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help.html
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<!DOCTYPE html>
<html>
<head>
<meta charset="UTF-8">
<title>Help - MDPD</title>
<link rel = "stylesheet" type = "text/css" href = "css/main.css" />
<link rel = "stylesheet" type = "text/css" href = "css/browse.css" />
<script type = "text/javascript" src = "js/browse.js"></script>
<style>
body{
background-color: #ffffff;
}
p{
font-size: 1.2em;
}
img{
max-width: 100%;
width: auto;
}
</style>
</head>
<body>
<div class = "section_header">
<center><p class="title">MDPD - Microbiome Database of Pulmonary Diseases</p></center>
</div>
<div class = "section_menu">
<center>
<table cellpadding="3px">
<tr class="nav">
<td class="nav"><a href="index.php" class="side_nav">Home</a></td>
<td class="nav"><a href="browse.php" class="side_nav">Browse</a></td>
<td class="nav"><a href="statistics.php" class="side_nav">Statistics</a></td>
<td class="nav"><a href="about.php" class="side_nav">About</a></td>
<td class="nav"><a href="#" class="active">Help</a></td>
<td class="nav"><a href="team.html" class="side_nav">Team</a></td>
</tr>
</table>
</center>
</div>
<div class = "section_middle">
<ol type="1">
<li>
<p>The <b>Search Option</b> on the home page allows users to query the database with specific
keywords for <i>Disease</i>, <i>Assay type</i>, <i>Country</i>, <i>Isolation source</i>,
<i>Instrument</i> and <i>Year</i>.</p>
<center><img src="resource/search.jpg" height="300px" /></center>
<ol type="A">
<li>
<p>The <b>search result page</b> provides information about the Run ID, BioProject ID,
SRA Study ID, Disease, Disease Sub-group, Isolation Source, Instrument, Assay Type,
Country, and Year. The table displayed in the search result can be downloaded in CSV
format by clicking on the <i>"Download table"</i> button located at the top of the
page.</p>
<center><img src="resource/search_result.jpg" height="400px" /></center>
</li>
<li>
<p>The <b>Run page</b> gives the information of the Experiment ID, BioSample ID, Average
Spot Length, Number of Bases, Center Name, Biome, and Therapeutics. The link beneath
the title leads to NCBI SRA page and BioProject ID links to <b>BioProject page</b> in MDPD.</p>
<center><img src="resource/run_page.jpg" height="400px" /></center>
</li>
<li>
<p>The <b>BioProject page</b> shows the information related to the study and the total number of
runs of the BioProject. If subgroups are present for the study, then a plot of differential
taxa can be visualized as LDA plot. Taxonomic profiles can be visualized with Krona plots for
group or subgroup. The Run ID(s) link to the <b>Run page</b> and the link just beneath the title
leads to the NCBI BioProject page.</p>
<center><img src="resource/bioproject_page.jpg" height="500px" /></center>
</li>
<li>
<p>The <b>LDA (Linear Discriminant Analysis) plot</b> provides information about the
differential biomarkers (genus for amplicon; and species for WMS). The horizontal
bars represent the genus/species and the length of the bar denotes the LDA score
(log<sub>10</sub>). LDA score signifies the effect size of each differentially
abundant microbe. A cut-off of <i>log<sub>10</sub> LDA ≥ 2</i> was chosen for
making the plot. The Kruskal-Wallis cutoff <i>p-value < 0.01</i> was chosen. The
LDA plot can be downloaded as a SVG image by clicking on the <i>"Export as SVG"</i>
<svg xmlns="http://www.w3.org/2000/svg" height="1em" viewBox="0 0 512 512">
<path d="M288 32c0-17.7-14.3-32-32-32s-32 14.3-32 32V274.7l-73.4-73.4c-12.5-12.5-32.8-12.5-45.3 0s-12.5 32.8 0 45.3l128 128c12.5 12.5 32.8 12.5 45.3 0l128-128c12.5-12.5 12.5-32.8 0-45.3s-32.8-12.5-45.3 0L288 274.7V32zM64 352c-35.3 0-64 28.7-64 64v32c0 35.3 28.7 64 64 64H448c35.3 0 64-28.7 64-64V416c0-35.3-28.7-64-64-64H346.5l-45.3 45.3c-25 25-65.5 25-90.5 0L165.5 352H64zm368 56a24 24 0 1 1 0 48 24 24 0 1 1 0-48z"/>
</svg>
button in the menubar located at the top right corner of the plot.
<center><img src="resource/lda.jpg" height="650px" /></center>
</li>
<li>
<p>The taxonomic composition of microbiome data of different isolation sources of lung
conditions can be visualized by Krona plots. Two types of Krona plots are present in the
database, (i) for merged sequence runs and (ii) for each sequence runs. The hierarchical
taxonomic classification can be visualized with this plot with genus/species at the outer
ring and the inner ring denoting the domains. The color gradient shows the abundant taxa
(red) and green denotes the least abundant taxa.<br/>
For a better view, see the plot at <i>"max depth = 6"</i> for amplicon (genus) and
<i>"max depth = 7"</i> for WGS (species). The Krona plot can be downloaded as a SVG image
using the <i>"Snapshot"</i> button located at the upper left corner of the plot.
