Here we present a new visualization tool called Arena3D which introduces a new, staggered multi layer concept that allows the analysis of big networks in a three dimensional space representation. The different layers in the representation correspond to different data types respective concepts like sequences, structures, chemicals diseases, pathways etc. The data entries for one specific data type, like sequences, can be ordered or clustered on their respective layer by applying a data focused similarity measurement like sequence similarity. Several clustering methods are also supported to cluster several data types in different layers. The different nodes of the layers can be connected according to known or predicted relationships between the nodes. The relationships are typically extracted from available databases and available text minimg machineries and are predicted by various data mining methods or originate from experimentally generated data. Indirect connections that may hide some additional information can also be explored.
Maria Secrier, Georgios A. Pavlopoulos, Jan Aerts, and Reinhard Schneider. Arena3D: visualizing time-driven phenotypic differences in biological systems. BMC Bioinformatics 2012, 13:45.
Georgios A. Pavlopoulos, Sean I. O'Donoghue, Venkata P. Satagopam, Theodoros Soldatos, Evangelos Pafilis, and Reinhard Schneider. Arena3D: visualization of biological networks in 3D. BMC Systems Biology 2008, 2:104.