CEG Bioinformatics Projects

GeneServer

Integrate data for genes, transcripts, proteins, complexes, pathways, processes (ontologies)

SNPproteinStructureMapper

Visualize variations in known or predicted 3-D protein structures and domains

• Cell Cycle: E.g. CCNH; CDK2
• DNA Repair: E.g. MPG; APEX; XRCC1; OGG1

Cincinnati Genes:

• CCND1
• CCND3
• CHEK1
• CHEK2
• PLK3

TRAFAC

A web-accessible, gene regulatory region discovery tool.

• Cell Cycle
• DNA Repair

Cincinnati Genes:

List of Genes

Regulograms (1 & 2)

Pathways

PathMaker

To design and annotate all the elements in a pathway and also modify existing pathways

Components:

• Selector: Populates the Gene Objects
  • Select genes based on the Gene Ontology assignments
  • Selected genes are placed in the gene object tab of a palette
  • Selected gene used as a navigation point to gene related objects. For e.g.: adding a protein or a transcript or a polymorphism
• Assembler: Operates within Pathway Biological Object Model
  • Work from the PathMaker palette
  • Specify interactions between the genes
• Viewer: Displays a graphical image of the current Pathway

• Cell Cycle
• DNA Repair
  • Human DNA Repair Pathway (Ensembl Gene Views)

Expression Database

• Repository
• Mining
• MultiCenterProjects
• Predictive Phenotyping Approach