Download Bioinformatics Core (B) - Functional Glycomics Gateway

Bioinformatics Core (B)
Progress and Future Goals
www.functionalglycomics.org
Advancing Glycomics
Key Issues & Challenges
Challenges
• Chemical heterogeneity
• Challenges in isolation and analysis
• Challenges in representation/processing glycan Information
Non-template biosynthesis
Ensemble or group of glycan
structures resulting from
coordinated expression of
several biosynthetic enzymes
Glycan-Protein Interaction
Glycan
Structure-Function
Relationships
Multivalent interactions
involving multiple glycan
motifs with multivalent CRDs
on proteins
Challenges
• Understanding biochemical basis for glycan-protein interactions
• How glycan specific genotype governs whole organism phenotype
• Constructing biological pathways and interaction networks
Consortium for Functional Glycomics
www.functionalglycomics.org
• Active collaborative effort
to advance glycomics
• Goal: Understand role of
glycan–protein interactions
in cell-cell communication
• Develop technologies and
resources to obtain data at
various levels from
molecule  mouse
• Integrated approach to
glycan structure-function
Bioinformatics Core (B)
Vision & Approach
CARBORDER
CPATHEXP
CELLSOURCE
Corder_key: NUMBER
Cell_key: NUMBER
Corder_ID: VARCHAR2(20)
Corder_date: DATE
Carbinv_key: NUMBER
Order_receiver: VARCHAR2(50)
Order_address: VARCHAR2(200)
Order_quantity: NUMBER
shipping_flag: CHAR(1)
Cell_ID: VARCHAR2(20)
biosource_key: NUMBER
Cell_line: VARCHAR2(30)
Cell_linetype: VARCHAR2(20)
Cell_tissue: VARCHAR2(20)
Cell_Organ: VARCHAR2(20)
Cpathexp_key: INTEGER
Cpathexp_ID: VARCHAR2(20)
Cpathexp_title: VARCHAR2(20)
Cpath_key: INTEGER
Protocol_key: INTEGER
Cpathexp_keyword: VARCHAR2(20)
Cpathexp_Instrument: VARCHAR2(20)
Cpathexp_comment: VARCHAR2(20)
Cpathexp_date: DATE
User_key: INTEGER
BIOLOGICAL_SOURCE
ENZYMESEQUENCE
biosource_key: INTEGER
Enzyme_sequenceKey: INTEGER
Biosource_ID: VARCHAR2(20)
kingdom: VARCHAR2(20)
Phylum: VARCHAR2(20)
Class: VARCHAR2(20)
Genus: VARCHAR2(20)
Species: VARCHAR2(20)
Enzyme_sequence: VARCHAR2(20)
Enzyme_key: INTEGER
ENZYME
GENE
CARBINVENTORY
Carbinv_key: NUMBER
Carbinv_ID: VARCHAR2(20)
Carb_key: NUMBER
Carbexp_key: VARCHAR2(20)
Carbinv_Purity: NUMBER
Carbinv_color: VARCHAR2(10)
Carbinv_State: VARCHAR2(10)
Quantity: NUMBER
Carbexp_batchno: VARCHAR2(20)
DNASEQ
PROTEINSEQUENCE
Gene_key: INTEGER
DNASEQ_key: INTEGER
Genome: VARCHAR2(20)
Gene_name: VARCHAR2(20)
biosource_key: INTEGER
Gene_key: INTEGER
DNASEQ_ID: VARCHAR2(20)
DNASEQ_IDtype: VARCHAR2(20)
DNASEQ_sequence: VARCHAR2(20)
Protein_sequenceKey: INTEGER
Protein_sequence: VARCHAR2(20)
Protein_key: INTEGER
CARBPATHWAY
Cpath_key: INTEGER
Cpath_name: VARCHAR2(20)
Carb_key: INTEGER
Enzyme_key: INTEGER
Cpath__Reaction: VARCHAR2(20)
Cpath_condition: VARCHAR2(20)
Cpath_stepFromCarb: INTEGER
Cpath_yield: INTEGER
PROTEIN
Protein_key: INTEGER
BIOFUNCTION_CATEGORY
Protein_ID: VARCHAR2(20)
ProteinID_type: VARCHAR2(20)
Protein_name: VARCHAR2(20)
Protein_CommonName: VARCHAR2(20)
Protein_family: VARCHAR2(20)
Protein_subFamily: VARCHAR2(20)
