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Clicking on the "?" button from any search type will take you to the appropriate help section.

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With the Gene Search radio button selected (default) you can either select a gene only by typing the name of your gene of interest into the text box, or you can further restrict your selection criteria by selecting tumor features and/or donorstumors. Once you have made your selections, click the Search button. The search will not work unless a gene has been selected. You can further limit your search by selecting the box next to "Show exact matches only".

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Results will be returned in a heat map heatmap format with the genes on the y-axis (vertical) and the tumors/tumor features on the x-axis (horizontal). The heat map heatmap represents the normalized gene level RNA-Seq expression data in TPM (Transcripts per MillionFPKM (Fragments Per Kilobase Of Exon Per Million Fragments Mapped). By default, the columns in the heat map heatmap are sorted first by tumor, then by tumor feature. To toggle the initial change sort parameterorder, click the toggle button in the top right hand corner of the heat mapheatmap.

Clicking on a data point in the heat map heatmap will populate the metadata box above the heat map heatmap with information specific to that gene and tumor. This meta-information includes information regarding the tumor, the gene and a search box to search for genes that show similar expression patterns as your gene of interest. There are two links available from the tumor box, clicking on the "Tumor Sub-Block" link will open up a new tab with the Specimen Detail Page and clicking the "SNI" link will take you to the Swedish Neuroscience Institute page (registration is required to access the patient metadata). Gene information includes metadata on the gene selected including links to ISH data for that gene (when available) and links to other Allen Brain Atlas resources that include that gene.

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You can adjust the window and the level of the color scale on the heat map heatmap by adjusting the threshold bars or re-centering the color map scale bar. You can also zoom in or out to see the heat map heatmap at different magnification levels.

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To restrict the columns that are displayed, select the "Filter Heatmap" button below the heatmap. Filtering your heatmap is a two-step process: first, select the "..." box to restrict your features, making sure to save your selections and then toggle the filter heatmap feature by clicking the "Filter Heatmap" button.

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In using gene expression databases, a "search by example" feature is highly desirable as genes with similar expression patterns may be related in function. Using the "Find Correlates" search utility will accomplish this function. This search by example facility is also available in the Allen Human Brain Atlas, the BrainSpan Atlas of the Developing Brain, as well as in the Allen Mouse Brain Atlas and in the Allen Developing Mouse Brain Atlas.

Once you have selected a gene of interest (by clicking on the heat map heatmap that results from a #Gene Search or #Differential search), you can find genes with similar expression patterns. All Features and All Tumors are included in your search by default, but you can select one or more features or tumors from the drop down menus. Once you have selected the tumor feature(s) and donortumor(s) of interest, click "Find Correlates".

The search will return a list of genes enriched in the target domain(s) over the contrast domain(s) and ranked by it's Pearson's correlation, rresults highlight the genes whose expression profiles across the samples of interest resemble the expression profile of the example gene by ranking the genes according to the Pearson’s correlation coefficient (r) between their profile and that of the example gene.

If there is ISH data available for a gene, there sill be a link labeled "Yes" that will take you to the ISH Data for that gene.

You can adjust the window and the level of the color scale on the heat map heatmap by adjusting the threshold bars or re-centering the color map scale bar. You can also zoom in or out to see the heat map heatmap at different magnification levels.

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To restrict the columns that are displayed, select the "Filter Heatmap" button below the heatmap. Filtering your heatmap is a two-step process: first, select the "..." box to restrict your features, making sure to save your selections and then toggle the filter heatmap feature by clicking the "Filter Heatmap" button.

You can see "anti-correlated" genes by toggling the sort order on column "r" or scrolling to the bottom of the heat mapheatmap.

Differential Search

Another common usage of gene expression databases is to find genes that show enrichment of expression in one set of samples compared to another set of samples. This type of query is supported by the "Differential Search" feature. Select the "Differential Search" radio button. If you do not know what to search for, there are some suggestions in the "Browse by Differential Expression" box on the landing pageUnder the RNA-Seq tab, click on the examples in the “Browse by Differential Expression” box, or select the “Differential Search” radio button to start your own search. To find genes enriched in one "target set" of tumor features and/or donors tumors compared to a "contrast set" of tumor features and/or donorstumors, choose the target set using the "Target Tumor Features/Tumors" drop down menu, and the contrast set using the "Contrast Tumor Features/Tumors" drop down menu. The default setting selects all tumor features and donorstumors, but clicking in the "All Features" or "All Tumors" text boxes will allow you to select individual tumor feature(s)/tumor(s). Then click "Search".

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The search will return a list of genes enriched in the target domain(s) over the contrast domain(s) ranked by either the Fold change in expression or values. The results can be sorted also by the confidence statistical significance of the evidence (or p-Value) . Clicking on either of these features will return a different list of genes. The ranking type will be indicated by a triangle next to the by clicking on the desired sort parameter.

If there is ISH data available for a gene, there sill be a link labeled "Yes" that will take takes you to the ISH Data for that gene.

You can adjust the window and the level of the color scale on the heat map heatmap by adjusting the threshold bars or re-centering the color map scale bar. You can also zoom in or out to see the heat map heatmap at different magnification levels.

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To restrict the columns that are displayed, select the "Filter Heatmap" button below the heatmap. Filtering your heatmap is a two-step process: first, select the "..." box to restrict your features, making sure to save your selections and then toggle the filter heatmap feature by clicking the "Filter Heatmap" button.

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