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OverviewVANTED stands for Visualization and Analysis of Networks containing Experimental Data.This system makes it possible to load and edit graphs, which may represent biological pathways or functional hierarchies. It is possible to map experimental datasets onto the graph elements and visualize time series data or data of different genotypes or environmental conditions in the context of a the underlying biological processes. Built-in statistic functions allow a fast evaluation of the data (e.g. t-Test or correlation analysis). A demo session (video and screenshot list) is available from the Tutorials section, which additionally contains example pathways and measurement datasets.Support for SBGN Process Diagram Level 1 is included in VANTED since V1.53. Example: Glycolysis pathway [SVG, PNG, GRAPHML]. Additional example files are available for download directly from within VANTED. Use the side panel Help/Example Visualizations and select the SBGN tree node from the list.Data MappingCombining experimental measurement data with network data is possible by first loading or creating a network. The loading of network data was described before. It is also possible to edit or draw pathways manually as described here.The next step is the preparation and loading of experimental measurement data. This is described in more detail here. While preparing the measurement data it is of great importance to use common names or identifiers which can be mapped to the labels of the target network elements. In the case that a mapping with KEGG pathways is desired, the substance names for the measurements should be EC numbers or Compound IDs.As the mapping procedure also considers the name and any synonym of the EC and compound nomenclature, it is also possible to name the measurements accordingly.Measurement values which can not be mapped automatically may be omitted during the mapping procedure. The second checkbox at the bottom of the experiment dataset pane called Create new nodes for... determines if new nodes are created for nodes that can not be automatically mapped.During the mapping procedure optionally a user-given mapping can be performed. The third checkbox Ask for user-given mapping... determines this behavior. In the case that no automatic mapping is possible the user may select one of the available graph elements (identified by its labels) for mapping the particular measured substance manually to the corresponding graph element.
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