Versions Compared

Key

  • This line was added.
  • This line was removed.
  • Formatting was changed.

...

The Allen Human Brain Atlas offers three types of searches to allow a user to: (1) obtain gene expression data for specific genes (or probes) of interest (Gene Search); (2) compare expression between different anatomic regions (Differential Search); and (3) use a 'seed' gene to find other genes with similar expression patterns (Find Correlates).

...

Gene Search

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, Entrez Gene ID or probe ID in the search box (multiple genes searches require an OR between gene names) before clicking the "Search" button. To show exact matches to your search query click the "Show exact matches only" box.

...

To download your search results, click the "Download this data" link at the bottom left of the heatmap.

...

Differential Search

To find genes that show enrichment of expression in one region compared to another region, use the Differential Search mode. Select the "Differential Search" radio button. To find genes or probes with an enhanced gene expression profile in one or more brain regions when compared to one or more other brain regions by entering the target structure(s) in the top search box (separate structures with a semicolon) and your contrast structure(s) in the bottom search box and click the Search button.

...

To perform the previous search in reverse, click the toggle button to the left of the Search button. To download your search results, click the "Download this data" link at the bottom left of the heatmap.

...

Mouse Differential Search

The "Mouse Differential Search" function enables side by side viewing and comparison of differential search across the human microarray and the mouse ISH datasets. Select the "Mouse Differential Search" 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.

...

Search Results

The return list is generated by first executing a differential search query in the human microarray dataset. Experiments for each gene are grouped together and ordered by maximum fold-change. For each gene in the human microarray return list, associated experiments in the mouse ISH dataset 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 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.

...

Gene Classification

When you are viewing heatmap data, there will be a "Gene Classification" radio button available. When the gene classification radio button is selected, you can search for enhanced gene expression from one of the categories in the drop down menu.

...

To download your search results, click the "Download this data" link at the bottom left of the heatmap.

...

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, Allen Developing Mouse Brain Atlas and the BrainSpan atlas of the developing human brain.

...

To download your search results, click the "Download this data" link at the bottom left of the heatmap.

...

Download Search Results

To download your search results, click the "Download this data" link at the bottom left of the heatmap. You will have the option of downloading up to 2000 genes at a time starting from any position in the heatmap. Your start position can be determined from the counter in the top left corner of the heatmap (see screenshot).

...

The column headers, probe headers and expression data will be consistent with the settings from which you downloaded the heatmap (i.e. heatmaps illustrating z-score will result in an Expression.csv file with normalized z-score values).

...

Data Visualization

Based on your search, the resulting microarray datasets are presented as a matrix with brain structure (by individual donor) on the horizontal x-axis and gene probes on the vertical y-axis. Because multiple probes were used to measure gene expression for a gene, search returns are reported by probe rather than by gene. The microarray data is presented in a heatmap 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.

...