Signal metrics analysis of oscillatory patterns in bacterial multi-omic networks

TL;DR

This paper introduces a novel signal processing methodology to analyze and quantify oscillatory patterns in bacterial multi-omic networks, revealing synchronized responses and evolutionary insights across different bacteria.

Contribution

A new signal metrics approach for identifying and quantifying multi-omic oscillations in bacterial networks, integrating diverse biological data for deeper mechanistic understanding.

Findings

Oscillatory signals are detected across multiple omic levels in bacteria.

Network-level multi-omic signals show synchronized responses to perturbations.

Oscillations correlate with evolutionary relationships among bacteria.

Abstract

Motivation: One of the branches of Systems Biology is focused on a deep understanding of underlying regulatory networks through the analysis of the biomolecules oscillations and their interplay. Synthetic Biology exploits gene or/and protein regulatory networks towards the design of oscillatory networks for producing useful compounds. Therefore, at different levels of application and for different purposes, the study of biomolecular oscillations can lead to different clues about the mechanisms underlying living cells. It is known that network-level interactions involve more than one type of biomolecule as well as biological processes operating at multiple omic levels. Combining network/pathway-level information with genetic information it is possible to describe well-understood or unknown bacterial mechanisms and organism-specific dynamics. Results: Network multi-omic integration has led to the discovery of interesting oscillatory signals. Following the methodologies used in signal processing and communication engineering, a new methodology is introduced to identify and quantify the extent of the multi-omic oscillations of the signal. New signal metrics are designed to allow further biotechnological explanations and provide important clues about the oscillatory nature of the pathways and their regulatory circuits. Our algorithms designed for the analysis of multi-omic signals are tested and validated on 11 different bacteria for thousands of multi-omic signals perturbed at the network level by different experimental conditions. Information on the order of genes, codon usage, gene expression, and protein molecular weight is integrated at three different functional levels. Oscillations show interesting evidence that network-level multi-omic signals present a synchronized response to perturbations and evolutionary relations along with taxa.