KeggExp is a biologist-friendly web server to integrate KEGG pathways and expression profile data (data generated by Microarray, RNA-seq, or mass spectrometry). It aims to adopt interactive visualization techniques to help researchers find key kegg pathways or genes that are worth further attention in analyzing expression profile data. Compared with existing tools, it has following new features:
- It presents simultaneously pathway map and dendgrogram & heatmap of hierarchical clustering results of the genes in the pathway.
- It provides interactive operations connecting the pathway map and the dendgrogram & heatmap; users can click to select co-expressed genes in the dendgrogram & heatmap and then highlight them in the pathway map.
- It presents a button for each experimental group; users can click one button and then highlight the differentially-expressed genes/proteins in the pathway map.
- It provides interactive operations to visualize multiple pathways in sequence.
Visualize pathway map and dendgrogram & heatmap
After users select one pathway, KeggExp automatically downloads pathway map and perform clustering analysis for the genes in the pathway, then simultaneously presents pathway map and dendgrogram & heatmap.
Highlight co-expressed genes in the pathway map
Users could select co-expressed genes in the dendgrogram & heatmap, and highlight them in the pathway map.
Highlight differentially-expressed genes/proteins in the pathway map
When users click one experimental group, the up-expressed genes will become red and the down-expressed genes will become green.
Operations for visualizing multiple pathways
One pathway often have cross talks with other pathways. Users can click pathway box in the pathway map and then explore the corresponding pathway. The pathways that have been explored are listed in the left top, users can select one pathway they want to explore.
KeggExp is available at http://www.fgvis.com/expressvis/KeggExp. If any questions or suggestions, feel free to contact me.