<commit_before><h1>Baseline Atlas of Gene Expression: Help</h1>



<h2>About Baseline Atlas</h2>
	
<p>Baseline Atlas aims primarily at representing information about which gene
product is present (and at what abundance) in which "normal" condition (e.g.,
tissue, cell type). In the first instance Baseline Atlas will consist of
individual well understood and curated RNA&ndash;seq experiments from <a
	href="http://www.ebi.ac.uk/arrayexpress">ArrayExpress</a>, such as: </p>

<ul>
  <li><a class="externallink" href="http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-513" rel="nofollow" title="http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-513">Illumina Body Map</a></li>
  <li><a class="externallink" href="http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-599" rel="nofollow" title="http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-599">Transcriptome of DBAxC57BL/6J mice</a></li>
  <li><a class="externallink" href="http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26284" rel="nofollow" title="http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26284">RNA&ndash;seq of long coding and long non coding RNAs from ENCODE cell lines</a></li>
  <li><a class="externallink" href="http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30352" rel="nofollow" title="http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30352">RNA&ndash;seq of 6 tissues from 10 species to investigate the evolution of gene expression levels in mammalian organs</a></li>
</ul>

<p>The above experiments have been re&ndash;analyzed using an in&ndash;house RNA&ndash;seq
processing pipeline, ensuring the highest quality of the original data and of
subsequent experiment metadata curation. The resulting data matrix stores gene
expression profiles across the analyzed experimental factor values as a set of
normalized expression levels (<a
	title="FPKM"
	href="http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html">FPKM</a>s).
You can search the data by a combination of genes conditions, experimental
factor values, and a minimum FPKM cutoff. See below for more details on searching.</p>



<h2>Baseline Atlas At a Glance</h2>

<p><img alt="Baseline Atlas Experiment View 'At a Glance'" src="resources/images/help/exptPageHelp.png" align="bottom" /></p>

<p>Some pages have question marks beside some elements. Mouseover these for brief help with the corresponding elements.</p>



<h2>Filtering Baseline Atlas Data</h2>

<p><img alt="filtering" src="resources/images/help/filtering.png" align="bottom" /></p>
<p>Some experiments have <b>more than one</b> experimental variable (factor). For example, in
<a class="externallink"
	href="http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26284"
	rel="nofollow"
	title="http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30352">one experiment</a>,
three different <b>types of RNA</b> were extracted from <b>six cellular components</b> from <b>23
human cell lines</b>. Results for these experiments are limited to a certain
combination of variables, e.g. showing expression of <b>total RNA</b> in the
<b>whole cell</b>. To limit the search results differently, use the "Change
filters" menu. In a 3&ndash;factor experiment, you can choose one value from any two
of the factors, and then search among the values for the remaining factor.
E.g., if you choose to limit to <b>poly(A) RNA</b> extracted from the
<b>cytosol</b>, you can then search among the <b>cell lines</b> for which this
data is available.</p>



<h2>Searching Baseline Atlas</h2>


<h3>Searching by genes</h3>

<p>You can search by <a href="http://ensembl.org">Ensembl</a> gene symbols (e.g. SAA4), identifiers (e.g. ENSG00000148965) or <a title="Ensembl Glossary" href="http://www.ensembl.org/Help/Glossary">biotypes</a> (e.g. protein_coding), <a href="http://www.uniprot.org">UniProt</a> accessions (e.g. P35542), <a href="http://www.geneontology.org">GO</a> ("phosphoglycerate kinase activity") or <a href="http://www.ebi.ac.uk/interpro/">InterPro</a> terms (e.g. phosphatase). A <b>space&ndash;separated</b> list of gene attributes will bring back genes that match <b>at least one</b> of the attributes in the query.</p>


<h3>Searching by experimental factor values</h3>

<p>You can search for any combination of experimental factor (e.g. <i>organism part</i> or <i>cell line</i>) values available:</p>
	
<ul>
	<li>within a <b>single&ndash;factor</b> experiment, e.g. <a href="experiments/E-MTAB-513" title="E-MTAB-513">Illumina Body Map</a><a title="E-MTAB-513" href="experiments/E-MTAB-513">,</a> or</li>
	<li>within a pre&ndash;selected subset of a <b>multi&ndash;factorial</b> experiment, e.g. <a class="externallink" href="experiments/E-GEOD-26284" rel="nofollow" title="E-GEOD-26284">RNA&ndash;seq of long coding and long non coding RNAs from ENCODE cell lines</a></li>
</ul>

