Inference of miRNA‐target interactions with negative regulation

As the target gene is usually negatively reguated by the miRNA, the default selection in miRTalk is to infer the cell-cell communication mediated by the negatively regulated miRNA-target interactions with the parameter regulation = "negative" in the function find_miRNA, namely high expression of the miRNA gene in the sender cell type and low expression of the target gene in the receiver cell type. Step-by-step procedures are shown below:

[1] load the example data

> load(paste0(system.file(package = 'miRTalk'), "/extdata/example.rda"))

> dim(sc_data)
[1] 22898   515

> table(sc_celltype)
sc_celltype
  Bcell Myeloid Stromal   Tcell   Tumor 
     83      38      23      54     317 

[2] create miRTalk object using single-cell transcriptomics data

> obj <- create_miRTalk(sc_data = sc_data,
                        sc_celltype = sc_celltype,
                        species = "Human",
                        condition = rep("condition",length(sc_celltype)),
                        evbiog = evbiog,
                        risc = risc,
                        ritac = ritac)
Warning: The following features are not present in the object: AGO2, not searching for symbol synonyms

[3] Find highly variable target genes with DEGs and HVGs with find_hvtg

> obj <- find_hvtg(object = obj)

[4] Find expressed miRNAs among all cells and generate background distribution for permutation test with find_miRNA. Set the parameter regulation as negative for the inference of negatively regulated miRNA-target interactions. We use risc for negative regulation.

> obj <- find_miRNA(object = obj,
                    mir_info = mir_info,
                    mir2tar = mir2tar,
                    regulation = "negative")

[5] Infer cell-cell communication mediated by EV-derived miRNAs from senders to receivers

> obj <- find_miRTalk(obj, if_doParallel = F)
[condition] 
[++++++++++++++++++++++++++++++] Finished:100% time:00:04:57

> obj
An object of class miRTalk 
460 EV-derived miRNA-target interactions