Alliance of Genome Resources

2. www.alliancegenome.org

3. Now: worm gene

4. Now: fly gene

5. AGR portal
● Aims
○ A consistent view of model organism data for human geneticists
○ Integrative tools and views not present in individual MOD sites
○ (Eventually) A single portal for all of the MODs
● Timeline
○ First public release - October 2017
■ Search
■ Gene report pages
● Basic information
● Transcript structures (genome browser)
● Function (GO annotations)
● Orthology
● Disease
○ 2018 and beyond-
■ More data types
● Phenotype, Expression, Interaction...
■ Integrated views

6. AGR Gene report page

7. AGR Gene report page

8. Orthology

9. Common genome browser

10. Disease Human
gene
Model Organism gene
Name (DO) Subtype Symbol Genomic
location
Species Symbol Ortholog
score
Exp.
models?
Alzheimer's
disease
ALZHEIMER DISEASE 1
APP 21q21.3
Mouse App 10 108
Rat App 10 343
Frog app 6 -
Fish appb 6 -
Fly Appl 7 4
Fly HsapAPP n/a 36
Worm apl-1 7 4
APBB2 4p14-p13
Mouse Apbb2 8 -
Frog apbb2 5 -
Fish apbb2b 3 -
Worm feh-1 6 -
ALZHEIMER DISEASE 2
APOE 9q13.32
Mouse Apoe 8 -
etc… etc… etc… etc…
Integrative views - human disease models

11. Gene Species Gene ontology Disease Expression Phenotype Mutants
CDK1 Human + + - + +
Cdk1 Rat + + - - -
Cdk1 Mouse + - + + +
cdk1 Zebrafish + - - + -
Cdk1 Fly + + + + +
cdk-1 Worm + + + + +
CDC28 Yeast + - + + +
CDK2 Human + + - - +
CDK3 Human + + - - +
CDK5 Human + + - + +
CDK6 Human + + - + +
CDK4 Human + + - + +
Integrative views - available data summary

12. Gene Species
CDK1 Human
Cdk1 Rat
Cdk1 Mouse
cdk1 Zebrafish
Cdk1 Fly
cdk-1 Worm
CDC28 Yeast
Integrative views - comparative gene structure

13. Integrative views - gene ontology

14. Need input!
What do you want from the AGR portal?

15. Goodman, Josh
Grumbling, Gary
Kaufman, Thom
Strelets, Victor
Thurmond, Jim
Bolt, Bruce
Davis, Paul
Howe, Kevin
Kersey, Paul
Paulini, Michael
Russell, Matt
Shafie, Myriam
Williams, Gary
Balhoff, James
Carbon, Seth
Dunn, Nathan
Lewis, Suzi
Miyasato, Stuart
Muller, Hans-Michael
Mungall, Chris
Munoz-Torres, Monica
Muruganujan, Anushya
Nguyen-Xuan, Jeremy
Overton, James
Thomas, Paul
Bradford, Yvonne
Eagle, Anne
Fashena, David
Frazer, Ken
Howe, Doug
Kalita, Patrick
Mani, Prita
Martin, Ryan
Paddock, Holly
Pich, Christian
Ramachandran, Sridhar
Ruzicka, Leyla
Schaper, Kevin
Shao, Xiang
Singer, Amy
Taylor Moxon, Sierra
Toro, Sabrina
Van Slyke, Ceri
Westerfield, Monte
Anagnostopoulos, Anna
Baldarelli, Richard
Beal, Jonathan
Bello, Susan
Blake, Judy
Blodgett, Olin
Bult, Carol
Campbell, Jeff
Christie, Karen
Corbani, Lori
Dolan, Mary
Drabkin, Harold
Frost, Pete
Giannatto, Sharon
Hale, Paul
Hill, David
Hutchins, Lucie
Kadin, Jim
Knowlton, Michelle
Law, MeiYee
Lewis, Jill
McAndrews, Monica
Miers, David
Motenko, Howie
Neuhauser, Steve
Ni, Li
Recla, Jill
Reed, Deborah
Richards-Smith, Beverly
Richardson, Joel
Shaw, David
Sitnikov, Dmitry
Smith, Cindy
Stone, Kevin
Tomczuk, Monika
Wilming, Laurens
Zhu, Sophia
Assis, Pedro
Binkley, Gail
Cherry, Mike
Engel, Stacia
Hellerstedt, Sage
Karra, Kalpana
Lang, Olivia
MacPherson, Kevin
Miyasato, Stuart
Nash, Rob
Sheppard, Travis
Skrzypek, Marek
Weng, Shuai
Wong, Edith
Brodie, Kent
De Pons, Jeff
Ghiasvand, Omid
Hayman, Tom
Laulderkind, Stan
Petri, Victoria
Shimoyama, Mary
Smith, Jennifer
Thota, Jyothi
Tutaj, Marek
Tutaj, Monika
Wang, Shur-Jen
Zacher, Stacy
Antonazzo, Giulia
Attrill, Helen
Brown, Nick
Costa, Marta
Fexova, Sylvie
Jones, Tamsin
Larkin, Aoife
Marygold, Steven
Millburn, Gillian
Rey, Alix
Staudt, Nicole
Urbano, Pepe
Crosby, Lynn
dos Santos, Gil
Emmert, Dave
Falls, Kathleen
Gramates, Sian
Matthews, Beverley
Perrimon, Norbert
Russo Gelbart, Susan
Tabone, Chris
Zhou, Pinglei
Zytkovicz, Mark
Cain, Scott
Gao, Sibyl
Harris, Todd
Nuin, Paulo
Stein, Lincoln
Wright, Adam
Chan, Juancarlos
Chen, Wen
Grove, Chris
Lee, Raymond
Li, Yuling
Raciti, Daniela
Schindelman, Gary
Sternberg, Paul
Tuli, Mary Ann
Van Auken, Kimberly
Yook, Karen
The Alliance of Genome Resources