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Genomic Anatomy of the Hippocampus Carol Thompson 1 , Sayan Pathak 1 , Andreas Jeromin 1 , Lydia Ng 1 , Cameron MacPherson 2 , Marty Mortrud,1 Allison Cusick,1 Zackery Riley 1 , Susan Sunkin 1 , Amy Bernard 1 , Ralph Puchalski 1 , Fred Gage 3 , Allan Jones 1 , Vladimir Bajic 2 , Michael Hawrylycz,  1  and Ed Lein 1 1  Allen Institute for Brain Science, Seattle, WA 98103, USA 2  South African National Bioinformatics Institute, University of the  Western Cape, Bellville 7535, Cape Town, South Africa 3  Salk Institute for Biological Studies, La Jolla, CA 92037, USA
Authors ,[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],[object Object],Allan R. Jones, Chief Scientific Officer Michael J. Hawrylycz,  Director of Informatics Ed S. Lein,  Director in Neuroscience Ralph B. Puchalski, Research Alliance Manager Susan M. Sunkin, Research Alliance Manager
Authors Continued ,[object Object],Salk Institute for Biological Studies, California Vladimir B. Bajic, Director Cameron R. MacPherson, PhD Student Fred H. Gage, Chair for Research on Age-Related Neurodegenerative  Diseases
What is the Hippocampus? Temporal lobe Hippocampus
Why do we care? ,[object Object],[object Object]
No Hippocampus =  Anterograde Amnesia ,[object Object],[object Object],HM Interview
Other Famous Cases ,[object Object],[object Object]
Discovery of LTP ,[object Object],[object Object]
How does it work? ,[object Object],Cajal’s Hippocampus (1911)
A Conceptual Model: EC DG CA3 CA1 ParaHp- Sensory components of “where” Perirhinal-Sensory components of object identity = “what” Other sensory inputs
How do we study it? ,[object Object],[object Object]
How do we study it? Histology – slice up the brain into fine slices and examine them under the microscope Nissl Stains of the hippocampus
Problems with what we know ,[object Object],[object Object]
Genomic Anatomy ,[object Object],[object Object]
Allen Brain Atlas (ABA) List of In Situ Hybridization data for entire genome!
In Situ Hybridization
Nonnegative Matrix Factorization x This is a way to break down huge data sets into workable amounts that you can then compare against each other.  98 59 112 73 34 91 64 33 78 7 8 9 6 7 2 5 6 3 8 0 9 3 4 5 2 3 1
Hierarchical clustering of voxel-based hippocampal gene expression data ,[object Object]
What Happened?
NMF Data Matches our Known Anatomy!
Can we do better?
9 Subregions of CA3
Can we do better? ,[object Object],[object Object]
3-D Models of Hippocampus ,[object Object]
Retrograde Tracing ,[object Object]
Subregions = Functionally Different? ,[object Object],[object Object]
Conclusion ,[object Object],[object Object],EC DG CA1 CA3
Future Research ,[object Object],[object Object],[object Object]

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Genomic Mapping of Hippocampus

  • 1. Genomic Anatomy of the Hippocampus Carol Thompson 1 , Sayan Pathak 1 , Andreas Jeromin 1 , Lydia Ng 1 , Cameron MacPherson 2 , Marty Mortrud,1 Allison Cusick,1 Zackery Riley 1 , Susan Sunkin 1 , Amy Bernard 1 , Ralph Puchalski 1 , Fred Gage 3 , Allan Jones 1 , Vladimir Bajic 2 , Michael Hawrylycz, 1 and Ed Lein 1 1 Allen Institute for Brain Science, Seattle, WA 98103, USA 2 South African National Bioinformatics Institute, University of the Western Cape, Bellville 7535, Cape Town, South Africa 3 Salk Institute for Biological Studies, La Jolla, CA 92037, USA
  • 2.
  • 3.
  • 4. What is the Hippocampus? Temporal lobe Hippocampus
  • 5.
  • 6.
  • 7.
  • 8.
  • 9.
  • 10. A Conceptual Model: EC DG CA3 CA1 ParaHp- Sensory components of “where” Perirhinal-Sensory components of object identity = “what” Other sensory inputs
  • 11.
  • 12. How do we study it? Histology – slice up the brain into fine slices and examine them under the microscope Nissl Stains of the hippocampus
  • 13.
  • 14.
  • 15. Allen Brain Atlas (ABA) List of In Situ Hybridization data for entire genome!
  • 17. Nonnegative Matrix Factorization x This is a way to break down huge data sets into workable amounts that you can then compare against each other. 98 59 112 73 34 91 64 33 78 7 8 9 6 7 2 5 6 3 8 0 9 3 4 5 2 3 1
  • 18.
  • 20. NMF Data Matches our Known Anatomy!
  • 21. Can we do better?
  • 23.
  • 24.
  • 25.
  • 26.
  • 27.
  • 28.