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Overview

The Data Set

The Allen Human Brain Atlas consists of two primary sources of gene expression data: microarray numerical value data and in situ hybridization (ISH) image data.

For complete details please see the Microarray Platform Selection, Whole Brain Microarray and In SituHybridization white papers on our Documentation page.

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Supported Platforms

This application has been tested with the following configurations. You may notice irregularities with software that has not been tested. There are known issues when viewing heat map data using unsupported browsers.

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Before you install/upgrade Flash Player, uninstall existing players using the Adobe uninstall program.
There are uninstallers available for Windows or Macintosh.

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Microarray Data

The Data Set

The website offers three types of searches to allow a user to: (1) limit the visualization to a subset of probes (or genes) of interest (Gene Search); (2) use a 'seed' gene to find other genes with similar expression patterns (Find Correlates); and (3) compare expression between different anatomic regions (Differential Search).

Gene Search

To search for a gene category by disease, pathway, cell type or function, click on the relevant search term in the tag cloud. To search for probes associated with a specific gene or group of genes, select the Gene Search radio button and type the gene name, gene symbol or Entrez Gene ID in the search box (multiple genes searches require an OR between gene names) before clicking the Search button.

Boolean Syntax

The following special operators can be used to build queries:

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  • AND, OR and NOT may be used in place of their corresponding operators. They must be upper case.
  • 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 (&).
  • Parenthesis can be used to group criteria, but nested parenthesis are not supported at this time.
  • The NOT operator (!)is not supported within parenthesis.

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Correlative Search

In using gene expression databases, a "search by example" feature is also highly desirable as genes with similar expression patterns may be related in function. The "Find Correlates" search utility will accomplish this function. This search by example facility is also available in the Allen Mouse Brain Atlas and Allen Developing Mouse Brain Atlas and the NIMH Transcriptional Atlas of Human Brain Development.
To find other genes with profiles similar to your gene of interest, first select your probe by clicking on any cell in the heat map related to that probe. You will see that probe listed in the box above the right hand side of the heat map. Then select the brain structure(s) in which you would like to see a similar expression pattern, and click "Find Correlates". This action will return probes with a similar expression profile to brain region(s) in which you are interested. Only regions selected for the search will be displayed. To see the search results across the entire brain, turn off the "Restrict Domains" function at the bottom of the heat map.
You can see "anti-correlated" returns by toggling the sort order on column "r" or scrolling to the bottom of the heatmap.

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Differential Search

Another common usage of gene expression databases is to find genes that show enrichment of expression in one region compared to another region. This type of query is supported by the "Differential Search" mode. Select the "Differential Search" radio button. To find genes or probes with a higher expression in one structure when compared to another structure, enter the target brain structure in the top search box and your contrast region in the bottom search box and click on the Search button.
Your search will return results in the two brain regions selected. The results will show higher expression in the target region compared to the contrast region. (To view the expression patterns of the returned probes over the entire brain, turn off the "Restrict Domains" function below the heat map.) Search results are sorted either by p-value or fold change, indicated by the arrow on the buttons over the column of genes. To alter the sort parameter, click on either the "p value" or the "fold-change" buttons.
To perform the previous search in reverse, click the toggle button beside the Search button.

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Data Visualization

Based on your search, the resulting microarray data sets are presented as a matrix with brain structure (by individual donor) on the horizontal x-axis and gene probes on the vertical y-axis. The microarray data is presented in a "heat map" format where the colors of the heat map correspond either to raw data or to a normalized (z-score) expression level of a probe. Brain structures are organized such that moving left to right on the x-axis is analogous to moving from anterior to posterior first in the cortical areas, followed by subcortical areas, cerebellum and brainstem.

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