I want to integrate mRNA, miRNA, and protein data from cow (Bos taurus). After selecting the database, the following message appears: ‘At least one of the input lists has not been used to compute omics network! Are you sure that you want to proceed?’
The miRNA are not enriched in the integration. Am I doing something wrong?
Most likely this means that no features from an omics layer can be connected to the network. This is could be due to biology (they are not indeed close in the interaction network), or due to limited coverage of the underlying databases (especially for less common species).
You should explore the networks using features from each omics layers individually before creating the integrated network. You will have better idea this way