www.fludb.org Influenza Research Database (IRD) & Virus Pathogen Resource (ViPR) Bioinformatics Resource Centers (BRCs) and support for Systems Biology data 06 November 2011 Richard H. Scheuermann, Ph.D. Department of Pathology U.T. Southwestern Medical Center www.viprbrc.o rg
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06 November 2011 Richard H. Scheuermann, Ph.D. Department of Pathology
www.viprbrc.org. Influenza Research Database (IRD) & Virus Pathogen Resource ( ViPR ) Bioinformatics Resource Centers ( BRCs ) and support for Systems Biology data. 06 November 2011 Richard H. Scheuermann, Ph.D. Department of Pathology U.T. Southwestern Medical Center. ViPR Overview. - PowerPoint PPT Presentation
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www.fludb.orgAnalysis and Visualizationwww.fludb.org
www.fludb.orgAnalysis and Visualization Tools
www.fludb.orgWorkbench Access
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www.fludb.orgData Submission
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www.fludb.orgData Submission Page
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SYSTEMS BIOLOGY “OMICS” DATA
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Overview of Systems Biology & DBP Projects
• Four systems biology groups funded by NIAID, including:– Systems Virology (Michael Katze group, Univ. Washington)
• Influenza H1N1 and H5N1 and SARS Coronavirus• statistical models, algorithms and software, raw and processed gene expression
data, and proteomics data
– Systems Influenza (Alan Aderem group, Institute for Systems Biology)• various Influenza viruses• microarray, mass spectrometry, and lipidomics data
• ViPR Driving Biological Projects– Abraham Brass, Mass. General Hospital
• Dengue virus host factor database from RNAi screen
– Lynn Enquist / Moriah Szpara, Princeton University• Deep sequencing and neuronal microarrays for functional genomic analysis of
Herpes Simplex Virus
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Andrew R. Joyce & Bernhard Ø. Palsson, Nature Reviews Molecular Cell Biology 7, 198-210 (March 2006)
Omics Data
www.fludb.orgAcknowledgement
• Lynn Law, U. Washington• Richard Green, U. Washington• Jyothi Noronha, U.T. Southwestern• Eva Sadat, U.T. Southwestern• Brett Pickett, U.T. Southwestern
www.fludb.orgDiscussion Points
• Relationship between data archives (e.g. GEO, PRIDE) and the BRCs (e.g. IRD, ViPR, PATRIC)
– Integration– Metadata standards
• Metadata– What kind of data– What kind of standards – MIBBI vs. “MIBBI lite”
• Raw versus processed data• Primary results data
– Need to define what is considered “primary” data for each platform• Microarray example: raw image files (.tiff) vs probe intensity values (.cel)• Opportunity for re-processing leading to re-interpretation
• Derived/processed results– “Interesting gene/protein lists” from microarray, RNAi, proteomics, and other experimental platforms– “Interesting metabolite lists”– Data processing metadata
• Visualize and analyze “interesting gene/protein/metabolite lists”
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1. “Omics” data management (host)a) Project metadata
2. Add additional related datasets from other sources
3. Visualize Host Factor Biosets in context of biological pathways and networks
4. Statistical analysis of pathway sub-network overrepresentation
5. Re-analysis of primary data using assembled pipeline tools (?)
Proposal for “Omics” Data
www.fludb.orgGEO Representation
GEO data representations based on free text
www.fludb.orgNon-standard Descriptions
Guess samples details
www.fludb.org Metadata (MIBBI-compliant)
• Project Level Metadata– Hypothesis, rationale, study design, etc.– Publications and links pertaining to the project– Data providers - PI, other key personnel, affiliations, contact information
• Experiment/Assay Level Metadata– Experiment platform– Experiment data type
• Experiment Sample Level Metadata– Sample source and characteristics of source– Sample type– Source/sample treatment information– Assay details
• Data Processing/Analysis Level Metadata– Algorithm(s) used for transforming primary to derived data– Configuration parameters
Search Analyze Save to WorkbenchSearch our robust database for: Genomes Genes & proteins Immune epitopes 3D protein structures
Analyze your results online. We offer: Identify similar sequences (BLAST) Align sequences (MSA) Find short peptides in proteins Visualize aligned sequences
Sign up for a Workbench to: Store data in working sets for future analysis Integrate ViPR data with your laboratory data Store analysis results Share results and data with collaborators
Browse All Search Types Browse All Tools Sign Up! Sign In
HighlightsViPR Highlight for All FamiliesYou can now search for, and visualize, 3D protein structures from within the ViPR website. Simply navigate to the protein of interest and then follow the links to use this feature.