<p>When you click on the experiment factor value input box, a dropdown menu appears, containing the list of all factor values available for selection:</p>
<p><img alt="Factor values dropdown" src="resources/images/help/factor_values_dropdown.png" align="bottom" /></p>
<p>Select one or more factor values to search with, or start typing to see suggestions.</p>


<h4><i>Specific</i> vs. <i>non&ndash;specific</i> search</h4>
	
<p>The default Baseline Atlas search reports first genes with more "specific" expression (with the <i>Specific</i> option selected by default). What we mean by this is outlined below:</p>
	
	<ul>
		<li>If the query contains <b>no experimental factor values</b>, the <i>Specific</i> search will report genes expressed in just <b>one</b> experimental factor value, then genes expressed in just <b>two</b> factor values, then three and so on, reporting any genes expressed in all the available factor values at the end of the list of results. Within each group of genes expressed in N factor values only, genes are sorted by the highest average FPKM across the N factor values in which they are expressed.</li>
		<li>If the query contains <b>at least one</b> experimental factor value, the <i>Specific</i> search will promote genes with <b>higher FPKM</b> across the <b>queried</b> factor values, and at the same time penalize genes with the higher FPKM across the <b>non&ndash;queried</b> factor values. In other words, genes with the <b>greatest difference</b> in expression between queried and non&ndash;queried tissues will be pushed towards the top of the list.</li>
  </ul>
  
  <p>If the <i>Specific</i> option is not selected, Baseline Atlas search will ignore specificity of expression when ordering the results. In particular:</p>
 
  <ul>
	  <li>If the query contains <b>no experimental factor values</b>, genes with the highest expression across <b>all</b> factor values will be reported first.</li>
	  <li>If the query contains <b>at least one</b> experimental factor value, genes with higher FPKM across the <b>selected</b> factor values are reported first (expression levels across the non&ndash;selected factor values is <b>ignored</b> in the ordering of results).</li>
  </ul>




<h3>Specifying the minimum expression level</h3>

<p>You can specify a minimum expression level to act as a <b>cutoff</b>, and only genes expressed <b>above</b> this level are displayed. This is to aid distinction between "background noise" and "real" gene expression. Our default FPKM cutoff is 0.5. To change it, enter a new value into the "Expression level cutoff" input box, or drag the slider until the "Expression level cutoff" input box shows your desired cutoff value. A histogram showing the number of genes expressed above a range of cutoffs is also available. This lets you see how many genes you are excluding by selecting a given cutoff. If you see that you're excluding a lot of genes, you may wish to <b>decrease</b> the cutoff. Clicking on the <img alt="Histogram enable/disable button" src="resources/images/help/histogram_btn.png" align="bottom" /> button toggles display of the histogram.</p>

<ul>
	<li>If you have not selected any experimental factors, the histogram shows the number of genes expressed in <b>any</b> factor value for each of the shown cutoffs.</li>
	<li>If you have selected <b>at least one</b> factor value, the histogram shows the number of genes expressed in <b>at least one of the selected factor values</b>, for each of the shown cutoffs.</li>
</ul>



<h2>Heatmap Results Display</h2>

<p>Results for your query (or the default query) are shown in a heatmap table. The heatmap rows and columns are labelled with gene symbols and experimental factor values, respectively. By default, the heatmap shows expressions by <b>colour intensity</b>, according to the gradient legend,<img alt="heatmap colour gradient" src="resources/images/help/gradient.png" align="bottom" />, displayed above the heatmap. Greater colour intensity means higher relative gene expression. To see the exact FPKM for a given gene in a given factor value, click on the corresponding box. To reveal this for all genes, click on the <img alt="Display levels" src="resources/images/help/display_levels.png" align="bottom" /> button. This also reveals minimum and maximum FPKMs on each side of the colour gradient. The gradient shows intensities corresponding to expression levels for the <b>top 50</b> (default) genes currently displayed (rather than all FPKM values for all genes returned by the query).</p>

  <p>When displayed factor values are organism parts, a mouseover action over each heatmap column highlights thus selected tissue in the anatomogram on the left (if available). If the selected organism part is gender&ndash;specifc, and anatomogram is available for each gender (i.e. if you can see the <img alt="Gender selection button" src="resources/images/help/gender_sel.png" align="bottom" /> button), you may need to switch to the gender to which a given tissue applies before seeing it highlighted.</p>



