ArticleGigaScience2024
CAT Bridge: an efficient toolkit for gene-metabolite association mining from multiomics data.
Article in GigaScience, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 4 papers.
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Who cites it
4 citing papers in PubMed.
- ChatMDV: reducing technical barriers in bioinformatics analysis using large language models.GigaScience · 2026Article
- Artificial intelligence for extracellular vesicle engineering and therapeutic design.Extracellular vesicles and circulating nucleic acids · 2026Review
- Epigenetic Regulation of ITGB7 Promotes Coronary Heart Disease via Immune and Metabolic Pathways: A Multimodal Mendelian Randomization Study.Cardiovascular therapeutics · 2026Article
- Multi-omics analyses reveal regulatory networks underpinning metabolite biosynthesis in Nicotiana tabacum.Nature communications · 2025Article
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Authors and funding
11 authors.
Funding
Abstract
backgroundWith advancements in sequencing and mass spectrometry technologies, multiomics 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 nonlinear 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.
findingsHere, we introduce Compounds And Transcripts Bridge (abbreviated as CAT Bridge, available at https://catbridge.work), a free user-friendly platform for longitudinal multiomics 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 multiomics analysis. Additionally, CAT Bridge features an artificial intelligence agent to assist users interpreting the association results.
conclusionsWe applied CAT Bridge to experimentally obtained Capsicum chinense (chili pepper) and public human and Escherichia 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 method outperforms traditional approaches in longitudinal multiomics analyses. CAT Bridge simplifies access to various established methods for longitudinal multiomics analysis and enables researchers to swiftly identify associated gene-metabolite pairs for further validation.
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Registered trials
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