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
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  • Why can't I interact with the browser? I can see one column of data but I can't do anything.
  • Help! My gene is showing up as gray.

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  1. FAQ

Xena Browser

Why can't I interact with the browser? I can see one column of data but I can't do anything.

The Visual Spreadsheet wizard asks that you add at least TWO columns of data before interacting with the browser. This is because Xena was designed to allow you to find correlations within the data and you need more than one type of data on the screen to find a trend.

Add another column of data and click Done. You can always delete this column after you have completed the wizard if it is not needed.

Help! My gene is showing up as gray.

In general, we recognize genes from the HUGO gene name space. If you gene name isn't recognized, try looking at Gene Card and see if other names listed there are recognized.

Last updated 4 years ago

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