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mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data

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Item Type:Article
Title:mBISON: Finding miRNA target over-representation in gene lists from ChIP-sequencing data
Creators Name:Gebhardt, M.L. and Mer, A.S. and Andrade-Navarro, M.A.
Abstract:BACKGROUND: 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. FINDINGS: To 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 . CONCLUSION: mBISON 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.
Keywords:microRNA, ChIP-Sequencing, Enrichment, Target Genes, Gene Regulatory Networks, Transcription Factors, Data Integration
Source:BMC Research Notes
Publisher:BioMed Central
Page Range:157
Date:16 April 2015
Official Publication:https://doi.org/10.1186/s13104-015-1118-8
PubMed:View item in PubMed

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