Abstract
ABSTRACTA major goal in biology is to comprehensively understand molecular interactions within living systems. Visualization and analysis of biological networks play crucial roles in understanding these biochemical processes. Biological networks include diverse types, from gene regulatory networks and protein–protein interactions (PPIs) to metabolic networks. Metabolic networks include substrates, products, and enzymes, which are regulated by allosteric mechanisms and gene expression. Given this complexity, there is a pressing need to investigate trans-omics networks that include these various regulations to understand living systems. However, analyzing various omics layers is laborious due to the diversity of databases and the intricate nature of network analysis. We developed iTraNet, a user-friendly interactive web application that visualizes and analyzes trans-omics networks involving four major types of networks: gene regulatory networks (including transcription factor, microRNA, and mRNA); PPIs; metabolic networks (including enzyme, mRNA, and metabolite); and metabolite exchange networks (including transporter, mRNA, and metabolite). Using iTraNet, we found that in wild-type mice, hub molecules within the network tended to respond to glucose administration, whereas inob/obmice, this tendency disappeared. With its ability to facilitate network visualization and analysis, we anticipate that iTraNet will help researchers gain insights into biological systems. iTraNet is available at (https://transomics.streamlit.app/).GRAPHICAL ABSTRACT
Publisher
Cold Spring Harbor Laboratory