Search

All data associated with the Allen Brain Atlas resources have been indexed and can be searched. The data span many different modalities including colorimetric in situ hybridization (ISH), dual fluorescence ISH, histological staining, microarray, RNA-Seq and exon array data.

The list of indexed subjects includes:

Genes
Image Series/Experiments
Anatomic Regions/Structures
Reference Atlases
Content
Documentation Keywords

Images are grouped into "Image Series" that comprise an experiment. Experiments consist of slides from the same specimen and that receive the same treatment, whether it is Nissl staining or ISH with a probe for a particular gene.

Some data sets include anatomic reference atlases to provide a structural framework for the location of gene expression.

Boolean Syntax

Operator	Example Query
AND operator: &	mouse & Grik3
OR operator: \|	Abcc1 \| Ache \| Adcyap1
NOT operator: !	reference atlas ! spinal

AND, OR and NOT may be used in place of their corresponding operators.
The AND operator (&) is implicit, so spaces between words that are not separated by an operator will be treated like an &.
OR (|) has higher operator precedence than AND (&).
Parentheses can be used to group criteria, but nested parentheses are not supported at this time.
The NOT operator (!) is not supported within parentheses.
Enclose search phrases in quotation marks to avoid confusion with boolean operators.

Search Results

Clicking on "Search" returns a list of results that include data from all of the datasets associated with the Allen Brain Atlas resources that match your search. The search results' order is weighted by subject and type of dataset.

Column	Description
Subject	Succinct description of the resource
Dataset	Name of the dataset
Details	Metadata to aid in determining its relevance

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Cross Dataset Differential Search

A common usage of gene expression databases is to find genes that show enrichment of expression in one region (target) compared to another region (contrast). This type of "differential search" query is supported in several of the Allen Brain Atlas datasets. For example:

In the Allen Mouse Brain Atlas, differential search is based on automated expression measurement of ISH images. Expression values are averaged over a 200 micron (per side) cube and mapped into a standard canonical space. Note: this search is derived from a fully automated processing pipeline. False positive and false negative results can occur due to artifacts on the tissue section or slide and/or algorithmic inaccuracies. Users should confirm results with visual inspection of the ISH images.
In the Allen Human Brain Atlas, differential search is based on a large scale microarray study with samples covering the whole brain and multiple subjects.

The "Cross Dataset Differential" search function enables side by side viewing and comparison of differential search across multiple datasets. Select the "Cross Dataset Differential" radio button. To find genes with higher expression in one structure compared to another structure, select a target brain structure in the top drop-down box and a contrast region in the bottom drop-down box and click on the Search button. A "linked" differential search is performed.

Search results

The return list is generated by first executing a differential search query in the primary dataset (the first column). Experiments (e.g. ISH image-series, microarray probes) for each gene are grouped together and ordered by maximum fold-change. For each gene in the primary return list, associated experiments in the secondary dataset (the second column) are identified; fold-change values are computed and displayed. Note that NCBI HomoloGene data is used to link genes across organisms. Click on the dataset column heading to toggle the primary dataset selection.

For each experiment, a gestalt visualization of the brain wide expression pattern is also provided. The type of visualization depends on the dataset:

For mouse brain data, expression is visualized as rotating 3D thumbnails. Each view is generated by maximum density projection where denser expression area appears more solid and obscures areas of lower density. Each cube is color-coded by average expression intensity ranging from blue (low intensity) through green to red (high intensity). Move slider bar in the header to rotate thumbnail.
For human brain data, microarray data is visualized as a heatmap where each column represents a tissue sample in ontological order. Heatmap color represents the z-score over a probe ranging from green (z-score of -3 and below) through black to red (z-score of +3 and above). Hover over any position in the heatmap to obtain the associated tissue sample structural annotation.

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