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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.

Microsoft Windows XP SP3

Apple Macintosh OS X 10.6.7

Internet Explorer 8.0

Safari 5.0.5

Firefox 4.0

Firefox 4.0

Flash 10.2.159.1

Flash 10.2.159.1

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

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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:

Operator

Example Search Type

Example Query

AND operator: &

Gene

dopamine & receptor

OR operator: |

Gene

ABAT

NOT operator: !

Gene

"dopamine receptor" !DRD3

  • 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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