代谢组学网络的连接代谢分析和雅可比分析

IF 4.9 2区医学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS

Computer methods and programs in biomedicine Pub Date : 2025-02-18 DOI:10.1016/j.cmpb.2025.108672

Jana Schwarzerova , Erdő Gabor Mate , Jakub Idkowiak , Dominika Olesova , Ales Kvasnicka , Dana Dobesova , David Friedecky , Valentyna Provaznik , Jozef Skarda , Wolfram Weckwerth , Thomas Nägele

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引用次数: 0

摘要

背景与目的代谢组相互作用网络为代谢物及其调控机制之间的动态关系提供了重要的见解。本研究介绍了一种新的计算框架MInfer，该框架集成了广泛使用的代谢组学分析工具MetaboAnalyst的输出，并使用雅可比分析来增强这些网络的推导和解释。方法minfer将MetaboAnalyst的综合数据处理能力与雅可比分析法的数学建模能力相结合。该框架应用于各种代谢组学数据集，采用先进的统计测试来构建相互作用网络并确定关键的代谢途径。结果MInfer在多个数据集的应用揭示了重要的代谢途径和潜在的调控机制。该框架在识别相互作用方面表现出高精度、敏感性和特异性，实现了强大的网络解释。结论：通过提供详细的相互作用网络和揭示关键的调控见解，sminfer增强了对代谢组学数据的解释。这个工具对于推进复杂生物系统的研究具有重要的潜力。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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MInfer: Bridging MetaboAnalyst and Jacobian analysis for metabolomic networks

Background and Objective

Metabolomic interaction networks provide critical insights into the dynamic relationships between metabolites and their regulatory mechanisms. This study introduces MInfer, a novel computational framework that integrates outputs from MetaboAnalyst, a widely used metabolomic analysis tool, with Jacobian analysis to enhance the derivation and interpretation of these networks.

Methods

MInfer combines the comprehensive data processing capabilities of MetaboAnalyst with the mathematical modeling power of Jacobian analysis. This framework was applied to various metabolomic datasets, employing advanced statistical tests to construct interaction networks and identify key metabolic pathways.

Results

The application of MInfer revealed significant metabolic pathways and potential regulatory mechanisms across multiple datasets. The framework demonstrated high precision, sensitivity, and specificity in identifying interactions, enabling robust network interpretations.

Conclusions

MInfer enhances the interpretation of metabolomic data by providing detailed interaction networks and uncovering key regulatory insights. This tool holds significant potential for advancing the study of complex biological systems.

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来源期刊

Computer methods and programs in biomedicine 工程技术-工程：生物医学

CiteScore

12.30

自引率

6.60%

发文量

601

审稿时长

135 days

期刊介绍： To encourage the development of formal computing methods, and their application in biomedical research and medical practice, by illustration of fundamental principles in biomedical informatics research; to stimulate basic research into application software design; to report the state of research of biomedical information processing projects; to report new computer methodologies applied in biomedical areas; the eventual distribution of demonstrable software to avoid duplication of effort; to provide a forum for discussion and improvement of existing software; to optimize contact between national organizations and regional user groups by promoting an international exchange of information on formal methods, standards and software in biomedicine. Computer Methods and Programs in Biomedicine covers computing methodology and software systems derived from computing science for implementation in all aspects of biomedical research and medical practice. It is designed to serve: biochemists; biologists; geneticists; immunologists; neuroscientists; pharmacologists; toxicologists; clinicians; epidemiologists; psychiatrists; psychologists; cardiologists; chemists; (radio)physicists; computer scientists; programmers and systems analysts; biomedical, clinical, electrical and other engineers; teachers of medical informatics and users of educational software.