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

Gao, Jinfang; Tarcea, V. Glenn; Karnovsky, Alla; Mirel, Barbara; Weymouth, Terry E.; Beecher, Christopher W.W.; Cavalcoli, James D.; Athey, Brian D.; Omenn, Gilbert S.; Burant, Charles F.; Jagadish, H. V.

doi:10.1093/bioinformatics/btq048

Cited by 199 publications

(153 citation statements)

References 13 publications

Supporting

Mentioning

153

Contrasting

Order By: Relevance

“…25–27 MAVEN contains a built-in pathway visualization interface. In the interface, compounds appear as circular nodes and reactions as arrows between nodes.…”

Section: Resultsmentioning

confidence: 99%

Metabolomic Analysis and Visualization Engine for LC−MS Data

Melamud¹,

Vastag²,

Rabinowitz³

2010

Anal. Chem.

563

466

View full text Add to dashboard Cite

Metabolomic analysis by liquid chromatography–high-resolution mass spectrometry results in data sets with thousands of features arising from metabolites, fragments, isotopes, and adducts. Here we describe a software package, Metabolomic Analysis and Visualization ENgine (MAVEN), designed for efficient interactive analysis of LC–MS data, including in the presence of isotope labeling. The software contains tools for all aspects of the data analysis process, from feature extraction to pathway-based graphical data display. To facilitate data validation, a machine learning algorithm automatically assesses peak quality. Users interact with raw data primarily in the form of extracted ion chromatograms, which are displayed with overlaid circles indicating peak quality, and bar graphs of peak intensities for both unlabeled and isotope-labeled metabolite forms. Click-based navigation leads to additional information, such as raw data for specific isotopic forms or for metabolites changing significantly between conditions. Fast data processing algorithms result in nearly delay-free browsing. Drop-down menus provide tools for the overlay of data onto pathway maps. These tools enable animating series of pathway graphs, e.g., to show propagation of labeled forms through a metabolic network. MAVEN is released under an open source license at http://maven.princeton.edu.

show abstract

“…25–27 MAVEN contains a built-in pathway visualization interface. In the interface, compounds appear as circular nodes and reactions as arrows between nodes.…”

Section: Resultsmentioning

confidence: 99%

Metabolomic Analysis and Visualization Engine for LC−MS Data

Melamud¹,

Vastag²,

Rabinowitz³

2010

Anal. Chem.

563

466

View full text Add to dashboard Cite

show abstract

“…We used Metscape, the metabolic network analysis and visualization tool (http://www.metscape.ncibi. org/tryplugin.html) (19), to generate the gene and enzyme networks associated with each of the differentiating metabolites. Metscape is a plugin for Cytoscape (http://www.cytoscape.org/).…”

Section: Methodsmentioning

confidence: 99%

Metabolic consequences of sepsis-induced acute lung injury revealed by plasma ¹H-nuclear magnetic resonance quantitative metabolomics and computational analysis

Stringer

Serkova

Karnovsky

et al. 2011

American Journal of Physiology-Lung Cellular and Molecular Phys

Self Cite

142

136

View full text Add to dashboard Cite

Metabolomics is an emerging component of systems biology that may be a viable strategy for the identification and validation of physiologically relevant biomarkers. Nuclear magnetic resonance (NMR) spectroscopy allows for establishing quantitative data sets for multiple endogenous metabolites without preconception. Sepsis-induced acute lung injury (ALI) is a complex and serious illness associated with high morbidity and mortality for which there is presently no effective pharmacotherapy. The goal of this study was to apply ¹H-NMR based quantitative metabolomics with subsequent computational analysis to begin working towards elucidating the plasma metabolic changes associated with sepsis-induced ALI. To this end, this pilot study generated quantitative data sets that revealed differences between patients with ALI and healthy subjects in the level of the following metabolites: total glutathione, adenosine, phosphatidylserine, and sphingomyelin. Moreover, myoinositol levels were associated with acute physiology scores (APS) (ρ = -0.53, P = 0.05, q = 0.25) and ventilator-free days (ρ = -0.73, P = 0.005, q = 0.01). There was also an association between total glutathione and APS (ρ = 0.56, P = 0.04, q = 0.25). Computational network analysis revealed a distinct metabolic pathway for each metabolite. In summary, this pilot study demonstrated the feasibility of plasma ¹H-NMR quantitative metabolomics because it yielded a physiologically relevant metabolite data set that distinguished sepsis-induced ALI from health. In addition, it justifies the continued study of this approach to determine whether sepsis-induced ALI has a distinct metabolic phenotype and whether there are predictive biomarkers of severity and outcome in these patients.

