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Merge pull request #225 from monarch-initiative/update-tutorial
Update tutorial
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‎docs/_static/genophenocorr.css‎

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‎docs/img/tutorial/tbx5_protein_diagram.png‎

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‎docs/index.rst‎

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=============
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genophenocorr
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=============
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=====
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GPSEA
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=====
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The concept of phenotype denote the observable attributes of an individual, but in
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genetics, the focus is generally placed on the study of whether specific disease-causing alleles are associated with specific phenotypic
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manifestations of the disease.
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`genophenocorr` is a Python package designed to support genotype-phenotype correlation analysis.
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The input to `genophenocorr` is a collection of `Global Alliance for Genomics and Health (GA4GH) Phenopackets <https://pubmed.ncbi.nlm.nih.gov/35705716/>`_.
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`genophenocorr` ingests data from these phenopackets and performs analysis of the correlation of specific variants,
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`GPSEA` (genotypes and phenotypes - study and evaluation of associations) is a Python package designed to support genotype-phenotype correlation analysis.
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We pronounce GPSEA as "G"-"P"-"C". The input to `GPSEA` is a collection of `Global Alliance for Genomics and Health (GA4GH) Phenopackets <https://pubmed.ncbi.nlm.nih.gov/35705716/>`_.
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`gpsea` ingests data from these phenopackets and performs analysis of the correlation of specific variants,
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variant types (e.g., missense vs. premature termination codon), or variant location in protein motifs or other features.
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The phenotypic abnormalities are represented by `Human Phenotype Ontology (HPO) <https://hpo.jax.org/app/>`_ terms.
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Statistical analysis is performed using a `Fisher Exact Test <https://en.wikipedia.org/wiki/Fisher%27s_exact_test>`_,
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Feedback
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--------
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The best place to leave feedback, ask questions, and report bugs is the `genophenocorr Issue Tracker <https://github.com/monarch-initiative/genophenocorr/issues>`_.
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The best place to leave feedback, ask questions, and report bugs is the `GPSEA Issue Tracker <https://github.com/monarch-initiative/genophenocorr/issues>`_.
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.. toctree::
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:caption: Installation & Tutorial
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:name: tutorial
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:name: index-toc
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:maxdepth: 1
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:hidden:
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‎docs/report/tbx5_cohort_info.html‎

