CSHL Resources for Integrative Cancer Biology

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CSHL Resourcesfor Integrative CancerBiology
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Resources

• Databases
• GKB pathway database
• International HapMap Project database
• WormBase
• PromoterDB
• Data Exchange Protocols
• Distributed Annotation System
• MOBY

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Genome Knowledgebase (GK)

• An open, on-line database of fundamental
  biological processes in human.
• Authored created by experts in the field.
• Interconnected with whole genome catalogs at
  Ensembl, SwissProt and MODs

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GK Home Page
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Constellation View (in dev)
DNA Replication
Ethanol Catabolism
Amino Acid Biosynthesis
Glucose Metabolism
Oxidative Decarboxylation
TCA Cycle
RNA Splicing
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The International HapMap Project

• Genome project identified 6 million SNPs sites
  of human variation
• SNPs are next generation of diagnostic tool
• HapMap project characterizing variation patterns
  across 3 world populations
• 500,000,000 genotypes to track

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www.hapmap.org
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PromoterDB
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Data sources of TRED
Cell-cycle genes
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Current information content of TRED
All Data promoters (genes)
categorized by Promoter Quality
1. Known,curated 4. Predicted w/ mRNA 2.
Known, not curated 5. Predicted w/ EST 3.
Predicted w/ Refseq 6. Predicted w/ predicted
genes
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WormBase
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Worm Genome
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Worm Gene
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Worm Functional Genomics
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Worm Comparative Genomics
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Data Exchange Protocols

• Distributed Annotation System (DAS)
• Exchange of genome data
• Used by WormBase, FlyBase, EnsEMBL, UCSC, others
• MOBY
• Web services protocol
• Integration of data across MODs

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Data Producer/Consumer
caBIG
DAS coordinates genes
Pathways, genes
PromoterDB
EVS
TF TFB Annotations
MOBY Gateway
More MODs