Abstract
BackgroundOver-representation of predicted miRNA targets in sets of genes regulated by a given transcription factor (e.g. as defined by ChIP-sequencing experiments) helps to identify biologically relevant miRNA targets and is useful to get insight into post-transcriptional regulation.FindingsTo facilitate the application of this approach we have created the mBISON web-application. mBISON calculates the significance of over-representation of miRNA targets in a given non-ranked gene set. The gene set can be specified either by a list of genes or by one or more ChIP-seq datasets followed by a user-defined peak-gene association procedure. mBISON is based on predictions from TargetScan and uses a randomization step to calculate False-Discovery-Rates for each miRNA, including a correction for gene set specific properties such as 3’UTR length. The tool can be accessed from the following web-resource: http://cbdm.mdc-berlin.de/~mgebhardt/cgi-bin/mbison/home.ConclusionmBISON is a web-application that helps to extract functional information about miRNAs from gene lists, which is in contrast to comparable applications easy to use by everyone and can be applied on ChIP-seq data directly.
Highlights
Over-representation of predicted miRNA targets in sets of genes regulated by a given transcription factor helps to identify biologically relevant miRNA targets and is useful to get insight into post-transcriptional regulation
It has been demonstrated that sets of functionally related genes, e.g. genes from a protein complex [1] or sets regulated by a common transcription factor [2,3], may contain information about their regulation on post-transcriptional level, which can be uncovered by means of enrichment analysis of miRNA targets
An application of such enrichment analysis can facilitate the classification of predicted miRNA targets according to their likelihood of being biologically functional and can point to miRNA function [2]
Summary
Over-representation of predicted miRNA targets in sets of genes regulated by a given transcription factor (e.g. as defined by ChIP-sequencing experiments) helps to identify biologically relevant miRNA targets and is useful to get insight into post-transcriptional regulation. An application of such enrichment analysis can facilitate the classification of predicted miRNA targets according to their likelihood of being biologically functional and can point to miRNA function [2]. The mBISON (miRNA binding site over-representation) tool was developed to enable the direct use of gene lists or ChIP-seq data to address the above mentioned questions.
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a callDisclaimer: All third-party content on this website/platform is and will remain the property of their respective owners and is provided on "as is" basis without any warranties, express or implied. Use of third-party content does not indicate any affiliation, sponsorship with or endorsement by them. Any references to third-party content is to identify the corresponding services and shall be considered fair use under The CopyrightLaw.
