An anatomically comprehensive atlas of the adult human brain transcriptome

Michael J. Hawrylycz (), Ed S. Lein, Angela L. Guillozet-Bongaarts, Elaine H. Shen, Lydia Ng, Jeremy A. Miller, Louie N. van de Lagemaat, Kimberly A. Smith, Amanda Ebbert, Zackery L. Riley, Chris Abajian, Christian F. Beckmann, Amy Bernard, Darren Bertagnolli, Andrew F. Boe, Preston M. Cartagena, M. Mallar Chakravarty, Mike Chapin, Jimmy Chong, Rachel A. Dalley, Barry David Daly, Chinh Dang, Suvro Datta, Nick Dee, Tim A. Dolbeare, Vance Faber, David Feng, David R. Fowler, Jeff Goldy, Benjamin W. Gregor, Zeb Haradon, David R. Haynor, John G. Hohmann, Steve Horvath, Robert E. Howard, Andreas Jeromin, Jayson M. Jochim, Marty Kinnunen, Christopher Lau, Evan T. Lazarz, Changkyu Lee, Tracy A. Lemon, Ling Li, Yang Li, John A. Morris, Caroline C. Overly, Patrick D. Parker, Sheana E. Parry, Melissa Reding, Joshua J. Royall, Jay Schulkin, Pedro Adolfo Sequeira, Clifford R. Slaughterbeck, Simon C. Smith, Andy J. Sodt, Susan M. Sunkin, Beryl E. Swanson, Marquis P. Vawter, Derric Williams, Paul Wohnoutka, H. Ronald Zielke, Daniel H. Geschwind, Patrick R. Hof, Stephen M. Smith, Christof Koch, Seth G. N. Grant and Allan R. Jones
Additional contact information
Michael J. Hawrylycz: Allen Institute for Brain Science
Ed S. Lein: Allen Institute for Brain Science
Angela L. Guillozet-Bongaarts: Allen Institute for Brain Science
Elaine H. Shen: Allen Institute for Brain Science
Lydia Ng: Allen Institute for Brain Science
Jeremy A. Miller: Allen Institute for Brain Science
Louie N. van de Lagemaat: Genes to Cognition Programme, Edinburgh University
Kimberly A. Smith: Allen Institute for Brain Science
Amanda Ebbert: Allen Institute for Brain Science
Zackery L. Riley: Allen Institute for Brain Science
Chris Abajian: Allen Institute for Brain Science
Christian F. Beckmann: MIRA Institute, University of Twente & Donders Institute, Radboud University Nijmegen
Amy Bernard: Allen Institute for Brain Science
Darren Bertagnolli: Allen Institute for Brain Science
Andrew F. Boe: Allen Institute for Brain Science
Preston M. Cartagena: University of California
M. Mallar Chakravarty: Allen Institute for Brain Science
Mike Chapin: Allen Institute for Brain Science
Jimmy Chong: Allen Institute for Brain Science
Rachel A. Dalley: Allen Institute for Brain Science
Barry David Daly: University of Maryland School of Medicine, University of Maryland Medical Center
Chinh Dang: Allen Institute for Brain Science
Suvro Datta: Allen Institute for Brain Science
Nick Dee: Allen Institute for Brain Science
Tim A. Dolbeare: Allen Institute for Brain Science
Vance Faber: Allen Institute for Brain Science
David Feng: Allen Institute for Brain Science
David R. Fowler: University of Maryland School of Medicine
Jeff Goldy: Allen Institute for Brain Science
Benjamin W. Gregor: Allen Institute for Brain Science
Zeb Haradon: Allen Institute for Brain Science
David R. Haynor: University of Washington
John G. Hohmann: Allen Institute for Brain Science
Steve Horvath: Gonda Research Center, David Geffen School of Medicine
Robert E. Howard: Allen Institute for Brain Science
Andreas Jeromin: Banyan Biomarkers, Inc.
Jayson M. Jochim: Allen Institute for Brain Science
Marty Kinnunen: Allen Institute for Brain Science
Christopher Lau: Allen Institute for Brain Science
Evan T. Lazarz: Allen Institute for Brain Science
Changkyu Lee: Allen Institute for Brain Science
Tracy A. Lemon: Allen Institute for Brain Science
Ling Li: Office of the Chief Medical Examiner, Baltimore, MD, University of Maryland
Yang Li: Allen Institute for Brain Science
John A. Morris: Allen Institute for Brain Science
Caroline C. Overly: Allen Institute for Brain Science
Patrick D. Parker: Allen Institute for Brain Science
Sheana E. Parry: Allen Institute for Brain Science
Melissa Reding: Allen Institute for Brain Science
Joshua J. Royall: Allen Institute for Brain Science
Jay Schulkin: Georgetown University, School of Medicine
Pedro Adolfo Sequeira: Functional Genomics Laboratory, School of Medicine, University of California
Clifford R. Slaughterbeck: Allen Institute for Brain Science
Simon C. Smith: Histion LLC
Andy J. Sodt: Allen Institute for Brain Science
Susan M. Sunkin: Allen Institute for Brain Science
Beryl E. Swanson: Allen Institute for Brain Science
Marquis P. Vawter: Functional Genomics Laboratory, School of Medicine, University of California
Derric Williams: Allen Institute for Brain Science
Paul Wohnoutka: Allen Institute for Brain Science
H. Ronald Zielke: The Eunice Kennedy Shriver NICHD Brain and Tissue Bank for Developmental Disorders, University of Maryland
Daniel H. Geschwind: Program in Neurogenetics, and Semel Institute, David Geffen School of Medicine-UCLA
Patrick R. Hof: Mount Sinai School of Medicine
Stephen M. Smith: FMRIB, Oxford University
Christof Koch: Allen Institute for Brain Science
Seth G. N. Grant: Genes to Cognition Programme, Edinburgh University
Allan R. Jones: Allen Institute for Brain Science

Nature, 2012, vol. 489, issue 7416, 391-399

Abstract: Abstract Neuroanatomically precise, genome-wide maps of transcript distributions are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. Here we describe the generation and analysis of a transcriptional atlas of the adult human brain, comprising extensive histological analysis and comprehensive microarray profiling of ∼900 neuroanatomically precise subdivisions in two individuals. Transcriptional regulation varies enormously by anatomical location, with different regions and their constituent cell types displaying robust molecular signatures that are highly conserved between individuals. Analysis of differential gene expression and gene co-expression relationships demonstrates that brain-wide variation strongly reflects the distributions of major cell classes such as neurons, oligodendrocytes, astrocytes and microglia. Local neighbourhood relationships between fine anatomical subdivisions are associated with discrete neuronal subtypes and genes involved with synaptic transmission. The neocortex displays a relatively homogeneous transcriptional pattern, but with distinct features associated selectively with primary sensorimotor cortices and with enriched frontal lobe expression. Notably, the spatial topography of the neocortex is strongly reflected in its molecular topography—the closer two cortical regions, the more similar their transcriptomes. This freely accessible online data resource forms a high-resolution transcriptional baseline for neurogenetic studies of normal and abnormal human brain function.

Date: 2012
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DOI: 10.1038/nature11405

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