I applied “Pathview” to overlay my gene expression data (“limma” - logFC) with a KEGG pathway (TNF-alpha). In this pathway, there are 111 genes (http://www.genome.jp/dbget-bin/get_linkdb?-t+genes+path:mmu04668). However, not all the genes are included in the KEGG graphics ((http://www.genome.jp/kegg-bin/show_pathway?mmu04668). It seems one gene symbol on the graph can represent many genes from the pathway. For instance, if you move your coursor over “PI3K” on the graph, several gene symbols pop up (e.g Pik3ca, Pik3cd, Pik3r1, Pik3r2, Pik3r3, Pik3r5, Pik3cg, Pik3cb) but if you click on the gene symbol it takes you to a link indicating only one gene Pik3ca. 109 genes of TNFa pathway are represented on my gene expression array including the 8 “PIK3” genes: 2 of those 8 genes with negative logFC , 6 of them with positive logFC.
Q1.I am wondering what/how values and genes are signified by each symbol on the graph made by “Pathview” when the gene symbol has more than one representation on the array (= gene.data for “Pathview”) like “PIK3” as an example. I was searching for an answer on the KEGG website or in relevant articles but I have not found any clear answer to my question.
Q2.I would like to change the color-coding of the gene symbols on the "Pathview" graph. I would like to represent all the negative values(- logFC) with one color (green palette (bright green to dark green) shade and all the positive values (+logFC) with one color (red palette (dark red to bright red) shade divided at 0, no gray in the middle. I tried different combinations of colors and bins but I could not get the division exactly in the middle (at 0). In addition, when I increase the bin substantially, the color key is off the chart.
pv.out <- pathview(gene.data = limma_result[, 1] , pathway.id =”04668 “, species = "mmu", out.suffix = "TNFa", keys.align = "y", kegg.native = T, both.dirs = TRUE, low = "green", mid = "gray", high = "red", bin = 20)
Any help is highly appreciated.
Thank you in advacne.