ArticleBioinformatics (Oxford, England)2024
PhenoMultiOmics: an enzymatic reaction inferred multi-omics network visualization web server.
Article in Bioinformatics (Oxford, England), 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.
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6 authors.
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Abstract
motivationEnzymatic reaction play a pivotal role in regulating cellular processes with a high degree of specificity to biological functions. When enzymatic reactions are disrupted by gene, protein, or metabolite dysfunctions in diseases, it becomes crucial to visualize the resulting perturbed enzymatic reaction-induced multi-omics network. Multi-omics network visualization aids in gaining a comprehensive understanding of the functionality and regulatory mechanisms within biological systems.
resultsIn this study, we designed PhenoMultiOmics, an enzymatic reaction-based multi-omics web server designed to explore the scope of the multi-omics network across various cancer types. We first curated the PhenoMultiOmics database, which enables the retrieval of cancer-gene-protein-metabolite relationships based on the enzymatic reactions. We then developed the MultiOmics network visualization module to depict the interplay between genes, proteins, and metabolites in response to specific cancer-related enzymatic reactions. The biomarker discovery module facilitates functional analysis through differential omic feature expression and pathway enrichment analysis. PhenoMultiOmics has been applied to analyze the transcriptomics data of gastric cancer and the metabolomics data of lung cancer, providing mechanistic insights into interrupted enzymatic reactions and the associated multi-omics network. AVAILABILITY AND IMPLEMENTATION: PhenoMultiOmics is freely accessed at https://phenomultiomics.shinyapps.io/cancer/ with a user-friendly and interactive web interface.
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