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Computational challenges, tools and resources for analyzing co- and post-transcriptional events in high throughput #MMPMID25515586
Bahrami-Samani E; Vo DT; de Araujo PR; Vogel C; Smith AD; Penalva LOF; Uren PJ
Wiley Interdiscip Rev RNA 2015[May]; 6 (3): 291-310 PMID25515586show ga
Co- and post-transcriptional regulation of gene expression is complex and multi-faceted, spanning the complete RNA lifecycle from genesis to decay. High-throughput profiling of the constituent events and processes is achieved through a range of technologies that continue to expand and evolve. Fully leveraging the resulting data is non-trivial, and requires the use of computational methods and tools carefully crafted for specific data sources and often intended to probe particular biological processes. Drawing upon databases of information pre-compiled by other researchers can further elevate analyses. Within this review, we describe the major co- and post-transcriptional events in the RNA lifecycle that are amenable to high-throughput profiling. We place specific emphasis on the analysis of the resulting data, in particular the computational tools and resources available, as well as looking towards future challenges that remain to be addressed.