Searching

"Gene Search" appears on our landing page. A gene search will show you a list of all the experiments we've done involving a gene that matches your search criteria. You can perform a gene search by typing in the gene search box, or by directly clicking on the list of gene symbols listed on the page. In either case, the search results will be narrowed to include only the items that are checked under the Strain, Sex, and Plane categories.

The gene search box gives you additional flexibility in specifying a gene, recognizing gene names, gene symbols, and alternate gene symbols of the genes involved in the experiment. A "Match" in gene search means that the text you type in is contained somewhere in the name, symbol or alternate symbol of the gene involved in the experiment.

As you begin typing in the gene search box, a list of suggestions will appear. You can use your arrow keys or the mouse to move down, highlighting the desired entry. If you're using your mouse, click on the desired entry to select it, then hit your "Enter" key or click the Search button to perform the search. If you're using arrow keys, hit the "Enter" or "Tab" key to select the highlighted item. If you don't want to use any of the suggestions, hit your "Esc" key or click your mouse outside the list and it will disappear.

↑ Go back to Contents

Search Results

The result set shows a list of gene expression experiments corresponding to the selected gene, strains, sexes and planes:

Searchresults

Please note-- If you searched by gene, it may appear that some of the rows do not match your gene criteria. Keep in mind that by default all of the alternate gene symbols (which are not shown in the result set) are included in a gene search. To see the alternate symbols for a gene, click on the gene symbol link in the result set to bring up the Image Series Detail page.

Sorting

The results are initially sorted by Strain in ascending order. Click on any of the column headers to sort by that column; click on the same column header again to reverse the sort order. A small arrow will appear next to the currently sorted column, indicating the sort order, as shown in the image at right.

Getting more detailed information

The Gene Symbol links to detailed information about the gene in our experiments. The number in the "ImagesSeries" column links directly to an image browser of all the series of images for the given experiment.

Comparing Result Sets

In addition to the links found in each experiment row, you can select multiple rows to compare images side-by-side. Click the check boxes at the far left of the desired rows, or click the check box in the column header to toggle all of the row check boxes on or off. All checked boxes are saved until you click on the "Clear Selections" button; this is true even if you move to another page of results, or even if you conduct a search on a different gene. Once you have finished selecting rows, click the "Compare Selected Experiments" button, which will display images for all of the selected rows on the Image Browse/Compare page.

XML

As shown in the image above, at the bottom of the table there is a link to an XML document containing all of the data in the result set.

↑ Go back to Contents

Image Series Detail

This page provides detailed information about the image series and the gene, including any alternate names for the given gene, transcript and riboprobe information. Search links to the Allen Brain Atlas (Mouse Brain) and Developing Mouse Brain projects are provided so that you can query these projects for the same gene.

Information on the page can be viewed as XML by clicking on the XML link on the bottom of the page.

↑ Go back to Contents

Image Browse/Compare Page

The image browse/compare page displays the ISH images from one or more image series. A number of different display and formatting options are described below.

Using the Zoom and Pan (Zap) Image Viewer

The default layout shows one or more zoom-and-pan (zap) viewers. The zap viewer allows you to navigate through an image series' thumbnails to select an image to view at higher resolution. Once selected, you can use your mouse or keyboard to zoom and pan the larger image. Additional image manipulation tools are described below.

Image Manipulation

Select a thumbnail from the bottom of the image series' window to open its image in the viewer window. Drag the image with your mouse pointer to an area of interest, then use the plus (+) and minus (-) keys or the wheel on your mouse to zoom in and out.

	Move the slider bar to the left to intensify the contrast.
	Select ISH, Nissl or expression mask image type.
	Open the selected image in a high-resolution viewer in a new browser window.
	Open a new browser window to review metadata and gene information for the image series.
	Close the viewer.

Multiple image series can be opened on the same Web page to enable side-by-side comparisons. You can swap viewers' positions on the page by clicking on the first viewer's title bar and dragging it to the second viewer's position.

↑ Go back to Contents

High Resolution Image Viewer

Click on the high resolution image viewer button in the Zap viewer (See Image Browse/Compare Page) to launch the high resolution viewer in a new browser window. This viewer provides an efficient way of viewing very large, high resolution images over relatively low bandwidth.

Use the controls shown at left to zoom and pan around the image. You can also zoom by clicking on the image, and pan by click-and-dragging the image, or using the keyboard up/down/right/left arrow keys.

The tool box shown at right enables you to

Switch between an ISH image and its corresponding expression mask or closest Nissl image.
Page through all the images in the same image series.
Adjust contrast (on the "Properties" page.)
Email a link to the image (Tools page.)
Download a JPEG of the image (Tools page.)

The scale bar will change appropriately as you zoom in and out of the image. Click and drag the scale to any position on the image to measure regions of interest. Click on the text to flip the scale from horizontal to vertical.

↑ Go back to Contents