<commit_before><!DOCTYPE html>

<!--
  ~ Copyright 2008-2012 Microarray Informatics Team, EMBL-European Bioinformatics Institute
  ~
  ~ Licensed under the Apache License, Version 2.0 (the "License");
  ~ you may not use this file except in compliance with the License.
  ~ You may obtain a copy of the License at
  ~
  ~ http://www.apache.org/licenses/LICENSE-2.0
  ~
  ~ Unless required by applicable law or agreed to in writing, software
  ~ distributed under the License is distributed on an "AS IS" BASIS,
  ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  ~ See the License for the specific language governing permissions and
  ~ limitations under the License.
  ~
  ~
  ~ For further details of the Gene Expression Atlas project, including source code,
  ~ downloads and documentation, please see:
  ~
  ~ http://gxa.github.com/gxa
  -->

<html>
<head>
    <META HTTP-EQUIV="CACHE-CONTROL" CONTENT="NO-CACHE">
    <META HTTP-EQUIV="PRAGMA" CONTENT="NO-CACHE">
    <title></title>
</head>
<body>

<!--experiment header-->
<div id="experimentAcc">ArrayExpress experiment accession number</div>

<div id="experimentTitle">Experiment title</div>

<!-- request preferences -->
<div id="geneSearch">Enter Ensembl gene ID(s) or gene symbol(s) to search with genes of interest. Separate them
    with new lines or spaces. Leave blank to search all annotated
    genes in this data set.
</div>

<div id="factorSearch">Select tissue(s) to see gene expression profiles for. Leave blank to see expressions in all of
    them.
</div>

<div id="cutoff">Enter a <b>minimum expression level</b> (FPKM) cut-off. Only genes with expression
    above this level will be displayed. The default cut-off is 0.5; if you would like to
    see results for the entire data set, change this to 0.
    FPKM stands for "fragments per kilobase of transcript per million mapped reads", and
    is a normalized measure of expression used in RNA-sequencing analysis.
</div>

<div id="gene-distribution">The histogram shows the number of genes (y-axis) expressed above expression
    level cutoffs (x-axis) for the chosen tissues. You can use it to help you choose a minimum cut-off. Click on a
    bar to select its expression level as the minimum cut-off.
</div>

<div id="toggleHistogramButton">Click this button to toggle display of the histogram showing the distribution of
    expression
    levels.
</div>

<div id="slider">Choose a minimum expression level (FPKM) cut-off using the slider. Only genes with
    expression above this level will be displayed
</div>

<!--experiment -->
<div id="gradient">The colour gradient represents relative expression level: the more saturated the colour, the
    higher the expression level is.
</div>

<div id="anatomogram">Tissues studied in this data set are displayed on the figure. Mouseover a gene in the table
    to highlight the tissue(s) in which it is expressed above the selected minimum expression level. Mouseover tissues
    in the table to highlight them on the figure.
</div>

<div id="heatmapTable">How are the results sorted?
Genes are sorted in order of expression level, from highest to lowest.
* If you did not select any tissues, results are ordered so that genes with expression above the
chosen cut-off in any one tissue are shown first (with highest expression level first), and then genes
with expression above the cutoff in any two tissues, and so on.
* If you selected a set of tissues, results are ordered so that genes with expression above the chosen
cut-off in all your chosen tissues are shown first (with highest expression level first), followed by
genes with expression above the cut-off in all but one of your chosen tissues, followed by genes with
expression in all but two of your tissues, and so on.</div>

<div id="resultInfo">Only the top 50 genes are displayed on this page; please download your results to see them
    all.</div>

<div id="heatMapTableCellInfo">A coloured box indicates the gene is expressed in the
corresponding tissue(s). The colour saturation of the box
indicates the expression level. To see the exact expression level
(FPKM), click on the box, or click the "Display levels" button in
the top-left of the table to see them all. Expression levels greater
than or equal to 1 are rounded to the nearest whole value.
Expression levels less than 1 are rounded to 1 decimal place.</div>

<div id="exp">this is experiment help</div>
</body>
</html><commit_msg>updated help text<commit_after><!DOCTYPE html>

