I have a lists of mature miRNAs (in the format
mmu-mir-129-5p) from different cell types together with expression data (LFC vs Control). I would like to group those genes according to genomic distance (thereby also grouping miRNAs of the same cluster together). Then, I would like to make some sort of visualization, to compare the results between different cell types (expression differences of individual clusters and distribution of these expression differences across genome). The .gff file with genomic coordinates I need is available from mirBase. In this file, both mature and unprocessed forms can be found. I thought of first assigning my mature_mirna_ids to their primary transcripts, and then those transcripts to genes. But this seems a bit like a way around. Is there more straightforward approach?
I am sure there are tool for doing similar things I just don't know of. I would like to find miRNA gene clusters that are differentially expressed between my samples (cell types). Finally, I would love to hear from you about possible ways to visualize such differences with respect to genome methylation data of corresponding genes (assuming the latter is also available).
Thank in advance for helpful insights. Cheers, Lech