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
  • General recommendations
  • Differences between the GDC and the legacy TCGA data
  • Choosing a study by type of data
  • Choosing a study based on a specific analysis or sample type

Was this helpful?

Export as PDF
  1. Overview of public data

Choosing a study/cohort

Last updated 7 months ago

Was this helpful?

General recommendations

We recommend the TCGA Pan-Cancer (PANCAN) study for most analysis. Unless you need a specific type of data or need to run a type of analysis listed below, we recommend the TCGA Pan-Cancer (PANCAN) study.

Why do we recommend this study?

We recommend it because it has the data from the Cancer Genome Atlas (TCGA) Research Network, which generated the most comprehensive cross-cancer analysis to date: The Pan-Cancer Atlas. Xena displays the curated genomics and clinical data generated by the Pan-Cancer Atlas consortium working groups.

Note that if you use the TCGA Pan-Cancer (PANCAN) to study a specific cancer type, you will need to filter down to just that cancer type.

If you don't want to filter ...

Our second most recommended datasets are the cancer-specific GDC TCGA studies. These avoid the need to filter down to a single cancer type and contain harmonized data from the Genomic Data Commons.

Differences between the GDC and the legacy TCGA data

More information comparing the data in the GDC to the legacy TCGA data can be found here:

Choosing a study by type of data

The table below assumes that you are interested in TCGA data. These data types may also appear in other studies, but these are the recommended studies.

Data type

Study

Dataset name

Menu

Transcript expression

TCGA Pan-Cancer (PANCAN)

TOIL Transcript expression

Advanced

lncRNA expression

TCGA Pan-Cancer (PANCAN)

TOIL Gene expression

Advanced

Exon expression

legacy TCGA datasets (per cancer type)

Exon expression

Advanced

miRNA expression

TCGA Pan-Cancer (PANCAN)

Batch Effects normalized miRNA data

Advanced

DNA methylation

Any

DNA methylation

Advanced

ATAC-seq

GDC Pan-Cancer (PANCAN)

ATAC-seq

Advanced

Varied Survival endpoints

TCGA Pan-Cancer (PANCAN)

NA (run KM plot)

--

Choosing a study based on a specific analysis or sample type

Analysis

Study

Compare Tumor vs Normal

TCGA, TARGET, GTEx

GRCh38 coordinates

Any GDC study

Cell Line

CCLE

Disease specific survival, disease free survival, progression free survival

TCGA Pan-Cancer (PANCAN)

TCGA Pan-Cancer (PANCAN) study
GDC Data Hub
LogoBefore and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons | NCI Genomic Data CommonsNCIGDC_Updates