Learn to use the Allen Mouse Brain Atlas, from the Allen Brain Institute, a database of spatially mapped large-scale gene expression data from a genome wide survey of expression patterns in the C57BL/6J adult mouse brain. This digital atlas of gene expression includes RNA in situ hybridization data, a Reference Atlas, and tools for visualization of gene expression and display of expression by specific brain structures.

You will learn:

  • to access the Allen Reference Atlas, atlas legend, and structure ontology
  • to perform effective gene expression searches of the Allen Mouse Brain Atlas
  • to locate gene expression image datasets from the search results using the List View and Thumbnail Views
  • how to use the Single and Multiple Image Viewers
  • how to download and use the Brain Explorer application


This tutorial is a part of the tutorial group Expression resources. You might find the other tutorials in the group interesting:

Functional Glycomics Gateway: The home for Functional Glycomics research

CleanEx: A Database of Heterogeneous Gene Expression Data Based on A Consistent Gene Nomenclature

miRBase: microRNA sequences, targets and gene nomenclature

DBTSS: Database of Transcriptional Start Sites

Alternative Splicing and Transcript Diversity (ASTD) database: A bioinformatics resource for alternative splice events and transcripts for human, mouse, and rat

GENSAT: Provides an extensive amount of high quality images of gene expression in the central nervous system of the mouse.

Gene Expression Omnibus (GEO): A gene expression/molecular abundance repository and a curated, online resource for gene expression data

ArrayExpress: A public repository for microarray gene expression data at the EBI


Expression : This category may contain various expression data collections, annotation tools, or repositories of expression data.


Friday SNPpets: Welcome to our Friday feature link collection: SNPpets. During the week we come across a lot of links and reads that we think are interesting, but don't make it to a blog post. Here they are for your e...

Tip of the Week: Allen Institute's Brain Explorer: Not that long ago Mary posted on updates that occurred recently at the Allen Institute for Brain Science & hinted that there might be a tip coming about their cool 3D Brain Explorer tool - well, today...

Brainz! Now with updates...Allen Brain Atlas: We've long admired the Allen Brain Atlas tools. It contains really nice data, lots of it, and there are some really sweet tools to explore images and expression data of various sorts. I just got my ABA...

Cerebellar Development Transcriptome Database: Announcement today from the MGI-mailing list on the CDT-DB: Updated: Cerebellar Development Transcriptome Database (CDT-DB) Dear Colleagues, We are pleased to announce the release of the updated CDT-DB...


Recent BioMed Central research articles citing this resource

Zhu Qianglong et al., Comparative transcriptome analysis of two contrasting watermelon genotypes during fruit development and ripening Transcriptomic methods. BMC Genomics (2017) doi:10.1186/s12864-016-3442-3

Gu Chao et al., Multiple regulatory roles of AP2/ERF transcription factor in angiosperm Molecular Biology. Botanical Studies (2017) doi:10.1186/s40529-016-0159-1

Martin Christine et al., Assessing segmental versus non-segmental features in the ventral nervous system of onychophorans (velvet worms). BMC Evolutionary Biology (2017) doi:10.1186/s12862-016-0853-3

Cai Pengfei et al., A next-generation microarray further reveals stage-enriched gene expression pattern in the blood fluke Schistosoma japonicum. Parasites Vectors (2017) doi:10.1186/s13071-016-1947-x

Huang Yutao et al., Exogenous spermidine improves seed germination of sweet corn via involvement in phytohormone interactions, H 2 O 2 and relevant gene expression. BMC Plant Biology (2017) doi:10.1186/s12870-016-0951-9