Application of the PHENotype SIMulator for rapid identification of potential candidates in effective COVID-19 drug repurposing

tRFUniverse: A comprehensive resource for the interactive analyses of tRNA-derived ncRNAs in human cancer

“…In addition to the target enrichment analysis, a more complex way to investigate which pathways may be regulated by the user-selected tRNA-derived ncRNA is through a phenotype simulation analysis. In more detail, in tRFUniverse, we have included PHENSIM, 53 , 54 a phenotype simulator that relies on the target interactions identified from the AGO CLASH/CLEAR/CLIP-Seq data and the topological information encoded on the KEGG 55 , 56 , 57 and REACTOME 58 , 59 , 60 , 61 pathways to identify the metabolic and signaling pathways potentially regulated by a specific tRNA-derived ncRNA and, in turn, its effects on the cellular phenotype. This is important since both tRFs generated from the mature tRNA 34 , 51 and the 5′ leader and 3′ trailer tRFs generated from the precursor of the tRNA 19 have been shown to be bound to AGO proteins, functioning as active regulators of gene expression.…”