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.
{% hint style="info" %} TCGA Pan-Cancer (PANCAN) study {% endhint %}
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.
{% hint style="info" %} GDC Data Hub {% endhint %}
More information comparing the data in the GDC to the legacy TCGA data can be found here:
{% embed url="https://gdc.cancer.gov/about-data/publications/HG38QC" %}
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) | -- |
| 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) |