Dataset Information
PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps.
Ontology highlight
ABSTRACT: Background
The progress in mapping RNA-protein and RNA-RNA interactions at the transcriptome-wide level paves the way to decipher possible combinatorial patterns embedded in post-transcriptional regulation of gene expression.Results
Here we propose an innovative computational tool to extract clusters of mRNA trans-acting co-regulators (RNA binding proteins and non-coding RNAs) from pairwise interaction annotations. In addition the tool allows to analyze the binding site similarity of co-regulators belonging to the same cluster, given their positional binding information. The tool has been tested on experimental collections of human and yeast interactions, identifying modules that coordinate functionally related messages.Conclusions
This tool is an original attempt to uncover combinatorial patterns using all the post-transcriptional interaction data available so far. PTRcombiner is available at http://disi.unitn.it/~passerini/software/PTRcombiner/.
SUBMITTER: Corrado G
PROVIDER: S-EPMC4234518 | biostudies-literature | 2014 Apr
REPOSITORIES: biostudies-literature
Publications
PTRcombiner: mining combinatorial regulation of gene expression from post-transcriptional interaction maps.
BMC genomics 20140423
<h4>Background</h4>The progress in mapping RNA-protein and RNA-RNA interactions at the transcriptome-wide level paves the way to decipher possible combinatorial patterns embedded in post-transcriptional regulation of gene expression.<h4>Results</h4>Here we propose an innovative computational tool to extract clusters of mRNA trans-acting co-regulators (RNA binding proteins and non-coding RNAs) from pairwise interaction annotations. In addition the tool allows to analyze the binding site similarit ...[more]