User Help Pages
  • Welcome to the Help Pages for UCSC Xena
  • Tutorials and webinars
    • Webinars
    • Basic Tutorial: Section 1
    • Basic Tutorial: Section 2
    • Basic Tutorial: Section 3
    • Advanced Tutorial: Section 1
    • Advanced Tutorial: Section 2
    • Tutorial: Tumor vs Normal
    • Tutorial: Viewing your own data
    • Live examples
  • How do I ...
    • How do I make a KM plot?
    • How do I compare tumor vs normal expression?
    • How do I remove null data (gray lines) from view?
    • How do I make subgroups?
    • How do I make more than 2 subgroups?
    • How do I make subgroups with geneA high and geneB high?
    • How do I compare gene expression between subgroups?
    • How do I compare gene expression between different cancer types?
    • How do I remove duplicate samples from a KM plot?
    • How do I view multiple types of cancer together?
    • How do I filter to just one cancer type
    • How do I view my data with the data from TCGA?
    • How do I change the color of a column?
    • How do I interact with the tooltip?
    • How do I cite UCSC Xena?
  • Overview of features
    • Visual Spreadsheet
      • Coloring for Mutation Columns
      • Coloring for Segmented Copy Number Columns
    • Kaplan Meier Plots
    • Chart & Statistics View
    • Filtering and subgrouping
      • Supported search terms for finding samples
    • Differential Gene Expression
    • GSEA
    • Genomic Signatures
    • Bookmarks
    • Download Data
    • Xena Single Cell
    • TumorMap
    • MuPIT
    • Accessing data through python
    • Transcript View
    • Xena Gene Set Viewer
  • Overview of public data
    • Types of data we have
    • TCGA
    • GDC
    • More studies
    • Choosing a study/cohort
  • FAQ
    • Xena Browser
    • Data and datasets
  • Viewing your own data
    • Getting Started
    • Probes/transcripts/identifiers we recognize
    • Data format specifications and supported biological data types
    • KM plots using data from a Local Xena Hub
    • Hubs for institutions, collaborations, labs, and larger projects
    • Loading data from the command line
    • FAQ/Troubleshooting Guide
  • Technical documentation
    • Setting up Xena for your institution
    • Deep Linking Into Xena
    • Metadata Specification
  • Contact us
  • Cite us
  • Data Use Agreement
Powered by GitBook
On this page
  • Overview
  • Installing a Local Xena Hub
  • System requirements for Xena Hub
  • Starting/running a Local Xena Hub
  • Loading data into a Local Xena Hub
  • Viewing data from a Local Xena Hub
  • Gene names and identifiers for genomic data
  • Help! I don't see my study listed
  • Data security
  • How does Xena ensure the security of my data?
  • Is there any data that is considered to not be secure?

Was this helpful?

Export as PDF
  1. Viewing your own data

Getting Started

Step-by-step instructions to viewing your own data

Last updated 3 years ago

Was this helpful?

Overview

Get started viewing your own data:

We support most types of . 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 (), 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 or a publication.

We support tab-delimited (.tsv and .txt) and Microsoft Excel files (.xlsx and .xls). 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.

Please use Chrome to view your own data.

Installing a Local Xena Hub

Click on . 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 for Xena Hub

  • Mac: OSX 10.7 and above

  • Windows: 64-bit

  • Linux: ability to run a .jar file

Starting/running a Local Xena Hub

Loading data into a Local Xena Hub

Viewing data from a Local Xena Hub

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

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.

After installing a local Xena Hub, go back to 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 will take up to one minute to start up.

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

You can also load data .

Click on . 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 'My Study'.

You Local Xena Hub must be running to view any data that you have loaded into it. Please ensure it is running on your computer. You can also check which studies are on your hub and what data is in them by going to the .

VIEW MY DATA
website wizard
properly formatted
via the command line
VISUALIZATION
My Computer Hub page
genomic and/or phenotypic/clinical/annotation data
survival data for a KM plot
GEO
VIEW MY DATA
Install a Local Xena Hub on your computer
Start the Local Xena Hub
Load the data you want to view
View the data