Protein_superUnitKey: INTEGER
Protein_type: VARCHAR2(20)
Biosource_key: INTEGER
Biofunction_key: INTEGER
Gene_key: VARCHAR2(20)
DNASEQ_key: INTEGER
Protein_sequenceKey: INTEGER
Protein_biofunctionDesc: VARCHAR2(20)
Access_code: VARCHAR2(20)
Protein_listdate: DATE
Biofunction_key: INTEGER
Static Pages
(SHTML) for
Web Site
Dynamic pages (JSPs)
for database driven
Entry, Dissemination and
Queries
Biofunction_name: VARCHAR2(20)
CARBOHYDRATE
Carb_key: INTEGER
CARBEXP
Carbexp_key: INTEGER
carbexp_ID: VARCHAR2(20)
carbexp_title: VARCHAR2(30)
Protocol_key: NUMBER
Carb_key: NUMBER
Carbexp_keyword: VARCHAR2(100)
Carbexp_Instrument: VARCHAR2(100)
Carbexp_comment: VARCHAR2(200)
Carbexp_date: DATE
Cabexp_batchno: VARCHAR2(20)
User_key: NUMBER
biosource_key: INTEGER
Carb_ID: VARCHAR2(20)
Carb_Sciname: VARCHAR2(20)
Carb_commonName: VARCHAR2(20)
Carb_Family: VARCHAR2(20)
Carb_Subfamily: VARCHAR2(20)
Carb_Type: VARCHAR2(10)
Carb_MW: NUMBER
Biofunction_key: NUMBER
Carb_BiofunctionDesc: VARCHAR2(100)
Carb_listdate: DATE
Carb_structure: VARCHAR2(500)
Carb_structureImgtype: VARCHAR2(10)
Carb_structureImg: BLOB
Access_code: VARCHAR2(20)
CPBINDING
Cpb_key: NUMBER
CARBEXPIMG
carbExpImg_key: INTEGER
Carbexp_key: NUMBER
CarbExpImg_exptype: VARCHAR2(20)
CarbExpImg_filetype: VARCHAR2(20)
CarbExpImg_imageRaw: BLOB
Cpb_ID: VARCHAR2(20)
Cpb_IDtype: VARCHAR2(20)
Carb_key: NUMBER
Protein_key: NUMBER
Cpb_flag: CHAR(1)
Biofunction_key: NUMBER
Cpb_BiofunctionDesc: VARCHAR2(100)
Cpb_Keq: NUMBER
Cpb_DG: NUMBER
Cpb_DH: NUMBER
Cpb_DS: NUMBER
Cpb_listdate: DATE
PROTIENREF
Paper_key: NUMBER
Protein_key: INTEGER
CARBPATHREF
Paper_key: NUMBER
Carb_key: INTEGER
Paper_key: NUMBER
Protocol_key: INTEGER
CPBEXPIMG
•
CPROFILEEXPIMG
cpexpImg_key: INTEGER
Cpexp_key: INTEGER
CpexpImg_exptype: VARCHAR2(20)
CpexpImg_filetype: VARCHAR2(20)
CpexpImg_imageRaw: BLOB
CpexpImg_desc: VARCHAR2(20)
GLYCOARRAY
GAEXP
Gaexp_key: INTEGER
Gaexp_ID: VARCHAR2(20)
Gaexp_title: VARCHAR2(20)
Protocol_key: INTEGER
Garray_key: INTEGER
Gaexp_SampleID: VARCHAR2(20)
Gaexp_SampleDesc: VARCHAR2(20)
Gaexp_keyword: VARCHAR2(20)
Gaexp_readtype: VARCHAR2(20)
Gaexp_raw: VARCHAR2(20)
Gaexp_date: DATE
Gaexp_imgfiletype: VARCHAR2(20)
Gaexp_imgraw: BLOB
Dbuser_key: INTEGER
TARGETPROTEIN
Carbprofile_key: NUMBER
Carbprofile_ID: VARCHAR2(20)
Carbprofile_title: VARCHAR2(30)
Carbprofile_carbComp: VARCHAR2(200)
Carbprofile_avgMW: NUMBER
Mouseind_key: NUMBER
Carbprofile_source: VARCHAR2(100)
Biofunction_key: NUMBER
Carbprofile_biofunctionDesc: VARCHAR2(200)
Parentprofile_ID: VARCHAR2(20)
Enzexp_key: INTEGER
Enzexp_ID: VARCHAR2(20)
Enzexp_title: VARCHAR2(20)
Protocol_key: INTEGER
Enzyme_key: INTEGER
Enzexp_keyword: VARCHAR2(20)
Enzexp_Instrument: VARCHAR2(20)
Enzexp_comment: VARCHAR2(20)
Enzexp_date: DATE
User_key: INTEGER
Cbpexp_ID: VARCHAR2(20)
Cbpexp_title: VARCHAR2(20)
Protocol_key: INTEGER
Protein_key: INTEGER
Cbpexp_keyword: VARCHAR2(20)
Cbpexp_Instrument: VARCHAR2(20)
Cbpexp_comment: VARCHAR2(20)
Cbpexp_date: DATE
Dbuser_key: INTEGER
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.