<h2>Anatomogram</h2>

<p>The anatomogram provides an attractive focal point for the tissues studied in a given experiment. As a reciprocal functionality for column mouseover in the heatmap, the mouseover action over tissues visualised in the anatomogram highlights the corresponding column in the heatmap table.</p>



<h2>Downloading Query Results</h2>

<p>Only the <b>top 50</b> genes resulting from your search are displayed on the page by default. Click on the <img alt="Download button" src="resources/images/help/download_button.png" align="bottom" /> button to download the <b>full results</b> of your query in tab&ndash;delimited format with no ordering.</p>



<h2>Experiment Design Page</h2>

<p>The Experiment Design page (e.g. <a title="Illumina Body Map &mdash; Experiment Design page" href="experiments/E-MTAB-513/experiment-design">Illumina Body Map</a>) shows RNA&ndash;seq processing run acessions (from <a href="http://www.ebi.ac.uk/ena/">ENA</a>), along with their coresponding biological sample characteristcs and factor values. You can access it from the experiment page by clicking the <img alt="Experiment Design button" src="resources/images/help/expDes_btn.png" align="bottom" /> button. By default, only the runs used in Baseline Atlas are shown, although the dataset these were taken from may contain more. To see all runs in this dataset, including those not used for Baseline Atlas, uncheck <i>Show Analysed only</i>. You can sort the experiment design table by clicking on a column. To then sort by another column while retaining the ordering of the first column you clicked, hold down the <b>shift</b> key and click another column. The first selected column forms the primary sort order and the shift+click&ndash;ed columns form secondary, tertiary, etc. sort orders in turn.</p>
<p>Please note that a column may be in three states:</p>
  <ol>
    <li>sorted in ascending order <img alt="unsorted arrows" src="resources/images/help/ascArrow.png" align="center" /></li>
    <li>sorted in descending order <img alt="unsorted arrows" src="resources/images/help/descArrow.png" align="center" /></li>
	<li>unsorted <img alt="unsorted arrows" src="resources/images/help/unsortedArrows.png" align="center" /></li>
  </ol>
  <p>In <b>single&ndash;column</b> sort mode (without holding shift), clicking on a column heading jumps between ascending and descending. In <b>multi&ndash;column</b> sort mode (shift+click), clicking on a column heading alternates between ascending, descending and unsorted. If you shift+click a column to sort by it and then wish to undo this, just shift+click it again until the column is unsorted (<img alt="unsorted arrows" src="resources/images/help/unsortedArrows.png" align="center" />).</p>
  
  <p>The experiment design table is also searchable &mdash; entering a keyword automatically selects the subsection of the table that matches the keyword. Click on the <img alt="Download button" src="resources/images/help/download_button.png" align="bottom" /> button on the right&ndash;hand side to download the full results of the current query (with no ordering applied) in tab&ndash;delimited format.</p>



<h2>Analysis Methods Page</h2>

<p>The Analysis Methods page (e.g. <a title="Illumina Body Map &mdash; Analysis Methods page" href="experiments/E-MTAB-513/analysis-methods">Illumina Body Map</a>) lists the data analysis methods applied to the raw experimental data in <a title="FASTQ format" href="http://nar.oxfordjournals.org/content/38/6/1767.full">FASTQ</a> format, in the order in which the methods were applied, to arrive at the gene expression levels shown in Baseline Atlas. You can access it from the experiment page by clicking the <img alt="Analysis Methods button" src="resources/images/help/am_btn.png" align="bottom" /> button.</p>



<h2>Providing Feedback</h2>

<p>Baseline Atlas is still a prototype and thus more then ever we rely and value user feedback on what we are doing right, what does not work or what could be achieved more intuitively. We would also be grateful for any feedback on the analysis methods we have adopted &mdash; we are passionate about not only about intuitive data presentation, the highest level of experimental metadata curation, but also about the quality and biological validity of the expression data presented in Baseline Atlas.</p>

<p>To send us your valuable feedback, please fill in form accessed by clicking on the <i>Feedback</i> link on the top right of Baseline Atlas experiment page:</p>
<p><img alt="Feedback Pop-up" src="resources/images/help/feedback.png" align="bottom" /></p><commit_msg>added externallink class to links in help.html<commit_after><h1>Baseline Atlas of Gene Expression: Help</h1>



