ArticleBMC bioinformatics2009
MarVis: a tool for clustering and visualization of metabolic biomarkers.
Article in BMC bioinformatics, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed.
- Exploring the biochemical and biological functions of copper radical oxidases in the vascular wilt phytopathogenApplied and environmental microbiology · 2026Article
- Redox-inactive CC-type glutaredoxins interfere with TGA transcription factor-dependent repression of target promoters in roots.The Plant cell · 2025Article
- Unravelling induced resistance in strawberry: distinct metabolomic signatures define cultivar-specific resistance toFrontiers in plant science · 2025Article
- Article
- N-Hydroxy pipecolic acid methyl ester is involved in Arabidopsis immunity.Journal of experimental botany · 2023Article
- Sphingolipids are involved in insect egg-induced cell death in Arabidopsis.Plant physiology · 2022Article
- A non-targeted metabolomics analysis identifies wound-induced oxylipins inFrontiers in plant science · 2022Article
- Accurate and easy method for systemin quantification and examining metabolic changes under different endogenous levels.Plant methods · 2018Article
- Metabolite profiling of non-sterile rhizosphere soil.The Plant journal : for cell and molecular biology · 2017Article
- Divergent co-transcriptomes of different host cells infected with Toxoplasma gondii reveal cell type-specific host-parasite interactions.Scientific reports · 2017Article
- Ectopically expressed glutaredoxin ROXY19 negatively regulates the detoxification pathway in Arabidopsis thaliana.BMC plant biology · 2016Article
- Article
- Functional Characterization of CYP94-Genes and Identification of a Novel Jasmonate Catabolite in Flowers.PloS one · 2016Article
- TGA Transcription Factors Activate the Salicylic Acid-Suppressible Branch of the Ethylene-Induced Defense Program by Regulating ORA59 Expression.Plant physiology · 2014Article
- Article
- Verticillium longisporum infection affects the leaf apoplastic proteome, metabolome, and cell wall properties in Arabidopsis thaliana.PloS one · 2012Article
- MarVis-Filter: ranking, filtering, adduct and isotope correction of mass spectrometry data.Journal of biomedicine & biotechnology · 2012Article
- Metabolic priming by a secreted fungal effector.Nature · 2011Article
- *omeSOM: a software for clustering and visualization of transcriptional and metabolite data mined from interspecific crosses of crop plants.BMC bioinformatics · 2010Article
- MarVis-Pathway: integrative and exploratory pathway analysis of non-targeted metabolomics data.Metabolomics : Official journal of the Metabolomic SocietyArticle
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundA central goal of experimental studies in systems biology is to identify meaningful markers that are hidden within a diffuse background of data originating from large-scale analytical intensity measurements as obtained from metabolomic experiments. Intensity-based clustering is an unsupervised approach to the identification of metabolic markers based on the grouping of similar intensity profiles. A major problem of this basic approach is that in general there is no prior information about an adequate number of biologically relevant clusters.
resultsWe present the tool MarVis (Marker Visualization) for data mining on intensity-based profiles using one-dimensional self-organizing maps (1D-SOMs). MarVis can import and export customizable CSV (Comma Separated Values) files and provides aggregation and normalization routines for preprocessing of intensity profiles that contain repeated measurements for a number of different experimental conditions. Robust clustering is then achieved by training of an 1D-SOM model, which introduces a similarity-based ordering of the intensity profiles. The ordering allows a convenient visualization of the intensity variations within the data and facilitates an interactive aggregation of clusters into larger blocks. The intensity-based visualization is combined with the presentation of additional data attributes, which can further support the analysis of experimental data.
conclusionMarVis is a user-friendly and interactive tool for exploration of complex pattern variation in a large set of experimental intensity profiles. The application of 1D-SOMs gives a convenient overview on relevant profiles and groups of profiles. The specialized visualization effectively supports researchers in analyzing a large number of putative clusters, even though the true number of biologically meaningful groups is unknown. Although MarVis has been developed for the analysis of metabolomic data, the tool may be applied to gene expression data as well.
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Registered trials
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