UCSC Treehouse Public Data | Treehouse Childhood Cancer Initiative

<div id="main"> <h1 id="title" class="ui center aligned header">UCSC Treehouse Public Data</h1> <p> The Treehouse Childhood Cancer Initiative is a research arm of the <a href="https://ucscgenomics.soe.ucsc.edu/">UCSC Genomics Institute</a>. We enable the sharing of pediatric cancer genomic data using tools developed by our Genomics Institute colleagues. We use shared data to analyze a child's tumor against both child and adult patient cancer tumors using a "pan cancer" or cross-comparison gene expression analysis. Our goal is to identify situations where an an approved drug, often an adult drug, is predicted to work on a child with cancer. </p> <p> As part of our research, we have gathered a compendium of RNA gene expression data which we have made available for download and visualization. </p> <p> Our samples are derived from partner clinical sites and publicly available repositories, including TARGET and TCGA.  Expression data from over 11,000 samples is available along with clinical data including age, gender, and disease type. </p> <h3>Visualizations</h3> <div class="ui compact segment vizboxes"> <h4>Tumormap</h4> <div class="vizbox"> <a href="https://tumormap.ucsc.edu/help/overview.html"> <img src="https://treehousegenomics.soe.ucsc.edu/wp-content/uploads/2018/04/TumorMap-example-v5April2018-300x138.png"> </a> <p class="ui basic segment"> The <a href="https://tumormap.ucsc.edu/help/overview.html">UCSC TumorMap</a> interactively displays samples in the Treehouse dataset positioned according to their RNA profiles. Users can color the samples based on dataset features like Disease. This browser shows samples clustered using the OpenOrd algorithm and best separates smaller groups. (See  <a href="http://cancerres.aacrjournals.org/content/77/21/e111"> "TumorMap: Exploring the Molecular Similarities of Cancer Samples in an Interactive Portal." </a> Cancer Research November 2017). </p> </div> <h4>Cluster Browser</h4> <div class="vizbox"> <a href="http://tsne.treehouse.gi.ucsc.edu/"> <img src="https://treehousegenomics.soe.ucsc.edu/wp-content/uploads/2017/10/tsne-thped-by-disease-300x136.png"> </a> <p class="ui basic segment"> The UCSC Cluster Browser interactively displays samples in the Treehouse dataset positioned according to their RNA profiles. Users can color the samples based on dataset features like Disease. This browser quickly shows samples clustered using the t-SNE algorithm and best shows relationships among larger groups. </p> </div> <h4>Xena</h4> <div class="vizbox"> <a href="https://xenabrowser.net/heatmap/?bookmark=2ac4e86d1a597ea64de0fc9a7b1782ea"> <img src="https://treehousegenomics.soe.ucsc.edu/wp-content/uploads/2017/10/high-res-xena-screenshot-oct.16.2017-300x136.png"> </a> <p class="ui basic segment"> UCSC Xena allows users to explore the Treehouse dataset, finding correlations and trends within and across genomic and phenotypic variables. Users can interactively add, remove, and rearrange arbitrary slices of data including genes, transcripts and other dataset features.  <a href="https://xenabrowser.net/heatmap/?bookmark=2ac4e86d1a597ea64de0fc9a7b1782ea">This example from our July 2017 dataset</a> shows that neuroblastoma in comparison to other pediatric cancers has a much stronger ALK gene expression and younger patient population. </p> </div> </div> <h3>Files</h3> <p>Three different file types are available.</p> <div class="ui compact segment vizboxes"> <h4>Limited Clinical Data</h4> <div class="vizbox ui basic segment"> Age, gender, and disease are provided for RNASeq samples compiled by the UCSC Treehouse Childhood Cancer Initiative. Samples derived from clinical sites, publicly available repositories, TARGET, and TCGA. </div> <h4>TPM Gene Expression, log<sub>2</sub>-Normalized</h4> <div class="vizbox ui basic segment"> Values in this dataset use HUGO gene names and are TPM, transformed by log<span class="subscript">2</span>(x+1) of the TPM value. </div> <h4>Expected Counts Gene Expression</h4> <div class="vizbox ui basic segment"> Values in this dataset are expected_count and use Ensembl gene IDs.  </div> </div> <h2 id="datasets">Download</h2> <di
v class="ui compact segment vizboxes"> <h3 id="april2018">Compendium v5 Public (April 2018)</h3> <div class="vizbox"> <div> <h4>Visualize</h4> <ul class="ui"> <li><a href="https://tumormap.ucsc.edu/?p=Treehouse/TreehousePEDv5_April2018">Tumormap</a></li> <li><a href="#" class="disabled">Cluster Browser</a> (coming soon)</li> <li><a href="https://xenabrowser.net/datapages/?hub=https://xena.treehouse.gi.ucsc.edu:443">Xena</a></li> </ul> </div><div> <h4>Files</h4> <ul> <li><a href="https://xenabrowser.net/datapages/?dataset=TreehousePEDv5_clinical_metadata.2018-05-09.tsv&host=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443">Clinical Data</a></li> <li><a href="https://xenabrowser.net/datapages/?dataset=TreehousePEDv5_unique_hugo_log2_tpm_plus_1.2018-05-09.tsv&host=https%3A%2F%2Fxena.treehouse.gi.ucsc.edu%3A443">TPM Expression</a></li> <li><a href="#" class="disabled">Expected Counts Expression</a> (coming soon)</li> </ul> </div> </div> This compendium was released in April 2018. It includes a total of 11,258 samples from Treehouse (identifiers start with "TH"), TCGA and TARGET projects.This data was generated by library preparation methods including polyA selection and ribosomal depletion. </div> </div>