<h2>About Baseline Atlas</h2>
	
<p>Baseline Atlas aims primarily at representing information about which gene
product is present (and at what abundance) in which "normal" condition (e.g.,
tissue, cell type). In the first instance Baseline Atlas will consist of
individual well understood and curated RNA&ndash;seq experiments from <a
	href="http://www.ebi.ac.uk/arrayexpress">ArrayExpress</a>, such as: </p>

<ul>
  <li><a class="externallink" href="http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-513" rel="nofollow" title="http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-513">Illumina Body Map</a></li>
  <li><a class="externallink" href="http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-599" rel="nofollow" title="http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-599">Transcriptome of DBAxC57BL/6J mice</a></li>
  <li><a class="externallink" href="http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26284" rel="nofollow" title="http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26284">RNA&ndash;seq of long coding and long non coding RNAs from ENCODE cell lines</a></li>
  <li><a class="externallink" href="http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30352" rel="nofollow" title="http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30352">RNA&ndash;seq of 6 tissues from 10 species to investigate the evolution of gene expression levels in mammalian organs</a></li>
</ul>

<p>The above experiments have been re&ndash;analyzed using an in&ndash;house RNA&ndash;seq
processing pipeline, ensuring the highest quality of the original data and of
subsequent experiment metadata curation. The resulting data matrix stores gene
expression profiles across the analyzed experimental factor values as a set of
normalized expression levels (<a
	class="externallink"
	title="FPKM"
	href="http://www.nature.com/nbt/journal/v28/n5/full/nbt.1621.html">FPKM</a>s).
You can search the data by a combination of genes conditions, experimental
factor values, and a minimum FPKM cutoff. See below for more details on searching.</p>



<h2>Baseline Atlas At a Glance</h2>

<p><img alt="Baseline Atlas Experiment View 'At a Glance'" src="resources/images/help/exptPageHelp.png" align="bottom" /></p>

<p>Some pages have question marks beside some elements. Mouseover these for brief help with the corresponding elements.</p>



<h2>Filtering Baseline Atlas Data</h2>

<p><img alt="filtering" src="resources/images/help/filtering.png" align="bottom" /></p>
<p>Some experiments have <b>more than one</b> experimental variable (factor). For example, in
<a class="externallink"
	href="http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-26284"
	rel="nofollow"
	title="http://www.ebi.ac.uk/arrayexpress/experiments/E-GEOD-30352">one experiment</a>,
three different <b>types of RNA</b> were extracted from <b>six cellular components</b> from <b>23
human cell lines</b>. Results for these experiments are limited to a certain
combination of variables, e.g. showing expression of <b>total RNA</b> in the
<b>whole cell</b>. To limit the search results differently, use the "Change
filters" menu. In a 3&ndash;factor experiment, you can choose one value from any two
of the factors, and then search among the values for the remaining factor.
E.g., if you choose to limit to <b>poly(A) RNA</b> extracted from the
<b>cytosol</b>, you can then search among the <b>cell lines</b> for which this
data is available.</p>



<h2>Searching Baseline Atlas</h2>


<h3>Searching by genes</h3>

<p>You can search by <a class="externallink" href="http://ensembl.org">Ensembl</a> gene symbols (e.g. SAA4), identifiers (e.g. ENSG00000148965) or <a title="Ensembl Glossary" class="externallink" href="http://www.ensembl.org/Help/Glossary">biotypes</a> (e.g. protein_coding), <a class="externallink" href="http://www.uniprot.org">UniProt</a> accessions (e.g. P35542), <a class="externallink" href="http://www.geneontology.org">GO</a> ("phosphoglycerate kinase activity") or <a href="http://www.ebi.ac.uk/interpro/">InterPro</a> terms (e.g. phosphatase). A <b>space&ndash;separated</b> list of gene attributes will bring back genes that match <b>at least one</b> of the attributes in the query.</p>


<h3>Searching by experimental factor values</h3>

<p>You can search for any combination of experimental factor (e.g. <i>organism part</i> or <i>cell line</i>) values available:</p>
	
<ul>
	<li>within a <b>single&ndash;factor</b> experiment, e.g. <a href="experiments/E-MTAB-513" title="E-MTAB-513">Illumina Body Map</a><a title="E-MTAB-513" href="experiments/E-MTAB-513">,</a> or</li>
	<li>within a pre&ndash;selected subset of a <b>multi&ndash;factorial</b> experiment, e.g. <a class="externallink" href="experiments/E-GEOD-26284" rel="nofollow" title="E-GEOD-26284">RNA&ndash;seq of long coding and long non coding RNAs from ENCODE cell lines</a></li>
</ul>

