Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

General information

Full name:
Description: The Allen Brain Atlas 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.
Year founded: 2003
Last update: 2017
Version: v1.0
Real time : Checking...
Country/Region: United States
Data type:
Data object:
Database category:
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Contact information

University/Institution: Allen Institute for Brain Science
Address: 551 North 34th Street, Seattle, WA 98103, USA
City: Seattle
Province/State: WA
Country/Region: United States
Contact name (PI/Team): Susan M. Sunkin
Contact email (PI/Helpdesk):


Neuroinformatics of the Allen Mouse Brain Connectivity Atlas. [PMID: 25536338]
Kuan L, Li Y, Lau C, Feng D, Bernard A, Sunkin SM, Zeng H, Dang C, Hawrylycz M, Ng L.

The Allen Mouse Brain Connectivity Atlas is a mesoscale whole brain axonal projection atlas of the C57Bl/6J mouse brain. Anatomical trajectories throughout the brain were mapped into a common 3D space using a standardized platform to generate a comprehensive and quantitative database of inter-areal and cell-type-specific projections. This connectivity atlas has several desirable features, including brain-wide coverage, validated and versatile experimental techniques, a single standardized data format, a quantifiable and integrated neuroinformatics resource, and an open-access public online database ( Meaningful informatics data quantification and comparison is key to effective use and interpretation of connectome data. This relies on successful definition of a high fidelity atlas template and framework, mapping precision of raw data sets into the 3D reference framework, accurate signal detection and quantitative connection strength algorithms, and effective presentation in an integrated online application. Here we describe key informatics pipeline steps in the creation of the Allen Mouse Brain Connectivity Atlas and include basic application use cases.

Methods. 2015:73() | 66 Citations (from Europe PMC, 2021-06-19)
A high-resolution spatiotemporal atlas of gene expression of the developing mouse brain. [PMID: 24952961]
Thompson CL, Ng L, Menon V, Martinez S, Martinez S, Lee CK, Glattfelder K, Sunkin SM, Henry A, Lau C, Dang C, Garcia-Lopez R, Martinez-Ferre A, Pombero A, Rubenstein JLR, Wakeman WB, Hohmann J, Dee N, Sodt AJ, Young R, Smith K, Nguyen TN, Kidney J, Kuan L, Jeromin A, Kaykas A, Miller J, Page D, Orta G, Bernard A, Riley Z, Smith S, Wohnoutka P, Hawrylycz MJ, Puelles L, Jones AR.

To provide a temporal framework for the genoarchitecture of brain development, we generated in situ hybridization data for embryonic and postnatal mouse brain at seven developmental stages for ?2,100 genes, which were processed with an automated informatics pipeline and manually annotated. This resource comprises 434,946 images, seven reference atlases, an ontogenetic ontology, and tools to explore coexpression of genes across neurodevelopment. Gene sets coinciding with developmental phenomena were identified. A temporal shift in the principles governing the molecular organization of the brain was detected, with transient neuromeric, plate-based organization of the brain present at E11.5 and E13.5. Finally, these data provided a transcription factor code that discriminates brain structures and identifies the developmental age of a tissue, providing a foundation for eventual genetic manipulation or tracking of specific brain structures over development. The resource is available as the Allen Developing Mouse Brain Atlas (

Neuron. 2014:83(2) | 96 Citations (from Europe PMC, 2021-06-19)
Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system. [PMID: 23193282]
Sunkin SM, Ng L, Lau C, Dolbeare T, Gilbert TL, Thompson CL, Hawrylycz M, Dang C.

The Allen Brain Atlas ( 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.

Nucleic Acids Res. 2013:41(Database issue) | 196 Citations (from Europe PMC, 2021-06-19)


All databases:
201/5061 (96.048%)
24/924 (97.511%)
Gene genome and annotation:
78/1350 (94.296%)
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Record metadata

Created on: 2015-06-20
Curated by:
Dong Zou [2020-01-13]
Lina Ma [2018-06-04]
Dong Zou [2018-03-08]
Mengwei Li [2016-03-31]
Mengwei Li [2016-03-28]
Mengwei Li [2015-11-23]
Mengwei Li [2015-06-26]