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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

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  1. Overview of public data

Choosing a study/cohort

Last updated 7 months ago

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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
Before and After: A Comparison of Legacy and Harmonized TCGA Data at the Genomic Data Commons | NCI Genomic Data CommonsNCIGDC_Updates
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