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<title>pMHC Data Compendium — Catalog</title>
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<h1>pMHC Data Compendium — Data Catalog</h1>
<p>Harmonized public data for a personalized cancer-vaccine immunogenicity pipeline: epitope–MHC
presentation, immunogenicity labels, thymic &amp; proteomic self references, foreign ligandomes,
and HLA population frequencies. Per-patient cohort data is private and excluded here.</p>
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<div class=kpis><div class="kpi"><div class="kn">15</div><div class="kl">datasets</div></div><div class="kpi"><div class="kn">7,423,658</div><div class="kl">records</div></div><div class="kpi"><div class="kn">5,263,507</div><div class="kl">distinct peptides</div></div><div class="kpi"><div class="kn">16</div><div class="kl">sources</div></div><div class="kpi"><div class="kn">5</div><div class="kl">tissues / origins</div></div><div class="kpi"><div class="kn">5</div><div class="kl">downstream tools</div></div></div>
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<div class=panel><h2>Records by category</h2><div class="bars"><div class="brow"><span class="blab">Immunogenicity</span><span class="btrack"><span class="bfill" style="width:100.0%;background:#c46ad0"></span></span><span class="bval">4,917,562</span></div><div class="brow"><span class="blab">Presentation</span><span class="btrack"><span class="bfill" style="width:45.5%;background:#3b82c4"></span></span><span class="bval">2,127,683</span></div><div class="brow"><span class="blab">Self reference</span><span class="btrack"><span class="bfill" style="width:9.2%;background:#39c5a8"></span></span><span class="bval">266,734</span></div><div class="brow"><span class="blab">Foreign reference</span><span class="btrack"><span class="bfill" style="width:6.0%;background:#e0873a"></span></span><span class="bval">104,508</span></div><div class="brow"><span class="blab">HLA frequencies</span><span class="btrack"><span class="bfill" style="width:4.1%;background:#8a8f98"></span></span><span class="bval">7,171</span></div></div></div>
<div class=panel><h2>Peptide–MHC records by species</h2><div class="bars"><div class="brow"><span class="blab">Human</span><span class="btrack"><span class="bfill" style="width:100.0%;background:#3b82c4"></span></span><span class="bval">7,084,713</span></div><div class="brow"><span class="blab">Mouse</span><span class="btrack"><span class="bfill" style="width:7.9%;background:#e0873a"></span></span><span class="bval">291,226</span></div></div></div>
<div class=panel><h2>Peptide–MHC records by MHC class</h2><div class="bars"><div class="brow"><span class="blab">MHC class I</span><span class="btrack"><span class="bfill" style="width:100.0%;background:#39c5a8"></span></span><span class="bval">6,456,191</span></div><div class="brow"><span class="blab">MHC class II</span><span class="btrack"><span class="bfill" style="width:14.7%;background:#c46ad0"></span></span><span class="bval">717,385</span></div></div></div>
<div class=panel><h2>Records by tissue / origin</h2><div class="bars"><div class="brow"><span class="blab">Tumor</span><span class="btrack"><span class="bfill" style="width:100.0%;background:#6e8bff"></span></span><span class="bval">4,127,087</span></div><div class="brow"><span class="blab">Viral</span><span class="btrack"><span class="bfill" style="width:6.0%;background:#6e8bff"></span></span><span class="bval">88,041</span></div><div class="brow"><span class="blab">Thymus</span><span class="btrack"><span class="bfill" style="width:5.5%;background:#6e8bff"></span></span><span class="bval">64,371</span></div><div class="brow"><span class="blab">Microbial / viral</span><span class="btrack"><span class="bfill" style="width:4.4%;background:#6e8bff"></span></span><span class="bval">16,467</span></div><div class="brow"><span class="blab">Population</span><span class="btrack"><span class="bfill" style="width:4.2%;background:#6e8bff"></span></span><span class="bval">7,171</span></div></div></div>
<div class=panel><h2>Datasets per downstream tool</h2><div class="bars"><div class="brow"><span class="blab">mhcmatch</span><span class="btrack"><span class="bfill" style="width:45.1%;background:#39c5a8"></span></span><span class="bval">3 ds</span></div><div class="brow"><span class="blab">ipred</span><span class="btrack"><span class="bfill" style="width:31.4%;background:#39c5a8"></span></span><span class="bval">2 ds</span></div><div class="brow"><span class="blab">public-epitope</span><span class="btrack"><span class="bfill" style="width:17.7%;background:#39c5a8"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">seqtree</span><span class="btrack"><span class="bfill" style="width:100.0%;background:#39c5a8"></span></span><span class="bval">7 ds</span></div><div class="brow"><span class="blab">model</span><span class="btrack"><span class="bfill" style="width:58.9%;background:#39c5a8"></span></span><span class="bval">4 ds</span></div></div></div>
