# GDC Xena Hub

The hub hosts open access data from the [GDC Data Release v41.0 - August 28, 2024](https://docs.gdc.cancer.gov/Data/Release_Notes/Data_Release_Notes/).

***The GDC Pan-Cancer (PANCAN) cohort still contains data from the v18.0 release.*** We are working to upgrade to the v41.0 release.

If you need data from the previous GDC Data Relase (v18.0), please email us at genome-cancer@soe.ucsc.edu.

New for this release, we worked to not have samples that have only have phenotype/clinical data and don't have any genomic data. This should make visualizing data in our Visual Spreadsheet easier.

## Supported data types

<table style="border:1px solid black;border-collapse:collapse;"><thead>
  <tr>
    <th style="border:1px solid black; text-align:left; padding:8px;"><span style="font-weight:bold">Type of data</span></th>
    <th style="border:1px solid black; text-align:left; padding:8px;">Data</span></th>
  </tr></thead>
<tbody>
  <tr>
    <td style="border:1px solid black; text-align:left; padding:8px;">Copy Number Variation</td>
    <td style="border:1px solid black; text-align:left; padding:8px;">* Allele-specific Copy Number Segment (ASCAT2, ASCAT3)<br>* Copy Number Segment (AscatNGS)<br>* Masked Copy Number Segment (DNAcopy)<br>* Gene Level Copy Number (ABSOLUTE, ASCAT2, ASCAT3, AscatNGS)</td>
  </tr>
  <tr>
    <td style="border:1px solid black; text-align:left; padding:8px;">Somatic Mutation</td>
    <td style="border:1px solid black; text-align:left; padding:8px;">* Ensemble Somatic Variant (WXS)<br>* Ensemble Somatic Variant (Targeted Sequencing)</td>
  </tr>
  <tr>
    <td style="border:1px solid black; text-align:left; padding:8px;">Gene Expression RNAseq</td>
    <td style="border:1px solid black; text-align:left; padding:8px;">* STAR (Counts, FPKM, FPKM-UQ, TPM)</td>
  </tr>
  <tr>
    <td style="border:1px solid black; text-align:left; padding:8px;">Protein expression</td>
    <td style="border:1px solid black; text-align:left; padding:8px;">* Protein Expression Quantification</td>
  </tr>
  <tr>
    <td style="border:1px solid black; text-align:left; padding:8px;">DNA Methylation</td>
    <td style="border:1px solid black; text-align:left; padding:8px;">* Illumina Human Methylation 27K<br>* Illumina Human Methylation 450K<br>* Illumina Human Methylation epic<br>* Illumina Human Methylation epic v2</td>
  </tr>
  <tr>
    <td style="border:1px solid black; text-align:left; padding:8px;">miRNA Expression</td>
    <td style="border:1px solid black; text-align:left; padding:8px;">* stem loop</td>
  </tr>
  <tr>
    <td style="border:1px solid black; text-align:left; padding:8px;">Phenotype, clinical, and survival data</td>
    <td style="border:1px solid black; text-align:left; padding:8px;"></td>
  </tr>
</tbody></table>

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