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.

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Presentation transcript:

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 Jack Chen Todd Harris Jason Stajich Peter D’Eustachio Fiona Cunningham

Genome KnowledgeBase Geeta Joshi-Tope Marcela Tello-Ruiz Peter D’Eustachio

Maize & Arabidopsis Insertion Databases Xiaokang Pan

Generic Model Organism Database Scott Cain Shulamit Avraham

Gramene Doreen Ware Chris Mahr Ken Clark (Dallas) Xiaokang Pan, Steve Schmidt, Lenny Teytelman, Wei Zhang

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 candidate 1 candidate 2 candidate 3 trait Maize, Barley, Sorghum, Oat, Wheat… Rice

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

Find Candidates in a Maize Interval

Add Rice Genetic & Physical Maps

Zoom in on Contig

Zoom to Rice Genome

Examine Individual Gene

Gene Prediction Details

Protein Page

Rice Mutant: semidwarf-1

Anatomy Ontology  Term: Stem

Trait Ontology  Term: Cum length

Development 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.

Next Steps  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 CSHLCornell University Ken Clark Susan McCouch Chris Mahr Pankaj Jaswal Xiaokang Pan Jun-Jian Ni Steve Schmidt Immanuel Yap Lenny Teytelman Wei Zhang Doreen Ware Peter VanBuren

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