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Visualizing metabolic network dynamics through time-series metabolomics data [article]

Lea F. Buchweitz, James T. Yurkovich, Christoph M. Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, Freyr Jóhannsson, Ólafur E. Sigurjónsson, Óttar Rolfsson, Julian Heinrich, Andreas Dräger
2018 bioRxiv   pre-print
Here, we present a new method for the visualization of time-course metabolomics data within the context of metabolic network maps.  ...  Here, we present a new method for the visualization of time-course metabolomics data that integrates data into an existing metabolic network map.  ...  of time-course metabolomics data in the context of large-scale 124 metabolic network maps.  ... 
doi:10.1101/426106 fatcat:q577o6cygfg5rj5dnkrmyskk4u

Visualizing metabolic network dynamics through time-series metabolomic data

Lea F. Buchweitz, James T. Yurkovich, Christoph Blessing, Veronika Kohler, Fabian Schwarzkopf, Zachary A. King, Laurence Yang, Freyr Jóhannsson, Ólafur E. Sigurjónsson, Óttar Rolfsson, Julian Heinrich, Andreas Dräger
2020 BMC Bioinformatics  
Here, we present GEM-Vis, an original method for the visualization of time-course metabolomic data within the context of metabolic network maps.  ...  This method can be applied to any system with data and a metabolic map to promote visualization and understand physiology at the network level.  ...  This work was made possible by the friendly support of yWorks GmbH (https://www.yworks.com) who provided their diagram visualization library yFiles for Java (https://www.yworks.com/products/yfiles-for-java  ... 
doi:10.1186/s12859-020-3415-z pmid:32245365 fatcat:b2on4jftybaf3lklq5nrkjtqwq

Metscape: a Cytoscape plug-in for visualizing and interpreting metabolomic data in the context of human metabolic networks

Jing Gao, V. Glenn Tarcea, Alla Karnovsky, Barbara R. Mirel, Terry E. Weymouth, Christopher W. Beecher, James D. Cavalcoli, Brian D. Athey, Gilbert S. Omenn, Charles F. Burant, H. V. Jagadish
2010 Computer applications in the biosciences : CABIOS  
Metscape is a plug-in for Cytoscape, used to visualize and interpret metabolomic data in the context of human metabolic networks.  ...  Metscape allows users to upload experimental data, and visualize and explore compound networks over time, or experimental conditions.  ...  Visualizing metabolites with node color and size changes in a network at a series of time points can help users to predict functions of metabolites.  ... 
doi:10.1093/bioinformatics/btq048 pmid:20139469 pmcid:PMC2844990 fatcat:zefqcgfbunajtfck3zmhwbp3hm

Mathematical Modeling and Dynamic Simulation of Metabolic Reaction Systems Using Metabolome Time Series Data

Kansuporn Sriyudthsak, Fumihide Shiraishi, Masami Yokota Hirai
2016 Frontiers in Molecular Biosciences  
It also highlights the potential for constructing a large-scale mathematical model by estimating model parameters from time series metabolome data in order to comprehensively understand metabolism at the  ...  Time series data are useful for predicting the most likely metabolic pathways because they provide important information regarding the accumulation of metabolites, which implies causal relationships in  ...  Time series metabolome data is suited for this task.  ... 
doi:10.3389/fmolb.2016.00015 pmid:27200361 pmcid:PMC4853375 fatcat:4ma6i74u7vgzzbni5agppwyabe

Systrip: A Visual Environment for the Investigation of Time-series Data in the Context of Metabolic Networks

J. Dubois, L. Cottret, A. Ghozlane, D. Auber, F. Bringaud, P. Thebault, F. Jourdan, R. Bourqui
2012 2012 16th International Conference on Information Visualisation  
In this article we present, Systrip, a visual environment for the analysis of time-series data in the context of biological networks. In particular we focus on the study of metabolism.  ...  It helps to interactively move through the different levels of analysis and to simultaneously investigate data with different point of views.  ...  Contextual visualization: The user can also visualize time-series data in the context of the metabolic network.  ... 
doi:10.1109/iv.2012.43 dblp:conf/iv/DuboisCGABTJB12 fatcat:6nm3q6gpinhpjlt6fhdddkssye