<!--
  ~ Copyright 2008-2012 Microarray Informatics Team, EMBL-European Bioinformatics Institute
  ~
  ~ Licensed under the Apache License, Version 2.0 (the "License");
  ~ you may not use this file except in compliance with the License.
  ~ You may obtain a copy of the License at
  ~
  ~ http://www.apache.org/licenses/LICENSE-2.0
  ~
  ~ Unless required by applicable law or agreed to in writing, software
  ~ distributed under the License is distributed on an "AS IS" BASIS,
  ~ WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
  ~ See the License for the specific language governing permissions and
  ~ limitations under the License.
  ~
  ~
  ~ For further details of the Gene Expression Atlas project, including source code,
  ~ downloads and documentation, please see:
  ~
  ~ http://gxa.github.com/gxa
  -->

<html>
<head>
    <META HTTP-EQUIV="CACHE-CONTROL" CONTENT="NO-CACHE">
    <META HTTP-EQUIV="PRAGMA" CONTENT="NO-CACHE">
    <title></title>
</head>
<body>

<!--experiment header-->
<div id="experimentAcc">ArrayExpress experiment accession number</div>

<div id="experimentTitle">Experiment title</div>

<!-- request preferences -->
<div id="geneSearch">Enter Ensembl gene ID(s) or gene symbol(s) to search with genes of interest. Separate them
    with new lines or spaces. Leave blank to search all annotated genes.
</div>

<div id="factorSearch">Select experimental factor value(s) to see gene expression profiles for. Leave blank to see expressions in all of
    them. Factor values are different experimental conditions, e.g. different tissues or cell types.
</div>

<div id="cutoff">Enter a <b>minimum expression level</b> (FPKM) cutoff. Only genes with expression
    above this level will be displayed. The default cutoff is 0.5; to
    see results for the entire data set, change it to 0.
    FPKM stands for "fragments per kilobase of transcript per million mapped reads", and
    is a normalized measure of gene expression.
</div>

<div id="gene-distribution">The histogram shows the number of genes (y-axis) expressed above expression
    level cutoffs (x-axis) for the chosen factor value(s). You can use it to help decide on a minimum cutoff. Click on a
    bar to select its expression level as the minimum cutoff.
</div>

<div id="toggleHistogramButton">Toggle display of histogram showing the distribution of expression levels.
</div>

<div id="slider">Choose a minimum expression level (FPKM) cutoff using the slider. Only genes with
    expression above this level will be displayed.
</div>

<!--experiment -->
<div id="gradient">The colour gradient represents relative expression level: the more saturated the colour, the
    higher the expression level is.
</div>

<div id="anatomogram">Tissues studied in this data set are displayed on the anatomogram. Mouseover a gene in the table
    to highlight the tissue(s) in which it is expressed above the selected minimum expression level. Mouseover tissues
    in the table to highlight them on the anatomogram.
</div>

<div id="heatmapTable">How are the results sorted?
Genes are sorted in order of expression level, from highest to lowest.
* If you did not select any factor values, results are ordered so that genes with expression above the
chosen cutoff in any one factor value are shown first (with highest expression level first), and then genes
with expression above the cutoff in any two factor values, and so on.
* If you selected a set of factor values, results are ordered so that genes with expression above the chosen
cutoff in all your chosen factor values are shown first (with highest expression level first), followed by
genes with expression above the cutoff in all but one of your chosen factor values, followed by genes with
expression in all but two of your factor values, and so on.</div>

<div id="resultInfo">Only the top 50 genes are displayed on this page; please download your results to see all genes.</div>

<div id="heatMapTableCellInfo">A coloured box indicates the gene is expressed under the
corresponding factor value(s). The colour saturation of the box
indicates relative expression level. To see the exact expression level
(FPKM), click on the box, or click the "Display levels" button in
the top-left of the table to see them all. Expression levels greater
than or equal to 1 are rounded to the nearest whole value.
Expression levels less than 1 are rounded to 1 decimal place.</div>

<div id="exp">this is experiment help</div>
</body>
</html>
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