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This interactive tutorial allows you to try out any of the functionality as you go.
To see our NEWEST features, jump to one of these steps:
You can re-enter the tutorial at any time from the Help menu at the top of the page.
Save your work or send it to others by creating bookmarks.
This menu also contains demonstrations of our tools.
Click "Add Datasets" to open the dataset browsing window.
Search for datasets by typing into the search box.
Datasets are organized into groups by data provider and cancer type.
To display a dataset, click on a group and then a dataset name.
Click button to download a dataset.
Note that this will download all the data from a dataset, not just the data that is currently in view.
Please see our data specification for information about our data files.
Data is organized with genomic information on the left and clinical information on the right.
Each row of data represents one sample with information from the genomic and clinical sides connected by the sample name.
Data is sorted by the left-most clinical column/feature and then sub-sorted on all columns following.
For gene expression data, red represents data values > 0 while green represents values < 0. For all other genomic data, red represents values > 0 while blue represents values < 0.
For clinical information, yellow indicates values > 0 or a different category, black indicates values near or at 0, while green represents values < 0.
Gray coloring indicates no data available.
To zoom in to a genomic location, click and drag over that region.
To zoom out a little, click .
To zoom out a lot, click the bigger .
Enter a genomic position in the search bar such as "chr1-chr4" or "chr1:800000-900000".
You can also enter a gene name and select it from the suggestion list. The coordinates will automatically be entered.
Zoom in vertically by clicking and dragging over the clinical heatmap.
To zoom out click at the top of the heatmap.
In addition to the current heatmap mode, there are two summary modes: Box Plot and Proportions, both of which can help users see overall patterns in the dataset.
More information about the summary modes can be found here.
Change the sorting of the heatmap by changing the order of the clinical feature columns. The left-most column is always the primary sort key.
Click on a feature to pull up a context menu to allow you to hide it or change its position.
Click "More Features" to bring up a list of clinical features available to add to the clinical heatmap.
Use the search box at the top of the menu to help find features of interest.
Kaplan-Meier Plots are graphs of the survival function of different groups of patients.
Patients are grouped by the left most clinical feature.
More information can be found here.
Click on the Tools menu to see tools to manipulate the clinical and genomic data.
Add your own clinical/phenotype data to the heatmap by selecting "Upload" from the Tools menu.
Paste in your data as patient/sample IDs and data values separated by a comma or tab, with each ID-value pair on a new line.
Enter a name for your data and click "Update"
Note that we currently do not display categorical data, only numerical.
Download the data behind the clinical heatmap by selecting "Download".
Click "About Dataset" to get more information about a dataset such as normalization done.
Signatures are gene expressions that can be used to predict things such as whether a patient will respond to a particular drug.
Signatures can also be used to display genes in the clinical heatmap, allowing sorting and other tools to be applied to genomic data.
Open the signature window by choosing "Signatures" from the Tools menu.
Add a favorite signature directly from the pull-down menu, or search for a signature using the search bar.
Make your own signature by entering genes into the gene expression box.
Enter one gene at a time to view genomic data in the clinical heatmap.
Creating groups of samples based on their clinical features is useful for visualizing differences between groups as well as performing statistics such as t-tests.
More information on Subgroups & Statistics can be found in our help.
Genes mode displays single or multiple genes side-by-side.
Click on the "Genes" button to switch to genes mode.
Gene names are along the bottom of the heatmap.
Similar to chromosome mode, genomic and clinical heatmaps are linked by the sample in heatmap mode and are independent in box plot and proportions modes.
You can zoom in by clicking and dragging.
Enter one gene, or multiple genes separated by spaces, into the search box to view them.
Use the Advanced Genes options to find predefined genesets, create genesets or have finer control over which genes are visible.
Signing up for an account allows you to save bookmarks, genesets and signatures.
Accounts are free and available from the sign in page.
Please see our user guide and FAQs for more help.
Please contact us with any feedback or questions.
Click the color legend to open the menu to adjust the genomic heatmap.
You can change the colors as well as normalize the heatmap by subtracting out the column mean.
Grab the bottom right corner of the heatmap to resize the heatmap.
Press 'Next' after the progress wheel disappears and the map is displayed.
If a subgroup were added, a statistics form would be displayed from which a statistical method and correction could be selected to apply to the subgroup.
The RefSeq Genes track from the Genome Browser shows gene locations.
Hover over the RefSeq Genes track to view the gene name.
The ideogram shows which chromosomes are being displayed.
The "View in Genome Browser" button will become activated if you view less than one chromosome.
Clicking this will open a new window at the UCSC Genome Browser with the same genomic coordinates.
Press the PDF button to display an image for generating a PDF.
To create a subgroup, click on a clinical feature.
This will bring up two sections - one for each subgroup - of either slider bars (for continuous features such as "age") or a small box of values (for categorical features such as "ER status").
Select either a range, one value or multiple values (shift-click) and click "Add".
Features used for each subgroup appear at the top under the Active Subgroups heading.
To delete a feature subgroup, click the "x" to the right of that feature subgroup.
Subgroups will appear as a "clinical feature" column in the clinical heatmap.
Add a subgroup to see how to generate statistics.
To test the differences between two subgroups, choose a test from the test drop down menu, then click "Show Statistics".
Statistics results appear below the heatmap for each genomic position.
For mean comparison tests, color indicates which group is significantly greater than the other. Gray indicates no statistical significance (p=0.05).
You can edit which genes are visible in Genes mode by using the geneset settings.
Click on "Genesets" to open the geneset settings.
The active (displayed) genesets is listed at the top.
Add a geneset directly from the pull-down menu or use the search bar to find a geneset by gene or geneset name.
Clicking on a geneset in the search results will fill the HUGO gene name box below with the genes in that geneset.
Edit the list of genes, if desired, and click "Replace".
You can also make your own geneset by typing in HUGO gene names, a geneset name and clicking "Replace".
Clicking on the geneset name in the active list will fill the HUGO gene names box with the genes in that geneset.
You can see all of your saved bookmarks, genesets and signatures by selecting the "My Account" link, which is visible after signing in.