Protocol_key: INTEGER
PAPER
Protocol_ID: VARCHAR2(20)
Protocol_Category: VARCHAR2(20)
Protocol_keyword: VARCHAR2(20)
Protocol_Title: VARCHAR2(20)
Protocol_overview: VARCHAR2(20)
Protocol_procedure: CHAR(18)
Protocol_trobleshooting: VARCHAR2(20)
Dbuser_key: INTEGER
Paper_key: NUMBER
Paper_ID: VARCHAR2(20)
ID_type: VARCHAR2(20)
Paper_title: VARCHAR2(200)
Paper_year: INTEGER
Journal_name: VARCHAR2(200)
Page_range: VARCHAR2(20)
ENZEXPIMG
EnzexpImg_key: INTEGER
Enzexp_key: INTEGER
EnzexpImg_exptype: VARCHAR2(20)
EnzexpImg_filetype: VARCHAR2(20)
EnzexpImg_imageRaw: BLOB
CBPEXPIMG
CbpexpImg_key: INTEGER
Cbpexp_key: INTEGER
CbpexpImg_exptype: VARCHAR2(20)
CbpexpImg_filetype: VARCHAR2(20)
CbpexpImg_imageRaw: BLOB
CPATHREAGENT
Protocol_key: INTEGER
Reagent_key: INTEGER
REAGENT
Reactant_Weightg: INTEGER
Reactant_mmol: VARCHAR2(20)
Reagent_key: INTEGER
Reagent_ID: VARCHAR2(20)
Reagent_IDtype: VARCHAR2(20)
Reagnet_name: VARCHAR2(20)
Reagent_formula: VARCHAR2(20)
Reagent_MW: INTEGER
CPROFILEID
Carbprofile_key: NUMBER
Carb_key: INTEGER
CPATHINSTRUMENT
Protocol_key: INTEGER
Instrument_key: INTEGER
Concentration: VARCHAR2(20)
CPROFILEEXP
Cpexp_key: INTEGER
cpexp_ID: VARCHAR2(20)
cpexp_title: VARCHAR2(20)
Protocol_key: INTEGER
Carbprofile_key: NUMBER
Cpexp_keyword: VARCHAR2(20)
Cpexp_instrument: VARCHAR2(20)
Cpexp_date: DATE
Cpexp_comment: VARCHAR2(20)
Dbuser_key: INTEGER
MOUSESTRAIN
Mouse_key: INTEGER
Mouse_ID: VARCHAR2(20)
Cell_key: NUMBER
Mouse_type: VARCHAR2(20)
Protocol_key: INTEGER
Mouse_keyword: VARCHAR2(20)
Mouse_desc: VARCHAR2(20)
MOUSEHISTOLOGY
MHS_key: INTEGER
MHS_ID: VARCHAR2(20)
Mouseind_key: INTEGER
MHS_date: DATE
MHS_age: INTEGER
MHS_weight: INTEGER
Protocol_key: INTEGER
MHS_purpose: VARCHAR2(20)
MHS_result: VARCHAR2(20)
MHS_comment: VARCHAR2(20)
Dbuser_key: INTEGER
MAREF
MICROARRAY
Marray_key: INTEGER
Paper_key: NUMBER
Marray_key: INTEGER
Marray_ID: VARCHAR2(20)
Marray_type: VARCHAR2(20)
Marray_desc: VARCHAR2(20)
Marray_imgtype: VARCHAR2(20)
Marray_img: BLOB
INSTRUMENT
Instrument_key: INTEGER
Instrument_category: VARCHAR2(20)
Instrument_name: VARCHAR2(20)
Instrument_model: VARCHAR2(20)
Instrument_Vender: VARCHAR2(20)
MAEXP
MAEXPANALYSIS
Maexp_key: INTEGER
Maexp_ID: VARCHAR2(20)
Maexp_title: VARCHAR2(20)
Protocol_key: INTEGER
Marray_key: INTEGER
Maexp_SampleID: VARCHAR2(20)
Maexp_SampleDesc: VARCHAR2(20)
Maexp_keyword: VARCHAR2(20)
Maexp_readtype: VARCHAR2(20)
Maexp_raw: VARCHAR2(20)
Maexp_date: DATE
Maexp_imgfiletype: VARCHAR2(20)
Maexp_imgraw: BLOB
Dbuser_key: INTEGER
Maexpanaly_key: INTEGER
Maexp_key: INTEGER
Maexpanaly_title: VARCHAR2(100)
Maexpanaly_desc: VARCHAR2(500)
DBUSER
Dbuser_key: INTEGER
Dbuser_username: VARCHAR2(20)
Dbuser_password: VARCHAR2(20)
Dbuser_lastname: VARCHAR2(20)
Dbuser_firstname: CHAR(18)
Dbuser_email: VARCHAR2(20)
Dbuser_employer: VARCHAR2(20)
