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<div class="main">
<div class="col-xs-3 options">
<div class="form-horizontal section-form-div">
<div class="form-group">
<label for="corr_type" class="col-xs-2 control-label">Method</label>
<div class="col-xs-3 controls">
<select name="corr_type" class="form-control">
<option value="sample">Sample r</option>
{% if dataset.type == 'ProbeSet' %}
<option value="lit">Literature r</option>
<option value="tissue">Tissue r</option>
{% endif %}
</select>
</div>
</div>
<div class="form-group">
<label for="corr_dataset" class="col-xs-2 control-label">Database</label>
<div class="col-xs-10 controls">
<select name="corr_dataset" class="form-control">
{% for tissue in corr_tools.dataset_menu %}
{% if tissue.tissue %}
<optgroup label="{{ tissue.tissue }} ------">
{% endif %}
{% for dataset in tissue.datasets %}
<option data-type="{% if tissue.tissue %}mrna_assay{% elif dataset[1][-4:] == 'Geno' %}geno{% else %}pheno{% endif %}" value="{{ dataset[1] }}"
{% if corr_tools.dataset_menu_selected == dataset[1] %}
selected
{% endif %}>
{{ dataset[0] }}
</option>
{% endfor %}
{% if tissue.tissue %}
</optgroup>
{% endif %}
{% endfor %}
</select>
</div>
</div>
<div class="form-group">
<label for="corr_return_results" class="col-xs-2 control-label">Limit to</label>
<div class="col-xs-4 controls">
<select name="corr_return_results" class="form-control">
{% for return_result in corr_tools.return_results_menu %}
<option value="{{ return_result }}"
{% if corr_tools.return_results_menu_selected == return_result %}
selected
{% endif %}>
Top {{ return_result }}
</option>
{% endfor %}
</select>
</div>
</div>
<div class="form-group">
<label for="corr_samples_group" class="col-xs-2 control-label">Samples</label>
<div class="col-xs-4 controls">
<select name="corr_samples_group" class="form-control">
{% for group, pretty_group in sample_group_types.items() %}
<option value="{{ group }}">{{ pretty_group }}</option>
{% endfor %}
</select>
</div>
</div>
<div id="corr_sample_method" class="form-group">
<label for="corr_sample_method" class="col-xs-2 control-label">Type</label>
<div class="col-xs-4 controls">
<select name="corr_sample_method" class="form-control">
<option value="pearson">Pearson</option>
<option value="spearman">Spearman Rank</option>
</select>
</div>
</div>
<div id="min_expr_filter" class="form-group" style="display: {% if dataset.type != 'Geno' %}block{% else %}none{% endif %};">
<label class="col-xs-2 control-label">Min Expr</label>
<div class="col-xs-4 controls">
<input name="min_expr" value="" type="text" class="form-control min-expr-field">
</div>
</div>
<div class="form-group">
<label for="location_type" class="col-xs-2 control-label">Location Type</label>
<div class="col-xs-4 controls">
<select name="location_type" class="form-control">
<option value="gene" {% if dataset.type == 'Publish' %}disabled{% endif %}>Gene</option>
<option value="highest_lod">Highest LOD</option>
</select>
</div>
</div>
<div id="location_filter" class="form-group">
<label class="col-xs-2 control-label">Location</label>
<div class="col-xs-10 controls">
<span>
Chr: <input name="loc_chr" value="" type="text" class="form-control corr-location">
Mb: <input name="min_loc_mb" value="" type="text" class="form-control corr-location"> to <input name="max_loc_mb" value="" type="text" class="form-control corr-location">
</span>
<br>
</div>
</div>
<div class="form-group">
<label class="col-xs-2 control-label">Range</label>
<div class="col-xs-5 controls">
<input name="p_range_lower" value="" type="hidden">
<input name="p_range_upper" value="" type="hidden">
<span class="inline-div">
<div id="p_range_slider" class="p-range-slider"></div>
<span id="p_range_lower" class="p-range-lower"></span>
<span id="p_range_upper" class="p-range-upper"></span>
</span>
</div>
</div>
<div class="form-group">
<label class="col-xs-2 control-label" >Use Cache</label>
<div class="col-xs-5 controls">
<input id="use_cache" name="use_cache" type="checkbox" checked>
</div>
</div>
<div class="form-group">
<label for="corr_sample_method" class="col-xs-2 control-label"></label>
<div class="col-xs-3 controls">
<input type="button" class="btn corr_compute submit_special btn-success" data-url="/corr_compute" title="Compute Correlation" value="Compute">
</div>
</div>
</div>
</div>
<div class="descriptions">
<div class="section-form-div">
<dl>
<dt class="map-method-text">Sample Correlation</dt>
<dd>The <a href="http://genenetwork.org/correlationAnnotation.html#genetic_r">Sample Correlation</a>
is computed
between trait data and any
other traits in the sample database selected above. Use
<a href="{{ url_for('gn_docs_blueprint.glossary') }}#Correlations">Spearman
Rank</a>
when the sample size is small (<20) or when there are influential outliers.</dd>
<dt class="map-method-text">Literature Correlation</dt>
<dd>The <a href="http://genenetwork.org/correlationAnnotation.html#literatureCorr">Literature Correlation</a>
(Lit r) between
this gene and all other genes is computed<br>
using the <span class="broken_link" href="https://grits.eecs.utk.edu/sgo/sgo.html">
Semantic Gene Organizer</span>
and human, rat, and mouse data from PubMed.
Values are ranked by Lit r, but Sample r and Tissue r are also displayed.<br>
<a href="{{ url_for('gn_docs_blueprint.glossary') }}#Literature">More on using Lit r</a></dd>
<dt class="map-method-text">Tissue Correlation</dt>
<dd>The <a href="http://genenetwork.org/webqtl/main.py?FormID=tissueCorrelation">Tissue Correlation</a>
(Tissue r)
estimates the similarity of expression of two genes
or transcripts across different cells, tissues, or organs
(<a href="http://genenetwork.org/correlationAnnotation.html#tissueCorr">glossary</a>).
Tissue correlations
are generated by analyzing expression in multiple samples usually taken from single cases.<br>
<strong>Pearson</strong> and <strong>Spearman Rank</strong> correlations have been
computed for all pairs of genes using data from mouse samples.<br></dd>
</dl>
</div>
</div>
</div>
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