• January 7, 2016
  • N/A

PPL Finder

The continuing discovery of new functions and classes of small non-coding RNAs is suggesting the presence of regulatory mechanisms far more complex than the ones identified so far. In our computational analysis of a large set of public available databases, we found statistical evidence of an inter-pathway regulatory motif, not previously described, that reveals a new protective role miRNAs may play in the successful activation of a pathway. We named this motif Pathway Protection Loop.

This tool provides the Bioinformatics PHP-MySQL pipeline used to integrate pathway and Micronome related data in order to search for miRNA mediated interactions at the pathway level, thus searching for the existence of PPLs.

Developers

Gianfranco Politano
Stefano_DiCarlo_1
Stefano Di Carlo

How to cite PPL Finder

The TestGroup development team  has invested a lot of time and effort in creating PPL Finder as it is today. Please give credit where credit is due and cite PPL Finder when you use it for your research activities.

PPL Finder can be cited through this papers:

Di Carlo, Stefano and Politano, Gianfranco and Savino, Alessandro and Benso, Alfredo “A systematic analysis of a mi-RNA inter-pathway regulatory motif.” Journal of clinical bioinformatics 3.1 (2013): 1. 10.1186/2043-9113-3-20

BibTEX

@Article{DiCarlo2013,
author="Di Carlo, Stefano
and Politano, Gianfranco
and Savino, Alessandro
and Benso, Alfredo",
title="A systematic analysis of a mi-RNA inter-pathway regulatory motif",
journal="Journal of Clinical Bioinformatics",
year="2013",
volume="3",
number="1",
pages="1--14",
issn="2043-9113",
doi="10.1186/2043-9113-3-20",
url="http://dx.doi.org/10.1186/2043-9113-3-20"
}

Downloads

v1.0-IWBBIO-2012-12-28.tgz : this release of the pipeline has been used to get the experimental results published in the paper : A. Benso, S. Di Carlo, G. Politano and A. Savino, “A New miRNA Motif Protects Pathways’ Expression in Gene Regulatory Networks”, International Work-Conference on Bioinformatics and Biomedical Engineering IWBBIO 2013

List of identified PPL

mirSVR < -0.3

mirSVR < -0.6

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