Dbuser_title: VARCHAR2(20)
Dbuser_Core: VARCHAR2(20)
Dbuser_listdate: DATE
TARGETGENE
Maexp_key: INTEGER
Gene_key: INTEGER
Targetgene_desc: VARCHAR2(20)
KOGENE
KOgene_key: INTEGER
MOUSEHEMA
KOgene_ID: VARCHAR2(20)
Mouse_key: INTEGER
Gene_key: INTEGER
Gene_ID: VARCHAR2(20)
KOgene_synonym: VARCHAR2(20)
KOgene_Mtype: VARCHAR2(20)
KOgene_UnigenDes: VARCHAR2(20)
KOgene_HumanGene: VARCHAR2(20)
MH_key: INTEGER
MH_ID: VARCHAR2(20)
Mouseind_key: INTEGER
MH_date: DATE
MH_age: INTEGER
MH_weight: INTEGER
MH_WBC: INTEGER
MH_Neutrophils: INTEGER
MH_Lymphocytes: VARCHAR2(20)
MH_HGB: INTEGER
MH_HCT: INTEGER
MH_PLT: INTEGER
MH_MPV: INTEGER
Dbuser_key: INTEGER
Gaexp_key: INTEGER
Protein_key: INTEGER
Targetcbp_desc: VARCHAR2(20)
Cpathexp_key: INTEGER
CpathexpImg_exptype: VARCHAR2(20)
CpathexpImg_filetype: VARCHAR2(20)
CpathexpImg_imageRaw: BLOB
CBPEXP
PROTOCOL
Paper_key: NUMBER
Cpb_key: NUMBER
CARBPROFILE
Garray_key: INTEGER
Garray_ID: VARCHAR2(20)
Garray_type: VARCHAR2(20)
Garray_desc: VARCHAR2(20)
Garray_imgtype: VARCHAR2(20)
Garray_img: BLOB
CpathexpImg_key: INTEGER
ENZEEXP
CPBREF
cpbExpImg_key: INTEGER
Cpbexp_key: NUMBER
CpbexpImg_exptype: VARCHAR2(20)
CpbexpImg_imageRaw: BLOB
Cpbexpimg_desc: VARCHAR2(20)
CpbexpImg_filetype: VARCHAR2(20)
CPATHEXPIMG
Cbpexp_key: INTEGER
Cpbexp_key: NUMBER
Middleware implemented
using Entity-Class
Operations, Servlets in
Java
Enzyme_ID: VARCHAR2(20)
Enzyme_type: VARCHAR2(20)
Enzyme_name: VARCHAR2(20)
Enzyme_CommonName: VARCHAR2(20)
Enzyme_family: VARCHAR2(20)
Enzyme_subFamily: VARCHAR2(20)
biosource_key: INTEGER
Biofunction_key: INTEGER
Enzyme_biofunctionDesc: VARCHAR2(20)
Gene_key: VARCHAR2(20)
DNASEQ_key: INTEGER
Enzyme_sequenceKey: INTEGER
Proteindb_ID: VARCHAR2(20)
SwissPort_ID: VARCHAR2(20)
Access_Code: VARCHAR2(20)
Protein_listdate: DATE
PROTOCOLREF
CPBEXP
cpbexp_ID: VARCHAR2(20)
cpbexp_title: VARCHAR2(20)
Protocol_key: INTEGER
Cpb_key: NUMBER
Cpbexp__keyword: VARCHAR2(20)
Cpbexp_Instrument: VARCHAR2(20)
Cpbexp_date: DATE
Cpbexp_comment: VARCHAR2(20)
Dbuser_key: INTEGER
Paper_key: NUMBER
Cpath_key: INTEGER
PAPER_REFERENCE
Enzyme_key: INTEGER
MOUSEIND
Mouseind_key: INTEGER
MIND_ID: VARCHAR2(20)
Mouse_key: INTEGER
Mind_sex: VARCHAR2(20)
MOUSEIMMU
MI_key: INTEGER
Object-based Relational
Database implemented using
Oracle
MI_ID: VARCHAR2(20)
Mouseind_key: INTEGER
MI_date: DATE
MI_age: INTEGER
MI_weight: INTEGER
MI_sampletype: VARCHAR2(20)
MI_CD4: INTEGER
MI_CD8: INTEGER
B220: INTEGER
IAB: INTEGER
IgM: INTEGER
IgD: INTEGER
Dbuser_key: INTEGER
MOUSEBEHAV
MB_key: INTEGER
MB_ID: VARCHAR2(20)
Mouseind_key: INTEGER
MB_date: DATE
MB_age: INTEGER
MB_weight: INTEGER
MB_GrossNero: VARCHAR2(20)
MB_SensorMotorReflex: VARCHAR2(20)
MB_PosturalReflex: VARCHAR2(20)
MB_motoractivity: VARCHAR2(20)
MB_Nocieption: VARCHAR2(20)
MB_AcousticStartle: VARCHAR2(20)
MB_SocialDomine: VARCHAR2(20)
