Topic 1-05: Get pathways from BioCarta

Zuguang Gu z.gu@dkfz.de

2024-01-26

BioCarta is a valuable source of biological pathways which not only provides well manually curated pathways, but also remarkable and intuitive pathway images.

The BioCartaImage package

The BioCartaImage is mainly for customizing BioCarta pathway images, but of source it contains gene sets for BioCarta pathways.

library(BioCartaImage)
head(PATHWAY2ENTREZ)

##         PATHWAY ENTREZ
## 1 h_RELAPathway   5970
## 2 h_RELAPathway   4790
## 3 h_RELAPathway   8772
## 4 h_RELAPathway   8737
## 5 h_RELAPathway   8717
## 6 h_RELAPathway   7189

The full name of pathways:

pathway_names = sapply(BIOCARTA_PATHWAYS, function(x) x$name)
head(pathway_names)

##                                                                                       h_RELAPathway 
##                                              "Acetylation and Deacetylation of RelA in The Nucleus" 
##                                                                                        h_no1Pathway 
##                                                              "Actions of Nitric Oxide in the Heart" 
##                                                                                         h_gsPathway 
##                                                  "Activation of cAMP-dependent protein kinase, PKA" 
##                                                                                        h_CSKPathway 
## "Activation of Csk by cAMP-dependent Protein Kinase Inhibits Signaling through the T Cell Receptor" 
##                                                                                        h_pkcPathway 
##                                              "Activation of PKC through G protein coupled receptor" 
##                                                                                    h_srcRPTPPathway 
##                                           "Activation of Src by Protein-tyrosine phosphatase alpha"

Highlight genes on the pathway image

library(grid)
grid.newpage()
grid.biocarta("h_RELAPathway", color = c("1387" = "yellow"))

Add more complicated graphics:

grob = biocartaGrob("h_RELAPathway")
grob2 = mark_gene(grob, "1387", function(x, y) {
    pos = pos_by_polygon(x, y)
    pushViewport(viewport(x = pos[1] - 10, y = pos[2], 
        width = unit(4, "cm"), height = unit(4, "cm"), 
        default.units = "native", just = "right"))
    grid.rect(gp = gpar(fill = "red"))
    grid.text("add whatever\nyou want here")
    popViewport()
}, capture = TRUE)
grid.draw(grob2)