In this analysis, we created an extended pathway, using the WikiPathways repository (Version 20210110) and the three -omics datasets. For this, each of the three -omics datasets was first analyzed to identify differentially expressed elements, and pathways associated with the significant miRNA-protein links were detected. A miRNA-protein link is deemed significant, and may possibly be implying causality, if both a miRNA and its target are significantly differentially expressed.
The peptidome and the proteome datasets were quantile normalized and log2 transformed (Pan and Zhang 2018; Zhao, Wong, and Goh 2020). Before transformation, peptide IDs were mapped to protein IDs, using the information provided by the data uploaders, and were summarized into single protein-level values using geometric mean. The miRNome dataset was already normalized and transformed; thus, the information of their targeting genes was simply added to each miRNA ID, using the information provided by miTaRBase (Huang et al. 2019). As a result, all three datasets had been mapped to their appropriate gene product-level (or, protein-level) identifiers.