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map, software, tool, visualize, 3d, Java, layout, cluster, large scale, gene, nodes, vector, conditions, data, probeset, normalized

BioLayout Express 3D is a Java platform for layout, visualization and clustering of large Graphs in 3D and 2D. The application is based on the original BioLayout 2D with significant changes to both layout and rendering. The express version has been designed to add functionality for the generation of graphs from large-scale gene expression studies such as Affymetrix chip experiments. In principle this functionality can be used to generate graphs of other data types whose input consists of unique nodes accompanied by a vector of measurements for that node across different conditions. In the case of Affymetrix data, nodes represent probesets and the vector consists of normalized expression measurements for each probeset across the conditions tested.