<p>When you click on the experiment factor value input box, a dropdown menu appears, containing the list of all factor values available for selection:</p>
<p><img alt="Factor values dropdown" src="resources/images/help/factor_values_dropdown.png" align="bottom" /></p>
<p>Select one or more factor values to search with, or start typing to see suggestions.</p>


<h4><i>Specific</i> vs. <i>non&ndash;specific</i> search</h4>
	
<p>The default Baseline Atlas search reports first genes with more "specific" expression (with the <i>Specific</i> option selected by default). What we mean by this is outlined below:</p>
	
	<ul>
		<li>If the query contains <b>no experimental factor values</b>, the <i>Specific</i> search will report genes expressed in just <b>one</b> experimental factor value, then genes expressed in just <b>two</b> factor values, then three and so on, reporting any genes expressed in all the available factor values at the end of the list of results. Within each group of genes expressed in N factor values only, genes are sorted by the highest average FPKM across the N factor values in which they are expressed.</li>
		<li>If the query contains <b>at least one</b> experimental factor value, the <i>Specific</i> search will promote genes with <b>higher FPKM</b> across the <b>queried</b> factor values, and at the same time penalize genes with the higher FPKM across the <b>non&ndash;queried</b> factor values. In other words, genes with the <b>greatest difference</b> in expression between queried and non&ndash;queried tissues will be pushed towards the top of the list.</li>
  </ul>
  
  <p>If the <i>Specific</i> option is not selected, Baseline Atlas search will ignore specificity of expression when ordering the results. In particular:</p>
 
  <ul>
	  <li>If the query contains <b>no experimental factor values</b>, genes with the highest expression across <b>all</b> factor values will be reported first.</li>
	  <li>If the query contains <b>at least one</b> experimental factor value, genes with higher FPKM across the <b>selected</b> factor values are reported first (expression levels across the non&ndash;selected factor values is <b>ignored</b> in the ordering of results).</li>
  </ul>




<h3>Specifying the minimum expression level</h3>

<p>You can specify a minimum expression level to act as a <b>cutoff</b>, and only genes expressed <b>above</b> this level are displayed. This is to aid distinction between "background noise" and "real" gene expression. Our default FPKM cutoff is 0.5. To change it, enter a new value into the "Expression level cutoff" input box, or drag the slider until the "Expression level cutoff" input box shows your desired cutoff value. A histogram showing the number of genes expressed above a range of cutoffs is also available. This lets you see how many genes you are excluding by selecting a given cutoff. If you see that you're excluding a lot of genes, you may wish to <b>decrease</b> the cutoff. Clicking on the <img alt="Histogram enable/disable button" src="resources/images/help/histogram_btn.png" align="bottom" /> button toggles display of the histogram.</p>

<ul>
	<li>If you have not selected any experimental factors, the histogram shows the number of genes expressed in <b>any</b> factor value for each of the shown cutoffs.</li>
	<li>If you have selected <b>at least one</b> factor value, the histogram shows the number of genes expressed in <b>at least one of the selected factor values</b>, for each of the shown cutoffs.</li>
</ul>



<h2>Heatmap Results Display</h2>

<p>Results for your query (or the default query) are shown in a heatmap table. The heatmap rows and columns are labelled with gene symbols and experimental factor values, respectively. By default, the heatmap shows expressions by <b>colour intensity</b>, according to the gradient legend,<img alt="heatmap colour gradient" src="resources/images/help/gradient.png" align="bottom" />, displayed above the heatmap. Greater colour intensity means higher relative gene expression. To see the exact FPKM for a given gene in a given factor value, click on the corresponding box. To reveal this for all genes, click on the <img alt="Display levels" src="resources/images/help/display_levels.png" align="bottom" /> button. This also reveals minimum and maximum FPKMs on each side of the colour gradient. The gradient shows intensities corresponding to expression levels for the <b>top 50</b> (default) genes currently displayed (rather than all FPKM values for all genes returned by the query).</p>

  <p>When displayed factor values are organism parts, a mouseover action over each heatmap column highlights thus selected tissue in the anatomogram on the left (if available). If the selected organism part is gender&ndash;specifc, and anatomogram is available for each gender (i.e. if you can see the <img alt="Gender selection button" src="resources/images/help/gender_sel.png" align="bottom" /> button), you may need to switch to the gender to which a given tissue applies before seeing it highlighted.</p>