show abstract

“…Those biomarkers that remained significant were pooled, and cancer-specific metabolite relationships were mapped to EHMN subdivisions using Kyoto Encyclopaedia of Genes and Genomes Compound identifiers, using the "Compound-Gene" function of the Metscape 3.2 plugin in Cytoscape (v3.0.2, National Resource of Network Biology, http://cytoscape.org; refs. [34][35][36]. However, pooled analysis of clinical metrics was not felt to be appropriate given the heterogeneity in analytics.…”

Section: Data Extractionmentioning

confidence: 99%

Diagnostic Metabolomic Blood Tests for Endoluminal Gastrointestinal Cancer—A Systematic Review and Assessment of Quality

Antonowicz

Kumar

Wiggins

et al. 2016

Cancer Epidemiology, Biomarkers &Amp; Prevention

View full text Add to dashboard Cite

Advances in analytics have resulted in metabolomic blood tests being developed for the detection of cancer. This systematic review aims to assess the diagnostic accuracy of blood-based metabolomic biomarkers for endoluminal gastrointestinal (GI) cancer. Using endoscopic diagnosis as a reference standard, methodologic and reporting quality was assessed using validated tools, in addition to pathway-based informatics to biologically contextualize discriminant features. Twenty-nine studies (15 colorectal, 9 esophageal, 3 gastric, and 2 mixed) with data from 10,835 participants were included. All reported significant differences in hematologic metabolites. In pooled analysis, 246 metabolites were found to be significantly different after multiplicity correction. Incremental metabolic flux with disease progression was frequently reported. Two promising candidates have been validated in independent populations (both colorectal biomarkers), and one has been approved for clinical use. Networks analysis suggested modulation of elements of up to half of Edinburgh Human Metabolic Network subdivisions, and that the poor clinical applicability of commonly modulated metabolites could be due to extensive molecular interconnectivity. Methodologic and reporting quality was assessed as moderate-to-poor. Serum metabolomics holds promise for GI cancer diagnostics; however, future efforts must adhere to consensus standardization initiatives, utilize high-resolution discovery analytics, and compare candidate biomarkers with peer nonendoscopic alternatives.Cancer Epidemiol Biomarkers Prev; 25(1); 6-15. Ó2015 AACR.

show abstract

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

Abstract: Metscape can be installed from within Cytoscape 2.6.x under 'Network and Attribute I/O' category. For more information, please visit http://metscape.ncibi.org/tryplugin.html.

Cited by 199 publications

References 13 publications

Metabolomic Analysis and Visualization Engine for LC−MS Data

Metabolomic Analysis and Visualization Engine for LC−MS Data

Metabolic consequences of sepsis-induced acute lung injury revealed by plasma ¹H-nuclear magnetic resonance quantitative metabolomics and computational analysis

Diagnostic Metabolomic Blood Tests for Endoluminal Gastrointestinal Cancer—A Systematic Review and Assessment of Quality

Contact Info

Product

Resources

About

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

Abstract: Metscape can be installed from within Cytoscape 2.6.x under 'Network and Attribute I/O' category. For more information, please visit http://metscape.ncibi.org/tryplugin.html.

Cited by 199 publications

References 13 publications

Metabolomic Analysis and Visualization Engine for LC−MS Data

Metabolomic Analysis and Visualization Engine for LC−MS Data

Metabolic consequences of sepsis-induced acute lung injury revealed by plasma 1H-nuclear magnetic resonance quantitative metabolomics and computational analysis

Diagnostic Metabolomic Blood Tests for Endoluminal Gastrointestinal Cancer—A Systematic Review and Assessment of Quality

Contact Info

Product

Resources

About

Metabolic consequences of sepsis-induced acute lung injury revealed by plasma ¹H-nuclear magnetic resonance quantitative metabolomics and computational analysis