Getting Started

Step-by-step instructions to viewing your own data

Overview

Viewing your own data is easy! Simply:

We support most types of genomic and/or phenotypic/clinical/annotation data. Genomic data needs to be values called on genes, transcripts, exons, probes or some other identifier. Phenotypic/clinical/annotation data can be almost anything, including patient data (e.g. age, set, etc), clinical data (survival data for a KM plot), and other data such as gene fusion calls, regulon activity, immune scores, and more. Samples can be bulk tissue, cell lines, cells, and more. We do not visualize raw data such as FASTQs or BAMs.

Data can be your own or from another source, like GEO or a publication. Data on a Local Xena Hub can only be viewed or accessed by the same computer on which it is running, keeping private data secure.

The Local Xena Hub must be installed and running in order to load data, as well as any time you want to view data. The Local Xena Hub will remember previously loaded data.

We currently do not support Safari for viewing your own data. Please use Chrome or Firefox

Installing a Local Xena Hub

Click on VIEW MY DATA and you will be prompted to download and install a local Xena Hub.

Double click on the download to begin the installation of the Xena Hub. Follow the wizard to finish the install.

System requirements

  • Mac: OSX 10.7 and above

  • Windows: 64-bit

  • Linux: ability to run a .jar file

Starting/running a Local Xena Hub

After installing a local Xena Hub, go back to VIEW MY DATA to auto-start the Hub. If it does not automatically start, refresh the page or double click on the Xena Hub application on your computer. The Xena Hub application should be in your Applications folder for Mac and Windows. Note that it typically takes a minute or two to start up.

Loading data into a Local Xena Hub

Most people load data into their Local Xena Hub through our website wizard, which leads you through the loading process step by step. Note that you will want to make sure your data is properly formatted ahead of time.

You can also load data via the command line.

Viewing data from a Local Xena Hub

Click on VISUALIZATION. If your study is not already selected as step 1 of the wizard, then select it from the drop down and click 'Done'. Note that if you did not enter a study name your data will be under 'New Study'.

Gene names and identifiers for genomic data

When you loaded your genomic data we asked what type of genes, transcripts or probes you used. If you selected one of the options from the drop down menu then you can enter HUGO gene names or the identifiers in your file. If you did not select one of the options then you will need to enter the identifiers as they appear in your file.

Help! I don't see my study listed

You Local Xena Hub must be running to view any data that you have loaded into it. Please ensure it is started up. You can also check which studies are on your hub and what data is in them by going to the My Computer Hub page: xenabrowser.net/datapages/?host=https%3A%2F%2Flocal.xena.ucsc.edu%3A7223.

Data security

How does Xena ensure the security of my data?

Xena does not utilize a central rendering service, or require hubs to be publicly accessible on the internet like, for example, the UCSC Genome Browser does. Data flows in one direction, from hubs to the user agent. If the user installs a Xena Hub on their laptop, the hub is as secure as the laptop. If the user installs a Xena Hub on a local network, behind a firewall, the hub is as secure as the local network.

The Xena Browser accesses data from a local Xena Hub on the same computer by requesting data from http://127.0.0.1. The local Xena Hub will make the data within it available at this address. The local Xena Hub will only answer requests made form the user's own computer.

Users will need to use a web browser that supports this if they wish to use a Xena Hub on the loopback interface. At the time of writing, this includes Chrome, and Firefox, but not Safari.

Is there any data that is considered to not be secure?

A very limited set of metadata is considered to be not secure in the Xena architecture model. This includes cohort names and samples names. This metadata is visible to other hubs in the following scenarios. When the user selects a cohort, all hubs are queried for samples on that cohort. When the user selects a data field, the hub holding that field is queried with the field ID (e.g. gene, probe, transcript, phenotype) and all cohort sample IDs. This means, for example, that two hubs holding data on the same cohort will see the union of sample IDs from that cohort. While data queries are not made available publicly, a malicious person could gain entry to a Xena Hub and comb through logs for these queries. For these reasons, these metadata fields should not contain private information.