Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system
By Susan Sunkin, Lydia Ng, C. Lau, Tim Dolbeare, Terri L. Gilbert, C. Thompson, M. Hawrylycz, Chinh Dang. Nucleic Acids Res., 2012
776 citations recorded by the source corpus.
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.
Subfields: Molecular Biology
View Paper: https://www.semanticscholar.org/paper/95ec1cfb1cd9cf9c83f0a905768c93d68ee75b64
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In Molecular Biology
Citations in the corpus
- The Scalable Brain Atlas: Instant Web-Based Access to Public Brain Atlases and Related Content (2013, methodology): “Prime examples of existing solutions for these tasks are the Brain Explorer software from the Allen Institute (Sunkin et al. 2013), the (discontinued) Brain Navigator product of Elsevier Inc. (http:// brainnav.com), the Java-based Whole Brain Catalog (http://wholebraincatalog.org), the urfacebased a”
- Enrichr: a comprehensive gene set enrichment analysis web server 2016 update (2016, methodology): “We created gene set libraries from HumanCyc (15), a Nucleic Acids Research, 2016, Vol. 44, Web Server issue W91 metabolic pathway resource stored in BioPAX format (16); gene and small-molecule perturbations from the LINCS L1000 data set; NCI-Nature pathways (17); protein complexes from the NURSA pro”
- The harmonizome: a collection of processed datasets gathered to serve and mine knowledge about genes and proteins (2016, background): “Allen Brain Atlas Adult Mouse Brain Tissue Gene Expression Profiles (38, 39, 45)”