George Mason University     |     Ganiraju Manyam, Ancha Baranova

How KPP works?

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a compendium of databases covering annotated genomes and protein interaction networks for all sequenced organisms. KEGG PATHWAY is a compilation of manually verified pathway maps displaying both the molecular interactions and the biochemical reactions. The recent version of this database includes a complete set of pathways related to signal transduction and other cellular processes.KPP will provide fast and comprehensive visualization of the global GE changes by consolidating a list of the color-coded candidate genes into the KEGG pathways.

KPP accepts the upregulated and downregulated gene lists as two different text files containing the gene identifiers of any organism. Permitted identifiers include GENBANK ID, NCBI GENE ID, NCBI GI ACCESSION, UNIGENE ID and UNIPROT ID. These identifiers are converted to KEGG gene identifiers and all the pathways associated with each of identified genes are extracted. Mapped genes are automatically consolidated within each pathway and color coded according to users’ preferences. Genes of interest can be also be highlighted using differentiating font color (see Examples). The number of the returned pathways could be minimized by filtering either the total number the painted genes in a given pathway or the ratio of the painted genes to the total number of genes in a given pathway.