Funm6AViewer: a web server and R package for functional analysis of context-specific m(6)A RNA methylation

Motivation: N-6-methyladenosine (m(6)A) is the most abundant mammalian mRNA methylation with versatile functions. To date, although a number of bioinformatics tools have been developed for location discovery of m(6)A modification, functional understanding is still quite limited. As the focus of RNA epigenetics gradually shifts from site discovery to functional studies, there is an urgent need for user-friendly tools to identify and explore the functional relevance of context-specific m(6)A methylation to gain insights into the epitranscriptome layer of gene expression regulation. Results: We introduced here Funm6AViewer, a novel platform to identify, prioritize and visualize the functional gene interaction networks mediated by dynamic m(6)A RNA methylation unveiled from a case control study. By taking the differential RNA methylation data and differential gene expression data, both of which can be inferred from the widely used MeRIP-seq data, as the inputs, Funm6AViewer enables a series of analysis, including: (i) examining the distribution of differential m6A sites, (ii) prioritizing the genes mediated by dynamic m6A methylation and (iii) characterizing functionally the gene regulatory networks mediated by condition-specific m6A RNA methylation. Funm6AViewer should effectively facilitate the understanding of the epitranscriptome circuitry mediated by this reversible RNA modification.