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. Similar 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 no shown). B) The KEGG biochemical pathway that appears following the selection of the pathway name "apoptosis" in Figure 5A depicts 4 differentially expressed genes within the apoptosis pathway by highlighted them in light green and red. The fact that the KEGG pathway highlights only 4 genes while the KeggChart maps 5 Affymetrix probesets to the apoptosis pathway is due to the fact that two probesets target the same "TRFα" gene.
Dennis et al. Genome Biology 2003 4:P3 doi:10.1186/gb-2003-4-5-p3