Dataset Information
Design tools for MPRA experiments.
Ontology highlight
ABSTRACT: Motivation
Genetic reporter assays are a convenient, relatively inexpensive method for studying the regulation of gene expression. Massively Parallel Reporter Assays (MPRA) are high-throughput functionalization assays that interrogate the transcriptional activity of many genetic variants at once using a library of synthetic barcoded constructs. Despite growing interest in this area, there are few computational tools to design and execute MPRA studies.Results
We designed an online web-tool and R package that allows for interactive MPRA experimental design encompassing both power analysis and design of constructs. Our tool is tuned using data from real MPRA studies. Users can adjust experimental parameters to examine the predicted effect on assay power as well as upload VCFs for automated construct sequence generation.Availability and implementation
The MPRA Design Tools web application is available here: https://andrewghazi.shinyapps.io/designmpra/, https://github.com/andrewGhazi/designMPRA and https://github.com/andrewGhazi/mpradesigntools.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Ghazi AR
PROVIDER: S-EPMC6454564 | biostudies-literature | 2018 Aug
REPOSITORIES: biostudies-literature
Publications
Design tools for MPRA experiments.
Bioinformatics (Oxford, England) 20180801 15
<h4>Motivation</h4>Genetic reporter assays are a convenient, relatively inexpensive method for studying the regulation of gene expression. Massively Parallel Reporter Assays (MPRA) are high-throughput functionalization assays that interrogate the transcriptional activity of many genetic variants at once using a library of synthetic barcoded constructs. Despite growing interest in this area, there are few computational tools to design and execute MPRA studies.<h4>Results</h4>We designed an online ...[more]