View Tutorial View Example Results Start Search
Data Summary Updated 2 Weeks Ago
Genome Statistics for Virus Families
Families 13
Genera 54
Species 661
Strains 38,886
Segments 45,154
FAMILY_NAME
TEXT SEARCH
Genomes
Genes & Proteins
Immune Epitopes
Host Factor Biosets
3D Protein Structures
Protein Domains
Protein Motifs
HISTORY
Your Analysis History
Retrieve a Download
Ortholog Groups
SEARCH OR FIND:
Quick Text Search
Sequence Feature Variant Type
ViPRVirus Pathogen Resource
...About Us Supported Projects Announcements Resources Support
SEARCH DATA ANALYZE & VISUALIZE ACCESS WORKBENCH VIRUS FAMILIES HOME
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ViPRVirus Pathogen Resource
SEARCH DATA ANALYZE & VISUALIZE ACCESS WORKBENCH VIRUS FAMILIES HOME FAMILY_NAMEYou are logged in as [email protected]
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Host Factor BiosetsBack to Previous Page
Please Select an Experiment to Explore to view the associated Bioset (Interesting Gene List )
Study Title Experiment Name Experiment Type
Host Species & Biomaterial (Cell Line)
Virus Strain Name
Host factors in DENV replication
Dengue whole-genome siRNA library screen siRNA Screen Human
(Huh-7) New Guinea C
About Us Supported Projects Announcements Resources Support
PI PI Institution Contract / Grant Title Description Keywords
Contract / Grant
NumberDate
Submitted
Abraham L. Brass
Massachusetts General Hospital
Dengue Virus-Host Interactiosn Using Functional Genomics
Identify host factors required for DENV replication by using siRNA libraries.
Dengue, DENV, siRNA, host factors
HHSN135711131(NIAID) Dec 2011
Cite ViPR Tutorials Report a Bug Request Web Training Contact Us Release Date: Jan 7, 2012This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, University of Texas Southwestern Medical Center and Vecna Technologies. Virus images courtesy of CDC Public Health Image Library and Wellcome Images.
Study Title Experiment Name Experiment Type
Host Species & Biomaterial (Cell Line)
Virus Strain Name
Host factors in HSV-1 replication
Host neuronal response to HSV-1
Gene Expression Microarray
Human Neurons(SHSY5Y ) 17
PI PI Institution Contract / Grant Title Description Keywords Contract /
Grant NumberDate
Submitted
Moriah SzparaLynn Enquist Princeton Univ.
Deep Sequencing and Neuronal Microarrays for Functional Genomic Analysis of HSV-1
Characterize the response to HSV-1 infection through differential gene
expression in human neuronal cells.
Herpes Simplex Virus 1, HSV-1,
neurons, HHSN24681012
(NIAID) Apr 2012
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ViPRVirus Pathogen Resource
SEARCH DATA ANALYZE & VISUALIZE ACCESS WORKBENCH VIRUS FAMILIES HOME FAMILY_NAME
Cite ViPR Tutorials Report a Bug Request Web Training Contact UsRelease Date: Jan 7, 2012
This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, University of Texas Southwestern Medical Center and Vecna Technologies. Virus images courtesy of CDC Public Health Image Library and Wellcome Images.
ViPRVirus Pathogen Resource
SEARCH DATA ANALYZE & VISUALIZE ACCESS WORKBENCH VIRUS FAMILIES HOME FAMILY_NAME
Cite ViPR Tutorials Report a Bug Request Web Training Contact UsRelease Date: Jan 7, 2012
This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, University of Texas Southwestern Medical Center and Vecna Technologies. Virus images courtesy of CDC Public Health Image Library and Wellcome Images.
ViPRVirus Pathogen Resource
SEARCH DATA ANALYZE & VISUALIZE ACCESS WORKBENCH VIRUS FAMILIES HOME FAMILY_NAME
Cite ViPR Tutorials Report a Bug Request Web Training Contact UsRelease Date: Jan 7, 2012
This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, University of Texas Southwestern Medical Center and Vecna Technologies. Virus images courtesy of CDC Public Health Image Library and Wellcome Images.
ViPRVirus Pathogen Resource
SEARCH DATA ANALYZE & VISUALIZE ACCESS WORKBENCH VIRUS FAMILIES HOME FAMILY_NAME
Cite ViPR Tutorials Report a Bug Request Web Training Contact Us Release Date: Jan 20, 2011This project is funded by the National Institute of Allergy and Infectious Diseases (NIH / DHHS) under Contract No. HHSN272200900041C and is a collaboration between Northrop Grumman Health IT, University of Texas Southwestern Medical Center and Vecna Technologies. Virus images courtesy of CDC Public Health Image Library and Wellcome Images.
Visualize Host Factor InteractionsPROTEIN-PROTEIN INTERACTIONS INFORMATIONNumber of “hits” from Interesting Gene List: 1 Number of Nodes: $num_nodes
Number of Edges: $num_edgesSave Analysis
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• 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