Bioinformatics Core B Progress and Future Goals

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Bioinformatics Core (B)Progress and Future Goals
www.functionalglycomics.org
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Advancing GlycomicsKey Issues Challenges
Glycan Structure-Function Relationships
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Consortium for Functional Glycomicswww.functional
glycomics.org

• Active collaborative effort to advance glycomics
• Goal Understand role of glycanprotein
  interactions in cell-cell communication
• Develop technologies and resources to obtain data
  at various levels from molecule ? mouse
• Integrated approach to glycan structure-function

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Bioinformatics Core (B) Vision Approach

• Vision Present the dynamic face of the
  Consortium via Internet to best utilize the value
  of the resources and datasets generated by its
  participants and the broader scientific
  community.

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Core B Organization
Administration Ram Sasisekharan (Core
Coordinator), Rahul Raman (Core Director)Ada
Ziolkowski (Admin Staff)
MIT Information Systems Server Maintenance
MIT Information Systems Database Administration
Bioinformatics Scientific liaisons, User
specifications, Bioinformatics applications
Information Technology Database, web, software
applications, user interface development
Core B Team Maha Venkataraman, Subu
Ramakrishnan, Savitri Subramanian, Thomas
LuttekeGanesh Venkataraman, Wei Lang, Eric
Berry, Nishla Keiser, Ishan Capila, Chipong Kwan
and Consultants
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Implementation StrategyDatabases and Interfaces
Consortium DB Data Objects, Relationships, Raw
and Parsable Data
User Interface Data Acquisition Web-based Forms
Annotation Tools
Public Databases GBP, Glycans, Glycoenzymes
User Interface for Information Dissemination
Glycan Structures Database
Consortium Data Dissemination
GBP Molecule Pages
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Implementation StrategySchema of CFG Data
Objects and Integration
Glycobiology, 16(5), 82R-90R
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Highlights of ProgressYears 1-4
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Highlights of ProgressQuarters 1-3 of Year 5

• CFG data acquisition and dissemination
• Streamlining the process to upload printed array
  data from Cores D and H
• Enhancing interfaces for disseminating scientific
  Core data
• Implementation of data dissemination and research
  tracking interfaces for PIs
• Specialized databases and molecule pages
• Data organization and implementation of
  glycosyltransferase database
• Updating expert contribution fields for C-type
  lectins in GBP database
• Other key highlights
• Bioinformatics satellite session at the Society
  for Glycobiology 2005 meeting discussion of
  glycan analysis methods and data exchange formats
• Renewal application and preparation for Council
  review
• Publications
• Glycomics An integrated systems approach to
  structure-function relationships of glycans.
  Nature Methods, 2(11) 817-24
• Advancing glycomics implementation strategies
  at the consortium for functional
  glycomics.Glycobiology, 16(5) 82R-90R

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CFG Scientific Core DataData Organization
Experiment Information Brief description of
scope of experiment or analysis
Protocols Standardized Protocols used in an
experiment or analysis
Sample/Resources Detailed information on sample
/ resource utilized mouse, tissue, cell, GBP
Data Summary Summary of interpretation of data
by Scientific Core
Raw Data Raw data files generated by the
analysis Images, Excel, binary formats
Annotated Data Processed information on entities
such as gene, mouse, GBP, etc. stored in DB tables
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CFG Scientific Core Data Statistics (as of June
2006)
Mouse Phenotyping (G) 16 KO Strains (11) 266
Experiments (149) 3116 data files (1100)
Glycotechnology (C) Mouse 11 tissues, 8 KO
strains, 92 MALDI-MS spectra Human 11 Tissues
108 MALDI-MS spectra Cell Lines 12 Cell Lines 27
Spectra
GBP-Glycan (H) 247 Samples (143)
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CFG Scientific Core DataEnhanced dissemination
interfaces
Navigation and downloading of CFG Data Gene
Expression, MALDI-MS Glycan Profiling, Mouse
Phenotyping and Glycan Array - DEMO
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Gene Microarray Data
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Gene Microarray Data
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Gene Microarray Data
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Mouse Phenotyping Data
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Mouse Phenotyping Data
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Mouse Phenotyping Data
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Mouse Phenotyping Protocols
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Glycan Array Data
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Glycan Array Data
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Glycan Array Data
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Glycan Array Data
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CFG Data Integration
Expression of glycan related genes in wildtype
mouse spleen
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CFG Data Integration
Glycan profile of spleen of FucT-VII KO mice with
differences in histology staining
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Tracking PI Research ProgressData dissemination
and resource tracking interface
Copy of submitted request emailed with Request ID
in database
Request Approval Process
Core A
Post Status Prioritizing/ Approved
PI
SC
Submit Online Request Form
Upload Datawith Request ID
Core
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Tracking PI Research ProgressData dissemination
and resource tracking interface
Navigating PI information page to find associated
resource requests and data - DEMO
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GBP Molecule Page InterfacesThree main components
Molecule Information Portal

• Glycan array data
• Mouse phenotyping data
• Transgenic mouse line

Contribution from experts obtained for C-type
lectins
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GBP Molecule PagesUpdating expert contributions
for C-type lectins
GBP Molecule Page example for C-type lectins with
filled expert contribution fields - DEMO
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GBP Molecule Pages
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DC-SIGN Molecule Page
Expert Contributions
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DC-SIGN Molecule Page
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DC-SIGN Molecule Page
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DC-SIGN Molecule Page
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DC-SIGN Molecule Page
Expert Contributions
PDB IDs of DC-SIGN complexed with glycan ligands
identified using PDB2LINUCS tool
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DC-SIGN Molecule Page
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GT Database DevelopmentExpert annotation of
glycosylation pathways
Type II Extension/ TerminationComposite Structure
343 Genes 40 Sialyl-T24 Fucosyl-T69 GlcNAc-T
47 Gal-T 54 GalNAc-T 78 Sulfo-T 31 Man-T
FucTs expert annotation
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GT Database DevelopmentGlycosylation interface
GT molecule pages
Molecule Information Portal

• Glycan profiling of GT KO mice
• Mouse phenotyping data
• Transgenic mouse line
• Gene expression (Year 6 goals)

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Glycan Structures Database
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Glycan Structure Search Interface
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Glycan Structure Search Interface
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Glycan Structure Search Interface
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Glycan Structure Search Interface
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Glycan DB Search Results
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Glycan DB Search Results