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bioRxiv · 10.1101/2020.08.03.234302

RAD: a web application to identify region associated differentially expressed genes

Liu, W.·Guo, Y.·Xue, Z.·Yuan, R.
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Abstract

With the advance of genomic sequencing techniques, chromatin accessible regions, transcription factor binding sites and epigenetic modifications can be identified at genome-wide scale. Conventional analyses focus on the gene regulation at proximal regions; however, distal regions are usually neglected, largely due to the lack of reliable tools to link the distal regions to coding genes. In this study, we introduce RAD (Region Associated Differentially expressed genes), a user-friendly web tool to identify both proximal and distal region associated differentially expressed genes. RAD maps the up- and down-regulated genes associated with any genomic regions of interest (gROI) and helps researchers to infer the regulatory function of these regions based on the distance of gROI to differentially expressed genes. RAD includes visualization of the results and statistical inference for significance. AvailabilityRAD is implemented with Python 3.7 and run on a Nginx server. RAD is freely available at http://labw.org/rad as online web service.

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Liu, W., Guo, Y., Xue, Z., Yuan, R.. 2020-08-04. RAD: a web application to identify region associated differentially expressed genes. https://doi.org/10.1101/2020.08.03.234302

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