VANTED: A system for advanced data analysis and visualization in the context of biological networks

By Björn H. Junker, Christian Klukas, Falk Schreiber. BMC Bioinformatics, 2006

550 citations recorded by the source corpus.

BackgroundRecent advances with high-throughput methods in life-science research have increased the need for automatized data analysis and visual exploration techniques. Sophisticated bioinformatics tools are essential to deduct biologically meaningful interpretations from the large amount of experimental data, and help to understand biological processes.ResultsWe present VANTED, a tool for the v isualization and a nalysis of n etworks with related e xperimental d ata. Data from large-scale biochemical experiments is uploaded into the software via a Microsoft Excel-based form. Then it can be mapped on a network that is either drawn with the tool itself, downloaded from the KEGG Pathway database, or imported using standard network exchange formats. Transcript, enzyme, and metabolite data can be presented in the context of their underlying networks, e. g. metabolic pathways or classification hierarchies. Visualization and navigation methods support the visual exploration of the data-enriched networks. Statistical methods allow analysis and comparison of multiple data sets such as different developmental stages or genetically different lines. Correlation networks can be automatically generated from the data and substances can be clustered according to similar behavior over time. As examples, metabolite profiling and enzyme activity data sets have been visualized in different metabolic maps, correlation networks have been generated and similar time patterns detected. Some relationships between different metabolites were discovered which are in close accordance with the literature.ConclusionVANTED greatly helps researchers in the analysis and interpretation of biochemical data, and thus is a useful tool for modern biological research. VANTED as a Java Web Start Application including a user guide and example data sets is available free of charge at http://vanted.ipk-gatersleben.de.

Subfields: Biophysics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/eb5d924f99745fa8eb2c6f0f8248ef758ca30e4c

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Citations in the corpus

Pathview Web: user friendly pathway visualization and data integration (2017, methodology): “Currently, several online tools offer intuitive and useful functions for pathway and data visualization, including MAPMAN (18), VANTED (19), iPath (15), Pathway Pro-jector (12), G-language Pathway Visualization Web Application (20) and Escher (21).”
Metabolomics and Multi-Omics Integration: A Survey of Computational Methods and Resources (2020, methodology): “VANTED follows SBGN specifications.”
Network visualization and analysis of gene expression data using BioLayout Express3D (2009, background): “There are now a range of academic and commercial programs that have been developed for the construction, display, editing and analysis of biological networks and pathways, as well as more generic network analysis and visualization platform”
PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments (2006, background): “Tools have also been developed that focus on the response of one (or several related) genes through multiple time points/experiments with a limited ontology structure [9].”
PathVisio 3: An Extendable Pathway Analysis Toolbox (2015, methodology): “A feature comparison table with other tools like Vanted [16], ProMeTra [17], KEGG Atlas [18] or Ingenuity [19] is available in S1 Table.”
Metabolomics in pesticide research and development: review and future perspectives (2011, unknown): “…Böcker et al. (2009) TargetSearch http://www.bioconductor.org/packages/2.5/bioc/html/TargetSearch.html Cuadros-Inostroza et al. (2009) VANTED http://vanted.ipk-gatersleben.de/ Junker et al. (2006), Klukas and Schreiber (2007) XCMS http://metlin.scripps.edu/download/ Smith et al. (2006)”