<table style="width:100%;">
<tr>
<td style="width:48%; margin:0 1% 0 1%;">(a)</td>
<td style="width:48%; margin:0 1% 0 1%;">(b)</td>
</tr>
</table>
<table>
<tr>
<td style="width:48%; margin:0 1% 0 1%;"><center><img src="resource/krona_merged.jpg" width="100%" /></center></td>
<td style="width:48%; margin:0 1% 0 1%;"><center><img src="resource/krona_runwise.jpg" width="100%" /></center></td>
</tr>
</table>
</li>
</ol>
</li>
<li>
<p>The browse page of MDPD has five sections.</p>
<ol type="A">
<li>
<p>The first section provides information about the <b>Disease-wise BioProjects</b>.</p>
<center><img src="resource/disease_wise_bioprojects.jpg" height="300px" /></center>
<p>Click any one of the diseases to view the list of BioProjects associated with the study.
Click one BioProject to go to the <b>BioProject page</b>.</p>
<center><img src="resource/disease_wise_bioprojects_1.jpg" height="400px" /></center>
<p>Click the checkbox to show only BioProjects with Healthy/Control.</p>
<center><img src="resource/disease_wise_bioprojects_2.jpg" height="400px" /></center>
</li>
<li>
<p>The second section provides information about the <b>Disease subgroup-wise BioProjects</b>.</p>
<center><img src="resource/subgroup_wise_bioprojects_1.jpg" height="300px" /></center>
<p>Click any one of the disease subgroups to view the list of BioProjects associated with
the study. Click one BioProject to go to the BioProject page.</p>
<center><img src="resource/subgroup_wise_bioprojects_2.jpg" height="300px" /></center>
</li>
<li>
<p>The third section provides the facility of <b>visualizing the taxonomic profile</b> of
the microbiome across different isolation sources of the lung conditions using a <b>Krona
plot</b>.</p>
<center><img src="resource/krona_table.jpg" height="500px" /></center>
</li>
<li>
<p>The fourth section enables the users to obtain the list of <b>shared prevalent taxa
between lung and gut microbiomes</b> of different lung conditions. The isolation sources
with the highest number of runs for lung and gut were taken for this analysis. Click
<b>"Get result"</b> to view the shared microbes plot.
<center><img src="resource/similarity_table.jpg" height="400px" /></center>
<p>The <b>UpSet plot</b> shows the number of organisms that are found in the lungs, gut,
and microbiomes. The <b>Likert plot</b> (diverging bar plot) depicts the prevalence of
the organisms that are found in both lung and gut microbiomes. A <i>prevalence cut-off</i>
of 50% at a <i>detection level ≥ 0.0001</i> was taken to get the prevalent taxa. The
UpSet plot can be downloaded as a SVG image by clicking on the <i>"Download UpSet plot"</i>
button located at the top of the page. The Likert plot can be downloaded as a SVG image by
clicking on the <i>"Download Likert plot"</i> button located at the top of the page.</p>
<center><img src="resource/similarity_figure.jpg" height="500px" /></center>
</li>
<li>
<p>The fifth section provides the facility to obtain the set of <b>differentially abundant
taxa between a pair of lung conditions </b>. The analyses were done on the isolation sources
where the data is available for both conditions. Click any button <b>"Show"</b> to view the
associated pair.</p>
<center><img src="resource/lda_disease_pair_table.jpg" height="500px" /></center>
<p>Users can obtain the LDA plot (horizontal bar plot) by clicking the <b>"Get LDA plot"</b>
to see the differentially abundant taxa for the pair of lung conditions/groups (cut-off
<i>log<sub>10</sub> LDA ≥ 2</i>). With the <b>"Get heatmap"</b> option users can get the
most abundant taxa (cut-off <i>log<sub>10</sub> LDA ≥ 3</i>) for the disease pair and the
BioProjects as the source of marker taxa.</p>
<center><img src="resource/heatmap.jpg" height="450px" /></center>
<p>There are few buttons to modify the plot.</p>
<center><img src="resource/symbols.jpg" height="250px" /></center>
</li>
</ol>
</li>
</ol>
<br/><hr/>
<p style="font-size:0.9em;text-align:center;">
© 2023 Bose Institute. All rights reserved. For queries, please contact Dr. Sudipto Saha
(<a style="color:#003325;" href="mailto:[email protected]">[email protected]</a>,
<a style="color:#003325;" href="mailto:[email protected]">[email protected]</a>).
</p>
</div>
</body>
</html>