Visualization of multiple experiment gene set analysis

Gene set analysis involves the association of genes that are relevant in certain biological experiments to knowledge sources such as pathways and gene ontologies. The experiments can correspond to patient groups or expression changes at different time points in response to certain stimuli. In this paper, we present the web-based system WEGA to associate gene sets with knowledge sources and conduct enrichment analysis to identify most affected pathways and ontology terms. Enrichment results are available in downloadable tabular format and interactively visualized. The most important features of WEGA is its ability to visualize the results of multiple experiments in a comparative manner using static and interactive graphs, highlighted and animated KEGG maps, hierarchy trees, and heatmaps. WEGA is free to use and it is accessible online at http://nubios.nileu.edu.eg/wega.