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Stein Lab. In-House Symposium 2002. The Plan. Overview of my lab’s activities Detailed look at the Gramene Database Run out of time Talk really fast Thunderous applause. The HapMap Project. Gudmundur Thorisson. Ravi Sachidanandam. WormBase. Peter D’Eustachio. Todd Harris. Jason

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Stein lab

Stein Lab

In-House Symposium 2002


The plan
The Plan

  • Overview of my lab’s activities

  • Detailed look at the Gramene Database

  • Run out of time

  • Talk really fast

  • Thunderous applause


The hapmap project
The HapMap Project

Gudmundur

Thorisson

Ravi

Sachidanandam


Wormbase
WormBase

Peter

D’Eustachio

Todd

Harris

Jason

Stajich

Fiona

Cunningham

Jack Chen


Genome knowledgebase
Genome KnowledgeBase

Peter

D’Eustachio

Geeta

Joshi-Tope

Marcela

Tello-Ruiz



Generic model organism database
Generic Model Organism Database

Scott Cain

Shulamit

Avraham


Gramene
Gramene

Doreen Ware

Chris Mahr

Xiaokang Pan, Steve Schmidt,

Lenny Teytelman, Wei Zhang

Ken Clark

(Dallas)


Rice as a model monocot
Rice as a Model Monocot

  • Rice genome is 400 Mbp

    • Maize is 2.8 Gbp

    • Wheat is 16 Gbp

  • Large-scale & microsynteny among grasses


Genomics by proxy
Genomics by Proxy

Maize, Barley, Sorghum, Oat, Wheat…

Rice

trait

candidate1

candidate2

candidate3


What s in gramene
What’s in Gramene

  • High-throughput data

    • Rice genome (two cultivars)

    • Gene predictions

    • Rice proteins

    • Functional annotation of gene products

    • EST collections (rice & other cereals)

  • Curated data

    • Genetic maps

    • Physical maps

    • Protein annotation

    • Mutants & phenotypes

    • QTLs









Rice mutant semidwarf 1
Rice Mutant: semidwarf-1


Anatomy ontology

Term: Stem

Anatomy Ontology


Trait ontology

Term: Cum length

Trait Ontology



What ontologies let you ask

Find all rice mutants in my favorite synteneic region associated with dwarfism.

What genes within a starch content QTL are predicted to be involved in carbohydrate metabolism?

Find protein orthologs between rice & maize whose stage-specific expression patterns have changed.

What Ontologies Let You Ask


Next steps
Next Steps associated with dwarfism.

  • Finished chromosomes

    • Rice chromosomes 1 & 4 have just been finished.

    • Rice chromosome 10 is in preparation.

    • Others finished over next year.

  • Produce uniform annotation of rice genome.

  • “Genes of Maize” project.

  • Panzea project: genetic variability among wild populations


Credits

CSHL associated with dwarfism.Cornell University

Ken ClarkSusan McCouch

Chris MahrPankaj Jaswal

Xiaokang PanJun-Jian Ni

Steve SchmidtImmanuel Yap

Lenny Teytelman

Wei Zhang

Doreen Ware

Credits

Peter VanBuren


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