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<div class='center1'>Framework for Inference of Regulation by miRNAs (FIRM)</div>
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<p>By integrating the three best performing algorithms to infer miRNA mediate regulation from co-expression signatures we have constructed a generalizable Framework for Inference of Regulation by miRNAs (FIRM). FIRM is available as a Python script capable of identifying putative miRNA mediated regulation from transcriptome co-expression signatures.</p>
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<div class='center1'>FIRM Dependencies</div>
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<p>FIRM was developed in Linux, but by ensuring the following dependencies are met could be modified to work in Windows. In order to function properly this script requires:
<ol>
<li><b>Python 2.6 or greater (but less than 3.X)</b> - the lastest python can be downloaded <a href='http://www.python.org/download/' target='_blank'>here</a>.</li>
<li><b>R</b> - the lastest R can be found <a href='http://cran.r-project.org/' target='_blank'>here</a>.</li>
<li><b>Weeder</b> - the lastest Weeder can be found <a href='http://159.149.109.9/modtools/downloads/weeder.html' target='_blank'>here</a>. The paths of this must be configured to identify the location of the frequency files packaged with FIRM. A successful installation of Weeder will allow a user to type 'weederlauncher' at the command line and will run the 'weederlauncher.out' program from Weeder 1.4.2.</li>
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<div class='center1'>Download FIRM</div>
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<p>We provide FIRM as a tarred and gzipped file:
<ul>
<li><a href='/static/firm/FIRM.tgz'>Download FIRM.tgz (16.5MB)</a></li>
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Once downloaded navigate a Linux command prompt to the directory containing the file and run:
<pre> prompt> tar xvzf FIRM.tgz</pre>
Here is a brief description of the files and folders in the FIRM directory:
<pre> prompt> ls FIRM
FIRM.py TargetPredictionDatabases common exp miRvestigator.py pssm.py weeder_FreqFiles</pre>
<ul>
<li><b>FIRM.py</b> - is the script to run the analysis.</li>
<li><b>TargetPredictionDatabases</b> - directory containing the target prediction databases PITA and TargetScan.</li>
<li><b>common</b> - directory containing general files needed to run the analysis.</li>
<li><b>exp</b> - directory where you should put your co-expression signatures files that are to be analyzed. The files should look like this:
<pre> Gene Group
NM_000014 32
NM_000015 23
...</pre>
This file is expected to have a header. It has two columns:
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<li>RefSeq Transcript ID</li>
<li>Co-expression signature number</li>
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</li>
<li><b>miRvestigator.py</b> - python module of the miRvestiagtor analysis script.</li>
<li><b>pssm.py</b> - python module to be a container for PSSM objects.</li>
<li><b>weeder_FreqFiles</b> - the Weeder frequence files that should be placed in the appropriate FreqFile location as determined by the way Weeder was installed.</li>
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<div class='center1'>Installing and Running FIRM</div>
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<p>If the dependencies above are met then to run FIRM will simply require the user to create the appropriate co-expression signature files and place them in the 'exp' directory. Then the analysis can be started by typing:
<pre> prompt> python FIRM.py</pre>
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<div class='center1'>Interpreting Results from FIRM</div>
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<p>FIRM limits the Weeder-miRvestigator method to only those inferences of miRNA mediated regulation with a perfect 7- or 8-mer miRvestigator complementarity p-value (p-value = 6.1 x 10<sup>-5</sup> or 1.5 x 10<sup>-5</sup>, respectively) to a miRNA seed in miRBase. Inferences of miRNA mediated regulation from the PITA and TargetScan enrichment of predicted miRNA target genes methods were filtered to include only those with Benjamini-Hochberg FDR = 0.001 and at least 10% of genes had a predicted miRNA binding site. After FIRM finished running it will produce a file 'combinedResults.csv' in the main FIRM directory. For the This file will contain a listing of all co-expression signatures that were predicted to be regualted by a miRNA. The column headings are:
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<li><b>Dataset</b> - the dataset where the co-expression signature was observed.</li>
<li><b>signature</b> - nubmer for the co-expression signature.</li>
<li><b>miRvestigator.miRNA</b> - miRvestigator predicted miRNA(s).</li>
<li><b>miRvestigator.model</b> - model that fit the miRNA to the PSSM found through Weeder, either 7mer or 8mer.</li>
<li><b>miRvestigator.mature_seq_ids</b> - the miRBase mature sequence IDs for the predicted miRNAs.</li>
<li><b>PITA.miRNA</b> - PITA predicted mirna(s)</li>
<li><b>PITA.percent_targets</b> - percent of co-expression cluster genes with predicted target sites in PITA.</li>
<li><b>PITA.P_Value</b> - p-value for the hypergeometric enrichment of miRNA(s).</li>
<li><b>PITA.mature_seq_ids</b> - the miRBase mature sequence IDs for the predicted miRNAs.</li>
<li><b>TargetScan.miRNA</b> - TargetScan predicted mirna(s)</li>
<li><b>TargetScan.percent_targets</b> - percent of co-expression cluster genes with predicted target sites in TargetScan.</li>
<li><b>TargetScan.P_Value</b> - p-value for the hypergeometric enrichment of miRNA(s).</li>
<li><b>TargetScan.mature_seq_ids</b> - the miRBase mature sequence IDs for the predicted miRNAs.</li>
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