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<!DOCTYPE html>
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<html lang="en">
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<head>
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<meta charset="utf-8">
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<title>Cohort</title>
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<style>
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table {
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border-collapse: collapse;
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margin: 25px 0;
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}
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}
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}
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div {
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}
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</style>
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</head>
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<body>
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<h1>genophenocorr cohort analysis</h1>
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<p>Successfully ingested 156 individuals.</p>
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<p>No errors encountered.</p>
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<table>
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<caption style="color: black;">
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<h3>Top 10 HPO Terms</h3>
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A total of 116 HPO terms were used to annotated the cohort.
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</caption>
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<tbody>
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<tr class="strng">
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<th class="lft">HPO Term</th>
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<th>ID</th>
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<th>Seen in <em>n</em> individuals</th>
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</tr>
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<tr>
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<td class="lft">Atrial septal defect</td>
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<td>HP:0001631</td>
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<td>50</td>
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</tr>
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<tr>
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<td class="lft">Ventricular septal defect</td>
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<td>HP:0001629</td>
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<td>41</td>
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</tr>
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<tr>
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<td class="lft">Hypoplasia of the radius</td>
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<td>HP:0002984</td>
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<td>40</td>
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</tr>
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<tr>
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<td class="lft">Triphalangeal thumb</td>
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<td>HP:0001199</td>
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<td>36</td>
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</tr>
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<tr>
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<td class="lft">Absent thumb</td>
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<td>HP:0009777</td>
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<td>32</td>
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</tr>
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<tr>
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<td class="lft">Short thumb</td>
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<td>HP:0009778</td>
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<td>32</td>
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</tr>
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<tr>
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<td class="lft">Abnormal carpal morphology</td>
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<td>HP:0001191</td>
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<td>30</td>
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</tr>
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<tr>
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<td class="lft">Secundum atrial septal defect</td>
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<td>HP:0001684</td>
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<td>27</td>
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</tr>
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<tr>
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<td class="lft">Absent radius</td>
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<td>HP:0003974</td>
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<td>15</td>
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</tr>
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<tr>
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<td class="lft">Cardiac conduction abnormality</td>
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<td>HP:0031546</td>
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<td>14</td>
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</tr>
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</tbody>
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</table>
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<table>
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<caption style="color: black;">
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<h3>Top 10 Variants</h3>
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Variants are shown according to NM_181486.4. A total of 156 unique variants were identified in the cohort.
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</caption>
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<tbody>
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<tr class="strng">
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<th>Count</th>
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<th class="lft">Variant key</th>
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<th>Variant Name</th>
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<th>Protein Variant</th>
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<th>Variant Class</th>
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</tr>
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<tr>
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<td>22</td>
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<td class="lft">12_114385521_114385521_C_T</td>
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<td>c.710G>A</td>
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<td>p.Arg237Gln</td>
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<td>MISSENSE_VARIANT</td>
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</tr>
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<tr>
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<td>20</td>
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<td class="lft">12_114401830_114401830_C_T</td>
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<td>c.238G>A</td>
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<td>p.Gly80Arg</td>
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<td>MISSENSE_VARIANT</td>
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</tr>
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<tr>
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<td>8</td>
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<td class="lft">12_114385563_114385563_G_A</td>
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<td>c.668C>T</td>
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<td>p.Thr223Met</td>
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<td>MISSENSE_VARIANT</td>
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</tr>
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<tr>
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<td>6</td>
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<td class="lft">12_114398675_114398675_G_T</td>
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<td>c.408C>A</td>
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<td>p.Tyr136Ter</td>
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<td>STOP_GAINED</td>
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</tr>
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<tr>
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<td>5</td>
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<td class="lft">12_114398682_114398682_C_CG</td>
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<td>c.400dup</td>
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<td>p.Arg134ProfsTer49</td>
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<td>FRAMESHIFT_VARIANT</td>
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</tr>
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<tr>
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<td>5</td>
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<td class="lft">12_114403792_114403792_C_CG</td>
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<td>c.106_107insC</td>
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<td>p.Ser36ThrfsTer25</td>
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<td>FRAMESHIFT_VARIANT</td>
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</tr>
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<tr>
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<td>5</td>
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<td class="lft">12_114399514_114399514_A_C</td>
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<td>c.361T>G</td>
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<td>p.Trp121Gly</td>
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<td>MISSENSE_VARIANT, SPLICE_REGION_VARIANT</td>
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</tr>
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<tr>
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<td>4</td>
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<td class="lft">12_114385474_114385474_A_G</td>
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<td>c.755+2T>C</td>
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<td>None</td>
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<td>SPLICE_DONOR_VARIANT</td>
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</tr>
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<tr>
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<td>4</td>
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<td class="lft">12_114398656_114398656_C_CG</td>
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<td>c.426dup</td>
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<td>p.Ala143ArgfsTer40</td>
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<td>FRAMESHIFT_VARIANT</td>
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</tr>
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<tr>
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<td>4</td>
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<td class="lft">12_114366360_114366360_C_T</td>
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<td>c.787G>A</td>
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<td>p.Val263Met</td>
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<td>MISSENSE_VARIANT</td>
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</tr>
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</tbody>
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</table>
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<table>
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<caption style="color: black;">
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<h3>Diseases</h3>
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</caption>
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<tbody>
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<tr class="strng">
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<th class="lft">Disease Name</th>
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<th >Disease ID</th>
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<th>Annotation Count</th>
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</tr>
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<tr>
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<td class="lft">Holt-Oram syndrome</td>
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<td>OMIM:142900</td>
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<td>156</td>
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</tr>
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</tbody>
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</table>
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<table>
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<caption style="color: black;">
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<h3>Variant categories for NM_181486.4</h3>
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</caption>
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<tbody>
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<tr class="strng">
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<th class="lft">Variant effect</th>
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<th>Annotation Count</th>
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</tr>
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<tr>
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<td class="lft">FRAMESHIFT_VARIANT</td>
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<td>38</td>
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</tr>
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<tr>
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<td class="lft">MISSENSE_VARIANT</td>
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<td>85</td>
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</tr>
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<tr>
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<td class="lft">STOP_GAINED</td>
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<td>19</td>
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</tr>
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<tr>
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<td class="lft">SPLICE_REGION_VARIANT</td>
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<td>10</td>
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</tr>
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<tr>
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<td class="lft">SPLICE_ACCEPTOR_VARIANT</td>
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<td>2</td>
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</tr>
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<tr>
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<td class="lft">SPLICE_DONOR_VARIANT</td>
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<td>7</td>
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</tr>
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<tr>
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<td class="lft">SPLICE_DONOR_5TH_BASE_VARIANT</td>
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<td>2</td>
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</tr>
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<tr>
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<td class="lft">INTRON_VARIANT</td>
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<td>2</td>
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</tr>
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<tr>
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<td class="lft">INFRAME_INSERTION</td>
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<td>2</td>
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</tr>
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<tr>
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<td class="lft">STOP_RETAINED_VARIANT</td>
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<td>2</td>
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</tr>
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<tr>
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<td class="lft">INFRAME_DELETION</td>
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<td>1</td>
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</tr>
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</tbody>
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</table>
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</body>
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</html>

‎docs/report/tbx5_frameshift_vs_missense.csv‎

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"Genotype group: Missense, Frameshift",Missense,Missense,Frameshift,Frameshift,,
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,Count,Percent,Count,Percent,p value,Corrected p value
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Ventricular septal defect [HP:0001629],31/60,52%,19/19,100%,5.6190936213143254e-05,0.0008990549794102921
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Abnormal atrioventricular conduction [HP:0005150],0/22,0%,3/3,100%,0.00043478260869565214,0.003478260869565217
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Atrioventricular block [HP:0001678],0/22,0%,2/2,100%,0.0036231884057971015,0.014492753623188406
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Heart block [HP:0012722],0/22,0%,2/2,100%,0.0036231884057971015,0.014492753623188406
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Absent thumb [HP:0009777],12/71,17%,14/31,45%,0.005628510156750059,0.018011232501600187
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Patent ductus arteriosus [HP:0001643],3/37,8%,2/2,100%,0.01349527665317139,0.03598740440845704
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Triphalangeal thumb [HP:0001199],13/72,18%,13/32,41%,0.02560162393963452,0.058517997576307476
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Cardiac conduction abnormality [HP:0031546],14/36,39%,3/3,100%,0.07440639019586388,0.14881278039172777
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Secundum atrial septal defect [HP:0001684],14/35,40%,4/22,18%,0.1424522583078588,0.2532484592139712
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Muscular ventricular septal defect [HP:0011623],6/59,10%,6/25,24%,0.1687456462342971,0.2699930339748754
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Pulmonary arterial hypertension [HP:0002092],4/6,67%,0/2,0%,0.42857142857142855,0.6233766233766234
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Hypoplasia of the ulna [HP:0003022],1/12,8%,2/10,20%,0.5714285714285713,0.7619047619047618
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Hypoplasia of the radius [HP:0002984],30/62,48%,6/14,43%,0.7735491022101784,0.9520604334894502
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Absent radius [HP:0003974],7/32,22%,6/25,24%,1.0,1.0
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Short humerus [HP:0005792],7/17,41%,4/9,44%,1.0,1.0
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Atrial septal defect [HP:0001631],42/44,95%,20/20,100%,1.0,1.0

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