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bioRxiv · 10.1101/2025.04.11.648356

panomiX: Investigating Mechanisms Of Trait Emergence Through Multi-Omics Data Integration

Sahu, A.·Psaroudakis, D.·Rolletschek, H.·Neumann, K.·Borisjuk, L.·Himmelbach, A.·Pinninti, K.·Töpfer, N.·Szymanski, J. J.
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Abstract

Complex omics approaches and high-throughput phenotyping generate large, heterogeneous datasets that make linking molecular signatures to plant traits challenging. To address this challenge, here we introduce panomiX, a user-friendly toolbox for multi-omics integration, designed to enable non-experts to apply advanced computational methods with ease. panomiX automates data preprocessing, variance analysis, multi-omics prediction, and interaction modeling through machine learning, revealing meaningful molecular interactions and synergies. We applied panomiX to a tomato heat-stress experiment combining image-based phenotyping, transcriptomics, and Fourier-transform infrared spectroscopy data, with the aim of identification of condition-specific, cross-domain relationships between gene expression, metabolite levels, and phenotypic traits. Our approach identified a network of such connections, with those linking photosynthesis traits with stress-responsive kinases in elevated temperatures among most significant ones. By simplifying complex analyses and improving interpretability, panomiX offers a platform to accelerate the discovery of trait emergence in plants and select specific candidate genes based on multi-omics analyses.

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Sahu, A., Psaroudakis, D., Rolletschek, H., Neumann, K., Borisjuk, L., Himmelbach, A., Pinninti, K., Töpfer, N., Szymanski, J. J.. 2025-04-17. panomiX: Investigating Mechanisms Of Trait Emergence Through Multi-Omics Data Integration. https://doi.org/10.1101/2025.04.11.648356

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