{% extends "base.html" %}

{% import "bootstrap/wtf.html" as wtf %}
{% import "bootstrap/fixes.html" as fixes %}
{% import "bootstrap/utils.html" as util %}

{% block title %}Differential Gene Expression Analysis Tutorial{% endblock %}

{% block content %}
    <div class="container">

        <ol class="breadcrumb">
            <li><a href="{{ url_for('help.index') }}">Help</a></li>
            <li class="active">Differential Gene Expression</li>
        </ol>

        {{ util.flashed_messages(dismissible=True, container=False) }}

        <div class="page-header">
            <h1>Differential Gene Expression Analysis Tutorial</h1>
        </div>

        <div class="panel panel-default">
            <div class="panel-body">
                <p>
                    This page outlines the ease in which differential gene expression data can be pre-processed
                    using <a href="http://dx.doi.org/10.1093/nar/gks1193">GEO2R</a>. The example used is series
                    <a href="https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE28146">GSE28146</a> from Blalock <i>et
                    al.</i>.
                </p>

                <h4>Citations</h4>
                <ul>
                    <li>
                        Barrett, T., <i>et al.</i> (2013). <a href="http://dx.doi.org/10.1093/nar/gks1193">NCBI
                        GEO: archive for functional genomics data sets—update</a>. Nucleic Acids Research, 41(D1),
                        D991–D995.
                    </li>
                    <li>
                        Blalock EM, <i>et al.</i> (2011). <a href="https://www.ncbi.nlm.nih.gov/pubmed/21756998">Microarray
                        analyses of laser-captured hippocampus reveal distinct gray and white matter signatures
                        associated with incipient Alzheimer's disease</a>. <i>J Chem Neuroanat</i> Oct;42(2):118-26.
                    </li>
                </ul>
            </div>
        </div>

        <div class="panel panel-default">
            <div class="panel-heading">
                <h3 class="panel-title">Step 1</h3>
            </div>
            <div class="panel-body">
                <p>
                    Visit the link of the dataset. For this tutorial, we will use <a
                        href="https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE28146">https://www.ncbi.nlm.nih.gov/geo/geo2r/?acc=GSE28146</a>
                    from Blalock <i>et al.</i> (2011).
                </p>
            </div>
        </div>

        <div class="panel panel-default">
            <div class="panel-heading">
                <h3 class="panel-title">Step 2</h3>
            </div>
            <div class="panel-body">
                <p>Select the corresponding groups to compare. The following steps must be repeated for each comparison.
                    In this example, GSE28146 is analyzed 3 times to compare experiments with the following labels:</p>
                <ul>
                    <li>Control vs. Incipient</li>
                    <li>Control vs. Moderate</li>
                    <li>Control vs. Severe</li>
                </ul>

                <img class="img-responsive" src="{{ url_for('static', filename='img/dgx_tutorial/1.png') }}"/>
            </div>
        </div>

        <div class="panel panel-default">
            <div class="panel-heading">
                <h3 class="panel-title">Step 3</h3>
            </div>
            <div class="panel-body">
                <p>
                    Scroll down, then click "Top 250" to perform the analysis with the default settings. If you
                    want to change the settings, then click the "Options" tab.
                </p>
                <img class="img-responsive" src="{{ url_for('static', filename='img/dgx_tutorial/2.png') }}"/>
            </div>
        </div>

        <div class="panel panel-default">
            <div class="panel-heading">
                <h3 class="panel-title">Step 4</h3>
            </div>
            <div class="panel-body">
                <p>
                    Wait (about a minute) for the analysis to run. The "Quick Start" box will be replaced with the
                    results; after which you can can select the columns and export. You must minimally
                    select <b>logFC</b> and <b>Gene.symbol</b> to run the <a>heat diffusion workflow</a> in BEL Commons.
                    Finally, click "Save all results".
                </p>
                <img class="img-responsive" src="{{ url_for('static', filename='img/dgx_tutorial/3.png') }}"/>
            </div>
        </div>

        <div class="panel panel-default">
            <div class="panel-heading">
                <h3 class="panel-title">Step 5</h3>
            </div>
            <div class="panel-body">
                <p>
                    As a quality control step, click "Value Distribution" to check for outliers within the groups
                    you have defined.
                </p>
                <img class="img-responsive" src="{{ url_for('static', filename='img/dgx_tutorial/4.png') }}"/>
            </div>
        </div>
    </div>

    {% include "footer.html" %}
{% endblock %}
