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 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 DalleyBarry 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, Allan R Jones

Research output: Contribution to journalArticlepeer-review


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.
Original languageEnglish
Pages (from-to)391-399
Number of pages9
Issue number7416
Early online date19 Sep 2012
Publication statusPublished - 2012


  • Neuroscience
  • Genetics
  • Genomics
  • Databases


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