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Visualizing metabolic network dynamics through time-series metabolomics data
[article]
2018
bioRxiv
pre-print
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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
2020
BMC Bioinformatics
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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
2010
Computer applications in the biosciences : CABIOS
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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
2016
Frontiers in Molecular Biosciences
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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
2012
2012 16th International Conference on Information Visualisation
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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
2019
Metabolites
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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
2013
Computational and Structural Biotechnology Journal
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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]
2012
Metabolomics
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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
2014
Computer applications in the biosciences : CABIOS
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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
2020
Metabolites
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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
2016
Briefings in Bioinformatics
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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
2017
RSC Advances
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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 identication 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
2014
Bioanalysis
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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
2022
Metabolites
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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
2016
International Journal of Molecular Sciences
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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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