PhenoMultiOmics：一种基于酶促反应的多组学网络可视化网页服务器

PhenoMultiOmics: an enzymatic reaction inferred multi-omics network visualization web server

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BIOINFORMATICS

影响因子:5.4

分区:生物学3区 / 生化研究方法3区生物工程与应用微生物3区数学与计算生物学3区

发表日期:2024 Nov 01

作者: Yuying Shi, Botao Xu, Zhe Wang, Qitao Chen, Jie Chai, Cheng Wang

DOI: 10.1093/bioinformatics/btae623

摘要

酶促反应在调控细胞过程中的作用至关重要，具有高度的生物学功能特异性。当疾病中酶促反应被基因、蛋白质或代谢物功能障碍破坏时，直观展示由此引起的扰动多组学网络变得尤为重要。多组学网络可视化有助于全面理解生物系统内的功能和调控机制。本研究设计了PhenoMultiOmics，一种基于酶促反应的多组学网页服务器，旨在探索多组学网络在多种癌症类型中的应用范围。我们首先整合了PhenoMultiOmics数据库，能够基于酶促反应检索癌症-基因-蛋白质-代谢物关系。随后开发了多组学网络可视化模块，展示基因、蛋白质和代谢物在特定癌症相关酶促反应中的相互作用。生物标志物发现模块通过差异表达和通路富集分析实现功能分析。PhenoMultiOmics已应用于胃癌转录组数据和肺癌代谢组数据的分析，为理解酶促反应中断及其相关多组学网络提供机制见解。该平台可在https://phenomultiomics.shinyapps.io/cancer/免费访问，界面友好且具有交互性。

Abstract

Enzymatic 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.In 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.PhenoMultiOmics is freely accessed at https://phenomultiomics.shinyapps.io/cancer/ with a user-friendly and interactive web interface.