Download presentation
Presentation is loading. Please wait.
Published byTaryn Birdsey Modified over 9 years ago
1
Stein Lab In-House Symposium 2002
2
The Plan Overview of my lab’s activities Detailed look at the Gramene Database Run out of time Talk really fast Thunderous applause
3
The HapMap Project Gudmundur Thorisson Ravi Sachidanandam
4
WormBase Jack Chen Todd Harris Jason Stajich Peter D’Eustachio Fiona Cunningham
5
Genome KnowledgeBase Geeta Joshi-Tope Marcela Tello-Ruiz Peter D’Eustachio
6
Maize & Arabidopsis Insertion Databases Xiaokang Pan
7
Generic Model Organism Database Scott Cain Shulamit Avraham
8
Gramene Doreen Ware Chris Mahr Ken Clark (Dallas) Xiaokang Pan, Steve Schmidt, Lenny Teytelman, Wei Zhang
9
Rice as a Model Monocot Rice genome is 400 Mbp Maize is 2.8 Gbp Wheat is 16 Gbp Large-scale & microsynteny among grasses
10
Genomics by Proxy candidate 1 candidate 2 candidate 3 trait Maize, Barley, Sorghum, Oat, Wheat… Rice
11
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
12
Find Candidates in a Maize Interval
13
Add Rice Genetic & Physical Maps
14
Zoom in on Contig
15
Zoom to Rice Genome
16
Examine Individual Gene
17
Gene Prediction Details
18
Protein Page
19
Rice Mutant: semidwarf-1
20
Anatomy Ontology Term: Stem
21
Trait Ontology Term: Cum length
22
Development Ontology
23
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.
24
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
25
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
Similar presentations
© 2025 SlidePlayer.com. Inc.
All rights reserved.