<h2>Anatomogram</h2>

<p>The anatomogram provides an attractive focal point for the tissues studied in a given experiment. As a reciprocal functionality for column mouseover in the heatmap, the mouseover action over tissues visualised in the anatomogram highlights the corresponding column in the heatmap table.</p>



<h2>Downloading Query Results</h2>

<p>Only the <b>top 50</b> genes resulting from your search are displayed on the page by default. Click on the <img alt="Download button" src="resources/images/help/download_button.png" align="bottom" /> button to download the <b>full results</b> of your query in tab&ndash;delimited format with no ordering.</p>



<h2>Experiment Design Page</h2>

<p>The Experiment Design page (e.g. <a title="Illumina Body Map &mdash; Experiment Design page" href="experiments/E-MTAB-513/experiment-design">Illumina Body Map</a>) shows RNA&ndash;seq processing run acessions (from <a href="http://www.ebi.ac.uk/ena/">ENA</a>), along with their coresponding biological sample characteristcs and factor values. You can access it from the experiment page by clicking the <img alt="Experiment Design button" src="resources/images/help/expDes_btn.png" align="bottom" /> button. By default, only the runs used in Baseline Atlas are shown, although the dataset these were taken from may contain more. To see all runs in this dataset, including those not used for Baseline Atlas, uncheck <i>Show Analysed only</i>. You can sort the experiment design table by clicking on a column. To then sort by another column while retaining the ordering of the first column you clicked, hold down the <b>shift</b> key and click another column. The first selected column forms the primary sort order and the shift+click&ndash;ed columns form secondary, tertiary, etc. sort orders in turn.</p>
<p>Please note that a column may be in three states:</p>
  <ol>
    <li>sorted in ascending order <img alt="unsorted arrows" src="resources/images/help/ascArrow.png" align="center" /></li>
    <li>sorted in descending order <img alt="unsorted arrows" src="resources/images/help/descArrow.png" align="center" /></li>
	<li>unsorted <img alt="unsorted arrows" src="resources/images/help/unsortedArrows.png" align="center" /></li>
  </ol>
  <p>In <b>single&ndash;column</b> sort mode (without holding shift), clicking on a column heading jumps between ascending and descending. In <b>multi&ndash;column</b> sort mode (shift+click), clicking on a column heading alternates between ascending, descending and unsorted. If you shift+click a column to sort by it and then wish to undo this, just shift+click it again until the column is unsorted (<img alt="unsorted arrows" src="resources/images/help/unsortedArrows.png" align="center" />).</p>
  
  <p>The experiment design table is also searchable &mdash; entering a keyword automatically selects the subsection of the table that matches the keyword. Click on the <img alt="Download button" src="resources/images/help/download_button.png" align="bottom" /> button on the right&ndash;hand side to download the full results of the current query (with no ordering applied) in tab&ndash;delimited format.</p>



<h2>Analysis Methods Page</h2>

<p>The Analysis Methods page (e.g. <a title="Illumina Body Map &mdash; Analysis Methods page" href="experiments/E-MTAB-513/analysis-methods">Illumina Body Map</a>) lists the data analysis methods applied to the raw experimental data in <a title="FASTQ format" class="externallink" href="http://nar.oxfordjournals.org/content/38/6/1767.full">FASTQ</a> format, in the order in which the methods were applied, to arrive at the gene expression levels shown in Baseline Atlas. You can access it from the experiment page by clicking the <img alt="Analysis Methods button" src="resources/images/help/am_btn.png" align="bottom" /> button.</p>



<h2>Providing Feedback</h2>

<p>Baseline Atlas is still a prototype and thus more then ever we rely and value user feedback on what we are doing right, what does not work or what could be achieved more intuitively. We would also be grateful for any feedback on the analysis methods we have adopted &mdash; we are passionate about not only about intuitive data presentation, the highest level of experimental metadata curation, but also about the quality and biological validity of the expression data presented in Baseline Atlas.</p>

<p>To send us your valuable feedback, please fill in form accessed by clicking on the <i>Feedback</i> link on the top right of Baseline Atlas experiment page:</p>
<p><img alt="Feedback Pop-up" src="resources/images/help/feedback.png" align="bottom" /></p>
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