Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system
- PMID: 23193282
- PMCID: PMC3531093
- DOI: 10.1093/nar/gks1042
Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system
Abstract
The Allen Brain Atlas (http://www.brain-map.org) provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search and viewing tools for the adult and developing brain in mouse, human and non-human primate. Here, we review the resources available at the Allen Brain Atlas, describing each product and data type [such as in situ hybridization (ISH) and supporting histology, microarray, RNA sequencing, reference atlases, projection mapping and magnetic resonance imaging]. In addition, standardized and unique features in the web applications are described that enable users to search and mine the various data sets. Features include both simple and sophisticated methods for gene searches, colorimetric and fluorescent ISH image viewers, graphical displays of ISH, microarray and RNA sequencing data, Brain Explorer software for 3D navigation of anatomy and gene expression, and an interactive reference atlas viewer. In addition, cross data set searches enable users to query multiple Allen Brain Atlas data sets simultaneously. All of the Allen Brain Atlas resources can be accessed through the Allen Brain Atlas data portal.
Figures
Similar articles
-
The Allen Human Brain Atlas: comprehensive gene expression mapping of the human brain.Trends Neurosci. 2012 Dec;35(12):711-4. doi: 10.1016/j.tins.2012.09.005. Epub 2012 Oct 5. Trends Neurosci. 2012. PMID: 23041053
-
If I only had a brain: exploring mouse brain images in the Allen Brain Atlas.Biol Cell. 2007 Jul;99(7):403-9. doi: 10.1042/BC20070031. Biol Cell. 2007. PMID: 17567264
-
High-resolution gene expression atlases for adult and developing mouse brain and spinal cord.Mamm Genome. 2012 Oct;23(9-10):539-49. doi: 10.1007/s00335-012-9406-2. Epub 2012 Jul 26. Mamm Genome. 2012. PMID: 22832508 Review.
-
The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content.Neuroinformatics. 2015 Jul;13(3):353-66. doi: 10.1007/s12021-014-9258-x. Neuroinformatics. 2015. PMID: 25682754 Free PMC article.
-
Neuroinformatics of the Allen Mouse Brain Connectivity Atlas.Methods. 2015 Feb;73:4-17. doi: 10.1016/j.ymeth.2014.12.013. Epub 2014 Dec 20. Methods. 2015. PMID: 25536338 Review.
Cited by
-
Imaging genetics of language network functional connectivity reveals links with language-related abilities, dyslexia and handedness.Commun Biol. 2024 Sep 28;7(1):1209. doi: 10.1038/s42003-024-06890-3. Commun Biol. 2024. PMID: 39342056 Free PMC article.
-
ST-SCSR: identifying spatial domains in spatial transcriptomics data via structure correlation and self-representation.Brief Bioinform. 2024 Jul 25;25(5):bbae437. doi: 10.1093/bib/bbae437. Brief Bioinform. 2024. PMID: 39228303 Free PMC article.
-
Single-cell spatial transcriptomics reveals distinct patterns of dysregulation in non-neuronal and neuronal cells induced by the Trem2R47H Alzheimer's risk gene mutation.Mol Psychiatry. 2024 Aug 5. doi: 10.1038/s41380-024-02651-0. Online ahead of print. Mol Psychiatry. 2024. PMID: 39103533
-
Neuromodulation modifies α-synuclein spreading dynamics in vivo and the pattern is predicted by changes in whole-brain function.Brain Stimul. 2024 Jul-Aug;17(4):938-946. doi: 10.1016/j.brs.2024.07.021. Epub 2024 Aug 2. Brain Stimul. 2024. PMID: 39096960
-
The myelin water imaging transcriptome: myelin water fraction regionally varies with oligodendrocyte-specific gene expression.Mol Brain. 2024 Jul 23;17(1):45. doi: 10.1186/s13041-024-01115-4. Mol Brain. 2024. PMID: 39044257 Free PMC article.
References
-
- Waterston RH, Lindblad-Toh K, Birney E, Rogers J, Abril JF, Agarwal P, Agarwala R, Ainscough R, Alexandersson M, An P, et al. Initial sequencing and comparative analysis of the mouse genome. Nature. 2002;420:520–562. - PubMed
-
- Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, et al. Initial sequencing and analysis of the human genome. Nature. 2001;409:860–921. - PubMed
-
- Lein ES, Hawrylycz MJ, Ao N, Ayres M, Bensinger A, Bernard A, Boe AF, Boguski MS, Brockway KS, Byrnes EJ, et al. Genome-wide atlas of gene expression in the adult mouse brain. Nature. 2007;445:168–176. - PubMed
-
- Jones AR, Overly CC, Sunkin SM. The Allen Brain Atlas: 5 years and beyond. Nat. Rev. Neurosci. 2009;10:821–828. - PubMed
-
- Ng L, Lau C, Young R, Pathak S, Kuan C, Sodt A, Sutram M, Lee C-K, Dang C, Hawrylycz M. NeuroBlast: a 3D spatial homology search tool for gene expression. BMC Neurosci. 2007;8:11. - PubMed
Publication types
MeSH terms
Grants and funding
LinkOut - more resources
Full Text Sources
Other Literature Sources