Figure 5.

Ouput of KeggCharts. (a) Visualization chart showing the distribution of 402 genes among KEGG biochemical pathways. The hit threshold was set to three and the output was sorted by hit count. The large number of unclassified identifiers is due to the fact that KEGG is biochemical-pathway centric and thus provides low coverage of gene lists. Similarly to the output of GoCharts, blue bars represent the number of genes in each pathway. Selecting a blue bar opens an HTML table showing the LocusLink, gene name, current classification, and other classification data for the genes in that pathway (data not shown). (b) The KEGG biochemical pathway that appears following the selection of the pathway name 'apoptosis' in (a) depicts four differentially expressed genes within the apoptosis pathway by highlighting them in light green and red. The fact that the KEGG pathway highlights only four genes whereas the KeggChart maps five Affymetrix probe sets to the apoptosis pathway is due to the fact that two probe sets target the same 'TNF-alpha' gene.