MB_conditionedFear: VARCHAR2(20)
MB_waterMaze: VARCHAR2(20)
MB_radialArmMaze: VARCHAR2(20)
Dbuser_key: INTEGER
MOUSEMETABOLISM
MM_key: INTEGER
MM_ID: VARCHAR2(20)
Mouseind_key: CHAR(18)
MM_date: DATE
MM_age: INTEGER
MM_weight: INTEGER
MM_Cardiac: VARCHAR2(20)
MM_BloodDiastol: INTEGER
MM_bloodSystol: INTEGER
MM_plumonary: VARCHAR2(20)
MM_FoodConsumption: INTEGER
MM_waterConsumption: INTEGER
MM_activityLevel: INTEGER
MM_OxygenConsumption: INTEGER
MM_CO2Output: INTEGER
MM_HeatOutput: INTEGER
Dbuser_key: INTEGER
Part of CFG database
overall ontology map
Core B Organization
Administration
Ram Sasisekharan (Core Coordinator), Rahul Raman (Core Director)
Ada Ziolkowski (Admin Staff)
MIT Information
Systems
Database Administration
Core Operations
&
Management
Bioinformatics
MIT Information
Systems
Server Maintenance
Information Technology
Scientific liaisons,
User specifications,
Bioinformatics applications
Database, web, software
applications, user interface
development
Core B Team
Maha Venkataraman, Subu Ramakrishnan, Savitri Subramanian, Thomas Lutteke
Ganesh Venkataraman, Wei Lang, Eric Berry, Nishla Keiser, Ishan Capila, Chipong
Kwan and Consultants
Implementation Strategy
Databases and Interfaces
Consortium DB
Data Objects,
Relationships, Raw
and Parsable Data
User Interface
Data Acquisition
Public
Databases
GBP, Glycans,
Glycoenzymes
Consortium
Data
Dissemination
User Interface for Information
Dissemination
GBP
Molecule
Pages
GlycoEnzyme
Molecule
Pages
Web-based Forms
Annotation Tools
Glycan
Structures
Database
Implementation Strategy
Schema of CFG Data Objects and Integration
Glycobiology, 16(5), 82R-90R
Highlights of Progress
Years 1-4
Years 1 - 2
Years 3-4
• Infrastructure set-up
• Acquisition of Core data
• Database implementation
• Public release of databases
• Software development
• CFG data dissemination
• Interactions with Cores for data
acquisition and dissemination
• GBP molecule pages
• Glycan structures DB
Highlights of Progress
Quarters 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
CFG Scientific Core Data
Data Organization
Experiment Information
Brief description of scope of
experiment or analysis
Protocols
Sample/Resources
Standardized Protocols
used in an experiment or
analysis
Detailed information on
sample / resource utilized
[mouse, tissue, cell, GBP]
Data Summary
Summary of interpretation
of data by Scientific Core
Raw Data
Annotated Data
Raw data files generated by
the analysis – Images, Excel,
binary formats
Processed information on
entities such as gene, mouse,
GBP, etc. stored in DB tables
CFG Scientific Core Data
Statistics (as of June 2006)
Gene Microarray (E)
47 Experiments (33)
617 Samples (387)
3546 data files (1826)
Glycotechnology (C)
Mouse: 11 tissues, 8 KO strains,
92 MALDI-MS spectra
Human: 11 Tissues 108 MALDIMS spectra
