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Data Portal

This is the online help for the Allen Institute for Brain Science Data Portal.

Overview

The Allen Brain Atlas resources are a growing collection of online public resources integrating extensive gene expression and neuroanatomical data, complete with a novel suite of search and viewing tools. This portal gives you access to each of these resources by clicking on the button for a particular project or by clicking the project from the banner tab or drop-down menu.

Key features of the Data Portal:

Announcements

  • Latest updates
  • Upcoming Events and Training
  • How to connect with us

Tutorials

A growing library of short video tutorials that demonstrate different aspects of using the Allen Brain Atlas resources.

Site Search

A way to search across the entire suite of datasets including a #Cross Dataset Differential Search, which allows you to search for brain regions with enhanced gene expression in both the Allen Mouse Brain Atlas and the Allen Human Brain Atlas.

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

Use of boolean syntax (i.e. AND, OR, NOT) is supported when using the search feature. Supported boolean operators include:

Operator

Example Query

AND

mouse AND Grik3

OR

Abcc1 OR Ache OR Adcyap1

NOT

reference atlas NOT spinal

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.
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.

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.

Data Highlights

On the portal page, a new image from one of the datasets will be displayed daily to highlight interesting data from the Allen Brain Atlas resources. Clicking on "More Highlights" will take you to a page with highlights from each of our projects. You can browse through the images from each project and click on any of the images to be taken to the experiment from which the highlight was taken.

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