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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., 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 |
| ISSN: | 1756-0500 |
| Publisher: | BioMed Central |
| Volume: | 8 |
| Number: | 1 |
| 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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