Cell Lines: 12 Cell Lines 27
Spectra
Mouse Phenotyping (G)
16 KO Strains (11)
266 Experiments (149)
3116 data files (1100)
GBP-Glycan (H)
247 Samples (143)
CFG Scientific Core Data
Enhanced dissemination interfaces
Navigation and downloading of CFG Data – Gene
Expression, MALDI-MS Glycan Profiling, Mouse
Phenotyping and Glycan Array - DEMO
Gene Microarray Data
Gene Microarray Data
Gene Microarray Data
Mouse Phenotyping Data
Mouse Phenotyping Data
Mouse Phenotyping Data
Mouse Phenotyping Protocols
Glycan Array Data
Glycan Array Data
Glycan Array Data
Glycan Array Data
CFG Data Integration
Expression of glycan related genes in wildtype mouse spleen
CFG Data Integration
Glycan profile of spleen of FucT-VII KO mice with differences in histology staining
Tracking PI Research Progress
Data dissemination and resource tracking interface
Copy of submitted request emailed
with Request ID in database
Core A
PI
Request
Approval
Process
Post Status
Database
Prioritizing/
Approved
SC
Request ID
Data IDs
Submit Online
Request Form
Upload Data
with Request ID
Core
Tracking PI Research Progress
Data dissemination and resource tracking interface
Navigating PI information page to find
associated resource requests and data DEMO
GBP Molecule Page Interfaces
Three main components
Data from Cores
Automated Acquisition
Data from public databases,
links to public resources
Interface to CFG
resources and data
Molecule
Information
Portal
• Glycan array data
• Mouse phenotyping data
• Transgenic mouse line
Expert Contribution
Filling out fields as
experts on the molecule
Contribution from experts
obtained for C-type lectins
GBP Molecule Pages
Updating expert contributions for C-type lectins
GBP Molecule Page example for C-type
lectins with filled expert contribution fields
- DEMO
GBP Molecule Pages
DC-SIGN Molecule Page
Expert
Contributions
DC-SIGN Molecule Page
DC-SIGN Molecule Page
DC-SIGN Molecule Page
DC-SIGN Molecule Page
Expert
Contributions
PDB IDs of DC-SIGN
complexed with glycan
ligands identified using
PDB2LINUCS tool
DC-SIGN Molecule Page
GT Database Development
Expert annotation of glycosylation pathways
Type II Extension/ Termination
Composite Structure
343 Genes
FucTs expert annotation
40 Sialyl-T
24 Fucosyl-T
69 GlcNAc-T
47 Gal-T
54 GalNAc-T
78 Sulfo-T
31 Man-T
GT Database Development
Glycosylation interface & GT molecule pages
Automated Acquisition
Data from public databases,
links to public resources
Molecule
Information
Portal
Data from Cores
Interface to CFG
resources and data
• Glycan profiling of GT KO mice
• Mouse phenotyping data
• Transgenic mouse line
• Gene expression (Year 6 goals)
Glycan Structures Database
Glycan Structure Search Interface
Glycan Structure Search Interface
Glycan Structure Search Interface
Glycan Structure Search Interface
Glycan DB Search Results
Glycan DB Search Results