usage
Slide5ViPR Overview
www.viprbrc.org
Slide6Database Search
Slide7Virus-specific Details
Slide8Search Page
Slide9Search Results
Slide10Strain Information
Slide11Clinical Metadata
Slide12Genome Data
Slide13Gene/Protein Data
Slide14Domain/Motif Annotation
Slide15ViPR Overview
www.viprbrc.org
Slide16Analysis Tools
Slide17Genome Annotator
Slide18ViPR Overview
www.viprbrc.org
Slide19Workbench
Slide20Sequence => Tools
Slide21Meta-CATS
Slide22Group Assignment
Slide23Meta-CATS Result
Slide24Workbench Updated
Slide25ViPR ChallengesDiverse research communitiesDiverse genome structuresVariable quality of gene/protein annotationsDeviation from the one gene – one functional protein paradigm (polyproteins)Growing complexity and inconsistency of metadataDriving Biological Projects taking us in a new direction that focuses on host genes
Slide26Diverse Genome Structures
Slide27Large DNA Virus Genome
Slide28Genome Browser for DNA Viruses
Slide29Single Strand RNA Virus Genome
Slide30Incomplete/InconsistentGene/Protein Annotations
Slide31Domain/Motif Annotation
Slide32Incomplete Annotation
Slide33Incomplete Annotation
Slide34Gene/Protein Data
Slide35Scaling Manual Curation
Slide36Polyproteins
Slide37Gene/Protein Data
Slide38Complexity of Clinical Metadata
Slide39Growing Clinical Metadata
Slide40Complex Query Pages
Slide41DBP and Host Gene Data
Slide42ViPR Driving Biological ProjectsAbraham Brass, Mass. General HospitalCreation of a Dengue virus-host interaction database using functional genomics and bioinformatics Lynn Enquist / Moriah
Szpara, Princeton UniversityDeep Sequencing and Neuronal Microarrays for Functional Genomic Analysis of Herpes Simplex Virus
Slide43Brass (DENV) DBP – Lab ComponentCarry out whole-genome screens with multiple siRNA librariesValidate DENV host factor “hits” w/ RT-PCRPerform viral lifecycle and primary cell experiments
on candidate genes
Slide44Brass (DENV) DBP – ViPR ComponentProviding Data storageSave “high-scoring” hits from the siRNA screensAssociate virus life cycle data with the respective hits
Developing Analytical CapabilityAssist in assessing validity of lower confidence hits from screensOver-representation of hits in biological pathways/networksEnhancing Resource UsabilityDeveloping visualization strategy to interpret siRNA
data (Interesting Gene Lists)
Slide45Enquist/Szpara (HSV-1) DBP – Lab ComponentObtain and assemble NGS dataOral and encephalitic HSV-1 isolatesUse gene expression microarrays to observe differences in
human neuronal cells during a time course of infection Temporally dissect results by blocking infection at several phasesEntry, viral gene expression, and genome replication
Test phenotype of
loci predicted to contribute to
neurovirulence
Swapping candidate gene(s)
Slide46Enquist/Szpara (HSV-1) DBP – ViPR ComponentProviding Data storageImport whole genome (consensus) sequences from GenBankImport microarray results from GEOAssociate virus life cycle data with respective genes
Enhancing Resource UsabilityMicroarray data Make results searchable and cross reference with other related studiesIncorporate genome browser into resourceIntegrate genotype-phenotype dataDeveloping visualization strategyInterpret microarray results (Interesting Gene Lists)
Slide47ViPR SummaryFunded by U.S. National Institute of Allergy and Infectious Diseases (NIAID)Free and open access with no use restrictionsDeveloped by a team of research scientists,
bioinformaticians and professional software developersComprehensive collection of public dataNovel derived data, novel analytical tools, unique functionsIntegration – Integration – Integration
www.viprbrc.org
Slide48ViPR ChallengesDiverse research communitiesDiverse genome structuresVariable quality of gene/protein annotationsDeviation from the one gene – one functional protein paradigm (polyproteins)Growing complexity and inconsistency of metadataDriving Biological Projects taking us in a new direction that focuses on host genes
Slide49ViPR AcknowledgementsUniv. 0f Texas SouthwesternRichard Scheuermann PhD (PI)Brett Pickett, PhDEva Sadat, PhDYun Zhang, MSVecna Technologies
Chris Larsen, Ph.D.Al Ramsey, Ph.D.Northrop GrummanMike 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)
N01AI2008038
Slide5050U.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
N01AI40041