Section 3 Pathway crosstalk

Figure 3.1: Gene-centric representation of the crosstalk, with nodes for genes and edges for interactions between nodes. Node are labelled by gene symbols along with the priority information (formatted as [rating@rank]) and color-coded by priority rating, and interactions derived from KEGG pathway map.

3.1 Identify crosstalk

# gene interaction information merged from KEGG pathways
ls_ig <- lapply(c("KEGG_environmental","KEGG_organismal"), function(network){
    g <- xDefineNet(network, guid=guid)
})
ig <- xCombineNet(ls_ig)

# keep the largest component
ig2 <- dNetInduce(g=ig, nodes_query=V(ig)$name) %>% as.undirected()

# search for a subset (with a desired node number [30,35]) of the gene network 
subg <- xPierSubnet(dTarget, network.customised=ig2, subnet.size=50)

# write into a file 'subg_nodes.txt'
dTarget$priority %>% select(name,rank,rating,description) %>% semi_join(tibble(name=V(subg)$name), by='name') %>% write_delim("subg_nodes.txt", delim='\t')

3.2 Crosstalk genes

Crosstalk genes identified above (subg_nodes.txt) can be explored: