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gene-expression.html
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gene-expression.html
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<!DOCTYPE html>
<html>
<head>
<title>MAPP reports</title>
</head>
<body style="background-color: rgb(219, 219, 219)">
<br>
<center>
<img src=mapp_logo.png width="4%">
<h1>MAPP Report</h1>
<h3>Test run with reduced parameters on a sampled dataset</h3>
<br>
<a href="gene-expression.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid #33a02c; background-color: #ffffff">Gene Expression</button>
</a>
<a href="transcript-expression.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Transcript Expression</button>
</a>
<a href="exon-inclusion.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Exon Inclusion Fractions</button>
</a>
<a href="pas-expression.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Poly(A) Site Expressions</button>
</a>
<br>
<br>
<a href="activities-3ss.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">3'SS Activities & Counts</button>
</a>
<a href="activities-5ss.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">5'SS Activities & Counts</button>
</a>
<a href="activities-pas.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">PAS Activities & Counts</button>
</a>
</center>
<br>
<br>
<center>
<div style="width: 50%; text-align: left; border: 2px solid black; background-color: #ffffff; padding: 20px; line-height: 1.5;">
Gene expression has been quantified with the Salmon tool
(<a href="https://www.nature.com/articles/nmeth.4197">Patro R. et al.</a>).
<br>
<br>
Expression scores are stored as Transcripts-per-Milion (TPM) values in a tab-separated format (TSV) table.
Transcript expression was aggregated over all transcripts for a specific gene.
<br>
<br>
Each row in the expression table represents a single, unique gene. The first column
corresponds to a gene ID. Each of the next columns stores TPM values of
a specific RNA-Seq sample, as in the scheme below:
<br>
<br>
<center>
<table border="2" style="border-collapse: collapse;">
<tr>
<th style="text-align: center; padding: 5px;"><b></b></th>
<th style="text-align: center; padding: 5px;"><b>Sample1</b></th>
<th style="text-align: center; padding: 5px;"><b>Sample2</b></th>
<th style="text-align: center; padding: 5px;"><b>...</b></th>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>Gene1</b></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>Gene2</b></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>Gene3</b></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
<tr>
<td style="text-align: center; padding: 5px;"><b>...</b></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
<td style="text-align: center; padding: 5px;"></td>
</tr>
</table>
</center>
</div>
<br>
<a href="report.html" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Main Menu</button>
</a>
<a href="results/quantification-genes.tsv" style="text-decoration: none;">
<button style="width: 180px; height: 40px; border: 2px solid black; background-color: #ffffff">Download Table</button>
</a>
</center>
</body>
</html>