MInfer: Bridging MetaboAnalyst and Jacobian analysis for metabolomic networks

IF 4.8 2区 医学 Q1 COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS Computer methods and programs in biomedicine Pub Date : 2025-05-01 Epub 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
{"title":"MInfer: Bridging MetaboAnalyst and Jacobian analysis for metabolomic networks","authors":"Jana Schwarzerova ,&nbsp;Erdő Gabor Mate ,&nbsp;Jakub Idkowiak ,&nbsp;Dominika Olesova ,&nbsp;Ales Kvasnicka ,&nbsp;Dana Dobesova ,&nbsp;David Friedecky ,&nbsp;Valentyna Provaznik ,&nbsp;Jozef Skarda ,&nbsp;Wolfram Weckwerth ,&nbsp;Thomas Nägele","doi":"10.1016/j.cmpb.2025.108672","DOIUrl":null,"url":null,"abstract":"<div><h3>Background and Objective</h3><div>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.</div></div><div><h3>Methods</h3><div>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.</div></div><div><h3>Results</h3><div>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.</div></div><div><h3>Conclusions</h3><div>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.</div></div>","PeriodicalId":10624,"journal":{"name":"Computer methods and programs in biomedicine","volume":"263 ","pages":"Article 108672"},"PeriodicalIF":4.8000,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Computer methods and programs in biomedicine","FirstCategoryId":"5","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S0169260725000896","RegionNum":2,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2025/2/18 0:00:00","PubModel":"Epub","JCR":"Q1","JCRName":"COMPUTER SCIENCE, INTERDISCIPLINARY APPLICATIONS","Score":null,"Total":0}
引用次数: 0

Abstract

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.
查看原文
分享 分享
微信好友 朋友圈 QQ好友 复制链接
本刊更多论文
代谢组学网络的连接代谢分析和雅可比分析
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。
求助全文
约1分钟内获得全文 去求助
来源期刊
Computer methods and programs in biomedicine
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.
期刊最新文献
Inhalation exposure and particle deposition across 16 nonhuman primate airway models using computational fluid–particle dynamics for allometric extrapolation Robust prediction of parameterized cardiovascular hemodynamics using deep operator networks with time normalization Towards lightweight stress monitoring on biometric data for IoMT environments CardioSynth: Parameter-driven cardiac MRI generation via oriented bounding boxes Emboli transport in a full patient-specific aortic tree: Assessment of abdominal organ injury risk during cardiopulmonary bypass
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
×
提示
您的信息不完整,为了账户安全,请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
0
微信
客服QQ
Book学术公众号 扫码关注我们
反馈
×
意见反馈
请填写您的意见或建议
请填写您的手机或邮箱
已复制链接
已复制链接
快去分享给好友吧!
我知道了
×
扫码分享
扫码分享
Book学术官方微信
Book学术文献互助
Book学术文献互助群
群 号:604180095
Book学术
文献互助 智能选刊 最新文献 互助须知 联系我们:info@booksci.cn
Book学术提供免费学术资源搜索服务,方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。
Copyright © 2023 Book学术 All rights reserved.
ghs 京公网安备 11010802042870号 京ICP备2023020795号-1