What are the typical miRNA microarray analysis workflow using R?

Question

[my1stbox]

Say just a test group of 5 replicates from bladder cancer tumor and corresponding control group from normal tissue of the same patients,like from the NMIBC part of GSE39093. What could I do to make the analysis seems more sophisticated. I have done differential expression analysis, target gene prediction, and GO, pathway enrichments of target genes. What else could I do? It would be better if you can specify some packages or codes, as well as some research papers to refer to. Regards, Allen

PS: Is paired (t)-test necessery? I found that DE gene number from paired t-test is about half of that from normal limma functions( which I don't know how to do paired test if it could).

Answer 1

[Kato]

You could try to realize an analysis to identify miRNA target genes in KEGG pathway maps. This is also used for the target gene candidates Here you can find information about a complex workflow.

I read about this analysis in some articles but I never tried to realize one.

[my1stbox]

Thank you! How do you think the workflow schematic been created?

[Kato]

I think that is an internal tool of the page. But if you are interested in make that kind of schemas you shall try LaTEX or this:

Draw.io

Glifffy