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index_backup.html
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<!-- back-up from before 6/21/2016 before the java-script textbox validation was added-->
<!-- saved from url=(0163)file:///C:/Users/Alexander/Desktop/PSEA-Quant_%20Protein%20set%20enrichment%20analysis%20on%20label-free%20and%20label-based%20protein%20quantification%20data.html -->
<html><head>
<style type="text/css">
.section {
display: none;
}
</style>
<script type="text/javascript">
function loading() {
document.getElementById('loading').style.display="block";
document.getElementById('formDiv').style.display="none";
document.getElementById('numControlReplicates').innerHTML=document.getElementsByName('ControlReplicates')[0].value;
document.getElementById('numDrugReplicates').innerHTML=document.getElementsByName('DrugReplicates')[0].value;
document.getElementById('numOfFractions').innerHTML=document.getElementsByName('fractions')[0].value;
document.getElementById('kValue').innerHTML=document.getElementsByName('kValue')[0].value;
document.getElementById('FDRThreshold').innerHTML=document.getElementsByName('FDRThreshold')[0].value;
document.getElementById('foldChangeThreshold').innerHTML=document.getElementsByName('FoldChange')[0].value;
}
</script>
<meta http-equiv="Content-Type" content="text/html; charset=windows-1252">
<title>TargetSeeker-MS</title>
<style type="text/css"></style></head>
<body>
<table width="100%" cellspacing="0" cellpadding="15">
<tbody>
<tr>
<td width="150">
<a href="http://fields.scripps.edu/">
<img border="0" src="./yateslab_small.gif">
</a>
</td>
<td style="margin:0 auto 0 auto">
</td>
<td width="150">
<a href="http://www.scripps.edu/">
<img border="0" src="./tsrilogo.gif">
</a>
</td>
</tr>
</tbody>
</table>
<table width="100%" cellspacing="0" cellpadding="15" bgcolor="#820004">
<tbody>
<tr>
<td valign="center" nowrap="" align="center">
<h1>
<font class="whitetitle" color="#FFFFFF">TargetSeeker-MS</font>
</h1>
</td>
</tr>
</tbody>
</table>
<!-- <h1 style="text-align: center;">
PSEA-Quant</h1> -->
<br>
<!--enctype="multipart/form-data"-->
<div id="formDiv">
<form method="post" action="http://sealion.scripps.edu:28080/Target_Seeker/TSForm" name="submit" enctype="multipart/form-data">
TargetSneeker-MS is a Bayesian Inference approach for drug target discovery, using protein fractionation coupled to mass spectrometry.<br>
It identifies proteins that are statistically significantly enriched via generating a noise-model using Bayesian Inference, which are measured with high reproducibility across a set of replicates.
<br>
<br>
<!--<br>
More information about TargetSeeker-MS is available <a href="http://pubs.acs.org/doi/abs/10.1021/pr500473n">here.</a>
<br>-->
Sample input and output files are accessible <a href="http://sealion.scripps.edu:28080/Target_Seeker/files/">here.</a>
<!--<br>
<br>
When using TargetSeeker-MS, please cite:<br>
Lavallée-Adam, M., Pelletier, A., Diedrich, J., Low, W., Petrascheck, M., Moresco, J., & Yates, J. R. (2016). <b>TargetSeeker-MS: A Bayesian Inference Approach for Drug Target Discovery using Protein Fractionation Coupled to Mass Spectrometry <br>
</b> <a href="http://pubs.acs.org/doi/abs/10.1021/pr500473n">Journal of proteome research.</a>
<br>
<br>-->
<hr>
<b><font color="#FF0000">Step 1. </font></b>Number of control replicates (at least 4):<br>
<input maxlength="7" name="ControlReplicates" size="2" type="text" value="4"> <br>
<br>
<b><font color="#FF0000">Step 2. </font></b>Number of drug replicates (recommended at least 2):<br>
<input maxlength="7" name="DrugReplicates" size="2" type="text" value="2"> <br>
<br>
<b><font color="#FF0000">Step 3. </font></b>Number of sample fractions per replicate (at least 2):<br>
<input maxlength="7" name="fractions" size="2" type="text" value="10"> <br>
<br>
<b><font color="#FF0000">Step 4. </font></b>Input data in the following tab-separated format (.txt file):<br>
The input file header must start with Protein and follow the following fraction format: xRyFz<br>
Where x is "C" for control replicate or "D" for drug replicate.<br>
Where y is the replicate number.<br>
Where z is the fraction number.<br>
The order of the columns after "Protein" does not need to be in order.<br>
However, each condition must have all replicates (1 to number of replicates) and all fractions (1 to number of fractions).<br>
Example:<br>
<em>Protein CR1F1 CR1F2 CR1F2 ...</em><br>
TO8B1.3 0 0 0<br>
W10C8.5 9 18 36<br>
F45D11.15 0 2 34<br>
<br>
<input type="file" name="file"><br><br>
<b><font color="#FF0000">Step 5. </font></b>k-nearest neighbor smoothing (integer greater than 0):<br>
<input maxlength="7" name="kValue" size="3" type="text" value="20"> <br>
<br>
<b><font color="#FF0000">Step 6. </font></b>False-Discovery Rate threshold (non-negative number less than 1):<br>
<input maxlength="7" name="FDRThreshold" size="5" type="text" value="0.1"> <br>
<br>
<b><font color="#FF0000">Step 7. </font></b>Fold-change threshold (non-negative number):<br>
<input maxlength="7" name="FoldChange" size="5" type="text" value="0.2"> <br>
<br>
<input type="submit" name="submit" value="Submit" onclick="loading()">
<hr>
This website is currently under development. If you encounter any problems, please contact mlaval "at" scripps "dot" edu
<hr width="100%" size="1" noshade="" color="#CCCCCC">
<div class="foot center">
Powered by <b> Yates Bioinformatics Team</b><br>
Copyright @2016 by Yates Lab, Department of Chemical Physiology, The Scripps Research Institute </div>
</em></form></div>
<div id="loading" class="section">
Your Target-Seeker-MS results are being computed. This may take a few minutes. Please wait...
</br>
</br>
</br>
</br>
<center>
<img src="./loading.GIF" height="142" width="142">
</center>
</br>
</br>
</br>
Parameters: </br>
Number of control replicates: <div id="numControlReplicates"></div> </br>
Number of drug replicates: <div id="numDrugReplicates"></div> </br>
Number of fractions: <div id="numOfFractions"></div> </br>
k-value: <div id="kValue"></div> </br>
FDR threshold: <div id="FDRThreshold"></div> </br>
Fold-change threshold: <div id="foldChangeThreshold"></div></br>
</div>
</body></html>