CAT Bridge: An Efficient Toolkit for Gene-Metabolite Association Mining from Multi-Omics Data

Background With advancements in sequencing and mass spectrometry technologies, multi-omics data can now be easily acquired for understanding complex biological systems. Nevertheless, substantial challenges remain in determining the association between gene-metabolite pairs due to the non-linear and multifactorial interactions within cellular networks. The complexity arises from the interplay of multiple genes and metabolites, often involving feedback loops and time-dependent regulatory mechanisms that are not easily captured by traditional analysis methods. Findings Here, we introduce Compounds And Transcripts Bridge (abbreviated as CAT Bridge, available at https://catbridge.work ), a free user-friendly platform for longitudinal multi-omics analysis to efficiently identify transcripts associated with metabolites using time-series omics data. To evaluate the association of gene-metabolite pairs, CAT Bridge is a pioneering work benchmarking a set of statistical methods spanning causality estimation and correlation coefficient calculation for multi-omics analysis. Additionally, CAT Bridge features an artificial intelligence (AI) agent to assist users interpreting the association results. Conclusions We applied CAT Bridge to experimentally obtained Capsicum chinense (chili pepper) and public human and Escherichia coli ( E. coli ) time-series transcriptome and metabolome datasets. CAT Bridge successfully identified genes involved in the biosynthesis of capsaicin in C. chinense . Furthermore, case study results showed that the convergent cross mapping (CCM) method outperforms traditional approaches in longitudinal multi-omics analyses. CAT Bridge simplifies access to various established methods for longitudinal multi-omics analysis, and enables researchers to swiftly identify associated gene-metabolite pairs for further validation.