I would like to get some advice or recommendations from you about the inetgrated miRNA-mRNA analysis pipeline. Here is what I would like to do:
- integrate the microarray data from microRNA and mRNA experiments, however taking into account their differential expression and, moreover, those data won't be matched (just microarray data from GEO for miRNA and mRNA in the same cancer, e.g. breast cancer),
- take into consideration the signaling pathways, which are altered, as miRNA targets some involved genes,
- and visualize the significantly altered miRNA and their targeted genes among my datasets in e.g. Cytoscape software.
I performed such analysis using MAGIA2 web-tool, however it was very simple and I am not sure about the differential expression calculation, as MAGIA calculates it on its own. There is a lot of papers with similar studies, but I can see that there is a lot of different approaches, a lot of available tools and different pipelines, so I am not sure which can I treat as the most reliable and the best recently available.
I will be grateful if you suggest something :)