RobExT: a tool to customize microarray data for CellDesigner and Cytoscape

CellDesigner and Cytoscape are popularly used tools in systems biology studies for biological network construction. Plug-ins for these tools are also available which enable visualization of the microarray data in the context to the constructed biological networks. However, a major limitation for these tools is that they accept inputs only in a specified format and not in the format generated routinely by secondary data analysis pipeline for microarray data. Generating an input file in the format acceptable to CellDesigner and/or Cytoscape is a non-trivial task for biologists with very limited computation experience. Hence, we developed an easy to use tool, RobExT (Robust Expression parsing Tool), that empowers biologists with capabilities to select, cleanse and filter microarray data relevant to their biological networks constructed using CellDesigner/Cytoscape.

Using RobExT, we extracted gene expression profile data for 100 genes constituting our biological network (could be used for any number of genes) from a normalized microarray dataset with more than 45000 gene probes. Input for RobExT was normalized microarray dataset, a text file listing 100 genes of our interest and appropriate p-value cut off (≤0.05). On processing, RobExT generated output files with expression profiles only for our genes of interest based on p-value cut off and in the format acceptable to CellDesigner and Cytoscape. Further, this data was overlaid on the biological network of 100 genes under consideration for easy visualization and analysis.

We have developed an easy to use tool RobExT that takes normalized microarray data, and, based on user inputs, generates output files that can be easily imported into CellDesigner and Cytoscape for easy visualization and further biological interpretation.