Using Expert Driven Machine Learning to Enhance Dynamic Metabolomics Data Analysis

Charlie Beirnaert, Laura Peeters, Pieter Meysman, Wout Bittremieux, Kenn Foubert, Deborah Custers, Anastasia Van der Auwera, Matthias Cuykx, Luc Pieters, Adrian Covaci, Kris Laukens
2019 Metabolites  
The results were compared to EDGE, a statistical method for time series data. This paper presents three novel outcomes.  ...  The first is a way to simulate dynamic metabolomics data with a known ground truth based on ordinary differential equations. This method is made available through the MetaboLouise R package.  ...  These simulated data are visually comparable to actual dynamic metabolomics data [10] .  ... 
doi:10.3390/metabo9030054 pmid:30897797 pmcid:PMC6468718 fatcat:nvvqbvdtvzfnbhx5ww6obvackq

COMPUTATIONAL TOOLS FOR THE SECONDARY ANALYSIS OF METABOLOMICS EXPERIMENTS

Sean C. Booth, Aalim M. Weljie, Raymond J. Turner
2013 Computational and Structural Biotechnology Journal  
While it is possible, and common, for experimenters to intuitively interpret these results using their knowledge of metabolism and the tested conditions, or manually map them onto known metabolic pathways  ...  organism metabolomics are somewhat limited.  ...  Through these functions MetPa can be used to visualize metabolomic data within known metabolic pathways, along with calculating which pathways are significantly affected.  ... 
doi:10.5936/csbj.201301003 pmid:24688685 pmcid:PMC3962093 fatcat:4zfhlfrvjnhzhbdzgx6dh63cpe

Computational Methods to Interpret and Integrate Metabolomic Data [chapter]

Feng Li, Jiangxin Wang, Lei Nie, Weiwen Zhang
2012 Metabolomics  
Computational methods for metabolic pathway analysis using metabolomic data Metabolomics data provides a series of snapshots of cellular metabolism, which can be combined with metabolic flux data for further  ...  data on a broad series of metabolites in an attempt to gain an overall understanding of metabolism and/or metabolic dynamics associated with conditions of interest, such as disease or drug exposure.  ...  Analytical chemistry is combined with sophisticated informatics and statistics tools to determine and understand metabolic changes upon genetic or environmental perturbations.  ... 
doi:10.5772/32517 fatcat:ety5vgnvfnaw5evchxhgbab3wy

ProbMetab: an R package for Bayesian probabilistic annotation of LC–MS-based metabolomics

Ricardo R. Silva, Fabien Jourdan, Diego M. Salvanha, Fabien Letisse, Emilien L. Jamin, Simone Guidetti-Gonzalez, Carlos A. Labate, Ricardo Z. N. Vêncio
2014 Computer applications in the biosciences : CABIOS  
This graph can be overlaid with other graph-based analysis, such as partial correlation networks, in a visualization scheme exported to Cytoscape, with web and stand alone versions.  ...  We present ProbMetab, an R package which promotes substantial improvement in automatic probabilistic LC-MS based metabolome annotation.  ...  Funding: Microsoft Research and FAPESP (09/53161-6); FAPESP Tema´tico grant (08/56100-5) and fellowships (10/ 14926-4, 12/05392-1 and 10/15417-6); CAPES through Po´s-graduac¸a˜o em Gene´tica FMRP-USP.  ... 
doi:10.1093/bioinformatics/btu019 pmid:24443383 pmcid:PMC3998140 fatcat:lvj5nyo5ujeind5ls2u26yctge

Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis

Svetlana Volkova, Marta R. A. Matos, Matthias Mattanovich, Igor Marín de Mas
2020 Metabolites  
These approaches enable integrating metabolomic data, among others, to enhance model predictive capabilities.  ...  Metabolic networks are regulated to ensure the dynamic adaptation of biochemical reaction fluxes to maintain cell homeostasis and optimal metabolic fitness in response to endogenous and exogenous perturbations  ...  To incorporate time-series of both intracellular and extracellular metabolomics data, a number of dynamic FBA variations have been proposed.  ... 
doi:10.3390/metabo10080303 pmid:32722118 fatcat:g7aq4jrsebbqrcu2wh3jcei3jm