<div class=panel><h2>Datasets per source</h2><div class="bars"><div class="brow"><span class="blab">IEDB</span><span class="btrack"><span class="bfill" style="width:100.0%;background:#8a8f98"></span></span><span class="bval">4 ds</span></div><div class="brow"><span class="blab">UniProt</span><span class="btrack"><span class="bfill" style="width:76.0%;background:#8a8f98"></span></span><span class="bval">3 ds</span></div><div class="brow"><span class="blab">NCI</span><span class="btrack"><span class="bfill" style="width:52.0%;background:#8a8f98"></span></span><span class="bval">2 ds</span></div><div class="brow"><span class="blab">HLA Ligand Atlas</span><span class="btrack"><span class="bfill" style="width:52.0%;background:#8a8f98"></span></span><span class="bval">2 ds</span></div><div class="brow"><span class="blab">TESLA</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">CEDAR</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">Gfeller</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">ITSNdb</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">GBM</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">VACCIMEL</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">Bjerregaard</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">TCGA</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">AFND</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">HPA</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">GSE272406</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div><div class="brow"><span class="blab">tsarina</span><span class="btrack"><span class="bfill" style="width:28.0%;background:#8a8f98"></span></span><span class="bval">1 ds</span></div></div></div>
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<div class=tablewrap><table>
<thead><tr><th>Dataset</th><th>Category</th><th>Species</th><th>MHC</th><th>Records</th>
<th>Distinct&nbsp;peptides</th><th>Tissue</th><th>Source</th><th>Feeds</th></tr></thead>
<tbody><tr><td><span class="dot" style="background:#3b82c4"></span>IEDB epitope–MHC</td><td>Presentation</td><td>human+mouse</td><td>I+II</td><td class=num>1,482,188</td><td class=num>689,421</td><td>—</td><td class=src>IEDB</td><td class=src>mhcmatch</td></tr><tr><td><span class="dot" style="background:#3b82c4"></span>IEDB epitope–MHC (≥2 refs)</td><td>Presentation</td><td>human+mouse</td><td>I+II</td><td class=num>645,102</td><td class=num>174,821</td><td>—</td><td class=src>IEDB</td><td class=src>mhcmatch</td></tr><tr><td><span class="dot" style="background:#c46ad0"></span>IEDB immunogenicity</td><td>Immunogenicity</td><td>human+mouse</td><td>I+II</td><td class=num>790,868</td><td class=num>516,092</td><td>—</td><td class=src>IEDB</td><td class=src>ipred, public-epitope</td></tr><tr><td><span class="dot" style="background:#c46ad0"></span>Neoantigens — tested</td><td>Immunogenicity</td><td>human</td><td>I+II</td><td class=num>525,989</td><td class=num>491,495</td><td>Tumor</td><td class=src>TESLA, NCI, CEDAR, Gfeller, ITSNdb, GBM, VACCIMEL, Bjerregaard</td><td class=src>model, ipred</td></tr><tr><td><span class="dot" style="background:#c46ad0"></span>Neoantigens — candidates</td><td>Immunogenicity</td><td>human</td><td>I</td><td class=num>1,355,926</td><td class=num>1,344,070</td><td>Tumor</td><td class=src>NCI</td><td class=src>model</td></tr><tr><td><span class="dot" style="background:#c46ad0"></span>TCGA neoantigens</td><td>Immunogenicity</td><td>human</td><td>I</td><td class=num>2,244,779</td><td class=num>1,948,737</td><td>Tumor</td><td class=src>TCGA</td><td class=src>model</td></tr><tr><td><span class="dot" style="background:#8a8f98"></span>HLA population freqs</td><td>HLA frequencies</td><td>—</td><td>—</td><td class=num>7,171</td><td class=num>—</td><td>Population</td><td class=src>AFND</td><td class=src>model</td></tr><tr><td><span class="dot" style="background:#39c5a8"></span>Thymus self-peptidome</td><td>Self reference</td><td>human</td><td>I+II</td><td class=num>53,878</td><td class=num>53,878</td><td>Thymus</td><td class=src>HLA Ligand Atlas</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#39c5a8"></span>Thymus expression</td><td>Self reference</td><td>—</td><td>—</td><td class=num>10,493</td><td class=num>—</td><td>Thymus</td><td class=src>HPA, HLA Ligand Atlas</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#39c5a8"></span>Human proteome</td><td>Self reference</td><td>human</td><td>—</td><td class=num>147,506</td><td class=num>—</td><td>—</td><td class=src>UniProt</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#39c5a8"></span>Mouse proteome</td><td>Self reference</td><td>mouse</td><td>—</td><td class=num>54,857</td><td class=num>—</td><td>—</td><td class=src>UniProt</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#e0873a"></span>Bacterial + viral proteomes</td><td>Foreign reference</td><td>foreign</td><td>—</td><td class=num>16,467</td><td class=num>—</td><td>Microbial / viral</td><td class=src>UniProt</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#e0873a"></span>Viral ligandome (IEDB)</td><td>Foreign reference</td><td>human+mouse</td><td>I+II</td><td class=num>82,368</td><td class=num>44,993</td><td>Viral</td><td class=src>IEDB</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#e0873a"></span>Pan-viral ORFs (GSE272406)</td><td>Foreign reference</td><td>—</td><td>—</td><td class=num>5,673</td><td class=num>—</td><td>Viral</td><td class=src>GSE272406</td><td class=src>seqtree</td></tr><tr><td><span class="dot" style="background:#3b82c4"></span>Cancer-testis antigens</td><td>Presentation</td><td>—</td><td>—</td><td class=num>393</td><td class=num>—</td><td>Tumor</td><td class=src>tsarina</td><td class=src>mhcmatch</td></tr></tbody></table></div>
<footer>
Generated by <code>pipeline/build_catalog.py</code> from the public compendium.
Immunopeptidome self-reference (thymus) from the HLA Ligand Atlas (Marcu&nbsp;2021, CC-BY&nbsp;4.0);
proteomes from UniProt; HLA frequencies from AFND. See <code>DESCRIPTION.md</code> for provenance.
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