How do I zoom in?

To zoom in on a section of the genome, click and drag horizontally across the genomic heatmap. To zoom in on a sample, click and drag vertically across the clinical heatmap. Vertical clinical heatmap zooming is only active when in "Heatmap" mode, not in any summary view.

How do I zoom out?

Click to zoom out incrementally and the bigger to zoom out to either the full chromosome or the full genome. To zoom out vertically, click the button over the clinical heatmap. Vertical clinical heatmap zooming is only active when in "Heatmap" mode, not in any summary view.

How do I view a gene?

There are a couple of ways to view a gene. First, you can type the gene name into the search bar and select it from the autocomplete list. This will autofill the search bar with the coordinates for that particular gene. If you know the genomic coordinates of your gene you can also directly enter them in the search bar.

Second, you can use the Genes view mode. Start by toggling the "Genes" button in the upper left corner of the heatmap display. Next, enter your gene(s) into the search box at the top of the screen. To save your gene as a geneset, use our advanced options

How do I sort the heatmap by a gene?

In order to sort the genomic and clinical heatmaps by a gene you need to add the gene as a signature. Adding a gene as a signature will add it to the clinical heatmap and, thus, allow you to sort on it.

First, open the signatures settings by clicking on the "Tools" menu for a dataset and then selecting "Signatures". Next, add your gene to the signature expression box near the bottom of the settings and click "Add". Your gene will now appear as a clinical feature and both heatmaps will be sorted by it. More information about the signature settings can be found here.

Why are multiple datasets updating at the same time?

Datasets in the same cohort update together. This means that changes to one clinical heatmap affect all the other clinical heatmaps in the cohort. More information about cohorts and how they are determined can be found here.

All the data is red. How can I see the difference between samples?

Genomic data are colored based on whether they are greater than, less than or equal to zero. Sometimes all the data in a dataset (e.g. gene expression datasets), will be greater than zero making it difficult to see the differences between samples. To visualize these differences users can click on the color legend in the top right corner of the genomic heatmap and then toggle the "Normalize", which will subtract the mean of each data column, making the mean of a data column equal to zero. Data will then be colored according to where they fall in relationship to the mean rather than zero.

Additionally, this option is helpful when there are vertical red/green/blue stripes at each genomic location or gene. This indicates that the vast majority of the data values for a specific gene are greater/lower than zero, which is often seen in many gene expression and DNA methylation datasets. This is due the data being normalized on the whole dataset level and not on the individual gene level. Thus, the difference in data values are more reflective of the difference between genes rather than between samples. The same browser "mean normalization" can be used to make the differences between samples more easily seen.

Note that the gain may need to be adjusted after this procedure to increase the intensity of the colors.

Why is the subgroup range for a clinical feature larger than what is displayed on the heatmap?

Datasets will often share a common clinical data file. The subgroup range for a clinical feature is determined by the entire range over all samples in the clinical file, not just the data that is displayed in a single dataset. Thus, if one sample is displayed in dataset X but not in dataset Y, the value for that sample will still appear in the subgroup range for dataset Y even though the sample is not being displayed. We are currently working to fix this.

How do I view a signature from one dataset on another?

You can view a signature generated from one dataset, such as copy number variation, on another dataset, such as gene expression, by first downloading the clinical heatmap. To do this, click on the download icon over the clinical heatmap. Next, upload the signature from the download as custom data.

Why are there multiple columns of data for one gene when in genes mode?

If more than one probe maps to a gene, the gene column will be divided into sub columns for each probe.

What is the p-value threshold for displaying red/green coloring in the statistics track?

The p-value threshold for all statistical tests is 0.05.

Which genome is the data annotated to?

All data is annotated to Human Mar. 2006 (NCBI36/hg18).

Can I use the Cancer Browser on all internet browsers?

We currently only support Firefox 3.0 and greater, Safari 5.0.3 and greater, and Chrome; we do not support Internet Explorer at the present time. If you discover a browser inconsistency, please contact us.

Why does the tutorial come up every time I open the browser?

The tutorial is set to automatically show if you have not visited the site since our last feature update. We use local storage in your browser to save the last time you visited. Your browser preferences may be set to prevent this information from being saved. Be sure these settings are enabled:

  • remember browser history
  • accept cookies from sites
  • keep cookies until they expire

How do I create a bookmark?

To bookmark a page, click on the "bookmark" button in the upper right corner and select "Create". This will give you the URL of the bookmark along with some text boxes to give your bookmark a name and description, if you are logged in. You do not need to be logged in in order to create a bookmark.

Please note that we don't guarantee any bookmarked view to remain exactly the same. We are continually updating data, especially data from TCGA, so views may change over time. This can include datasets, clinical features and values in clinical features.

You can also create a static link to the browser by building a URL.

How do I delete a bookmark?

You can delete a bookmark from your account by going to the My Account page, checking the box next to the bookmark and clicking "delete". Please note that the bookmark will still exist - it just won't be associated with your account. There is currently no way to permanently delete a bookmark.

How do I reset the browser to the defaults?

Click on the bookmark menu in the upper left corner and choose "Reset to defaults". Note that this will reset all the settings for the browser - it is equivalent to opening a new window or tab with the browser.

How do I cite the browser?

Please reference our most recent publications.

How do I save an image?

You can create an image of just the heatmaps and their titles by clicking on "PDF" in the upper right corner. Then use the innate capabilities of your computer and/or browser to make the image.

How do I download a dataset?

To download the processed files that make up a dataset click on the in the dataset header or the download button on the dataset details page.

You can download just the clinical data in the heatmap by clicking the download button above the clinical heatmap. There is currently no way to download just the genomic data in view.

How do I download just the data in view?

You can download just the clinical data in the heatmap by clicking the download button above the clinical heatmap. There is currently no way to download just the genomic data in view.

Is it possible to download statistical results?

It is not currently possible to download this information and are currently working on a solution to this issue. You can always download the data and perform the statistical test using a data package like R.

Is it possible to display my own data?

It is possible to display your own clinical data within one of our datasets. Click here for more information about what types of data we support. We hope to continue to provide more ways for users to view their data on our browser, including genomic data, in the future.

If you are part of a group or lab that would like to display data on the cancer browser please contact us to see if we could collaborate to set up a hosting service for you.