Analysis of metabolomic data: tools, current strategies and future challenges for omics data integration

Alice Cambiaghi, Manuela Ferrario, Marco Masseroli
2016 Briefings in Bioinformatics  
The two major goals of metabolomics are the identification of the metabolites characterizing each organism state and the measurement of their dynamics under different situations (e.g. pathological conditions  ...  Here, we review four main tools for number of users or provided features (MetaCore TM , MetaboAnalyst, InCroMAP and 3Omics) out of the several available for metabolomic data analysis and integration with  ...  InCroMAP provides metabolite mapping support through two different kinds of data visualizations: the integrated visualization and the global metabolic overview.  ... 
doi:10.1093/bib/bbw031 pmid:27075479 fatcat:2msu3y6zhfacdjl4q2nzdp362q

Discovery and verification of the potential targets from bioactive molecules by network pharmacology-based target prediction combined with high-throughput metabolomics

Aihua Zhang, Heng Fang, Yangyang Wang, Guangli Yan, Hui Sun, Xiaohang Zhou, Yuying Wang, Liang Liu, Xijun Wang
2017 RSC Advances  
Currently, plasma metabolome has suggested that compounds present in herbs may exert bioactivity.  ...  Further, with the deep exploration of metabolic pathway 3 The robust data processing and visualization procedure by the Progenesis QI data-processing platform.  ...  Then, we employed tutorial data using the Human Metabolome Database (HMDB) for identication within a few minutes. As a result, we selected 24 ions as ALD biomarkers through the above procedure.  ... 
doi:10.1039/c7ra09522h fatcat:g47ankaudnexvc57wvxbaxo7ea

Stable isotope-labeling studies in metabolomics: new insights into structure and dynamics of metabolic networks

Achuthanunni Chokkathukalam, Dong-Hyun Kim, Michael P Barrett, Rainer Breitling, Darren J Creek
2014 Bioanalysis  
However, advances in the mechanistic understanding of metabolic networks remain limited, as most metabolomics studies cannot routinely provide accurate metabolite identification, absolute quantification  ...  Here we describe some current approaches to stable isotope-labeled metabolomics and provide examples of the significant impact that these studies have had on our understanding of cellular metabolism.  ...  Another important challenge is the rapid visualization of information from isotope labeled metabolomics data within the context of metabolic pathways and networks.  ... 
doi:10.4155/bio.13.348 pmid:24568354 pmcid:PMC4048731 fatcat:zz5jdkjuyvg6lhbhadgrxlf62m

Guide to Metabolomics Analysis: A Bioinformatics Workflow

Yang Chen, En-Min Li, Li-Yan Xu
2022 Metabolites  
Such integration of different omics data requires specialized statistical and bioinformatics software.  ...  We also outline the most abnormal metabolic pathways in several cancers and diseases, and discuss the importance of multi-omics integration algorithms.  ...  The most common approach today is to simultaneously monitor transcript, protein and metabolite levels and obtain structural and dynamic changes in the underlying biological network of interest through  ... 
doi:10.3390/metabo12040357 pmid:35448542 pmcid:PMC9032224 fatcat:4lwn3jeeuvgnnichpbpscjbc5a

Clinical Metabolomics: The New Metabolic Window for Inborn Errors of Metabolism Investigations in the Post-Genomic Era

Abdellah Tebani, Lenaig Abily-Donval, Carlos Afonso, Stéphane Marret, Soumeya Bekri
2016 International Journal of Molecular Sciences  
Conventional biological diagnosis procedures are based on a time-consuming series of sequential and segmented biochemical tests.  ...  The function describes how the whole system behaves in space and time with regard to metabolic fluxes and response to stimuli [8] [9] [10] .  ...  ., diurnal variation in time series studies) or specific changes due to the intrinsic variability of metabolomic data [54, 122] .  ... 
doi:10.3390/ijms17071167 pmid:27447622 pmcid:PMC4964538 fatcat:bgxb5gotyffujacdtq44rvx7iu
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