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 ...

This workflow is based on the idea of comparing different gene sets through their semantic interpretation. In many cases, the user studies a specific phenotype (e.g. disease) by analyzing lists of genes resulting from different samples or patients. Their pathway analysis could result in different semantic networks, revealing mechanistic and phenotypic divergence between these gene sets. The workflow of BioTranslator Comparative Analysis compares quantitatively the outputs of pathway analysis, ...

BioTranslator performs sequentially pathway analysis and gene prioritization: A specific operator is executed for each task to translate the input gene set into semantic terms and pinpoint the pivotal-role genes on the derived semantic network. The output consists of the set of statistically significant semantic terms and the associated hub genes (the gene signature), prioritized according to their involvement in the underlying semantic topology.