This function retrieves all the regulation networks in regulonDB between TF-TF, GENE-GENE or TF-GENE depending on the parameter 'type'.
get_regulatory_network(
regulondb,
regulator = NULL,
type = "TF-GENE",
cytograph = FALSE
)A regulondb() object.
Name of TF or gene that acts as regulator. If NULL, the
function retrieves all existent networks in the regulonDB.
"TF-GENE", "TF-TF", "GENE-GENE"
If TRUE, displays network in Cytoscape. This option requires previous instalation and launch of Cytoscape.
A regulondb_result object.
## Connect to the RegulonDB database if necessary
if (!exists("regulondb_conn")) regulondb_conn <- connect_database()
## Build the regulon db object
e_coli_regulondb <-
regulondb(
database_conn = regulondb_conn,
organism = "E.coli",
database_version = "1",
genome_version = "1"
)
## Retrieve regulation of 'araC'
get_regulatory_network(e_coli_regulondb,
regulator = "AraC",
type = "TF-GENE"
)
#> regulondb_result with 14 rows and 3 columns
#> regulator regulated effect
#> <character> <character> <character>
#> 1 AraC araA +/-
#> 2 AraC araB +/-
#> 3 AraC araC +/-
#> 4 AraC araD +/-
#> 5 AraC araE +
#> ... ... ... ...
#> 10 AraC xylA -
#> 11 AraC xylB -
#> 12 AraC ygeA +
#> 13 AraC ydeM -
#> 14 AraC ydeN -
## Retrieve all GENE-GENE networks
get_regulatory_network(e_coli_regulondb, type = "GENE-GENE")
#> regulondb_result with 4405 rows and 3 columns
#> regulator regulated effect
#> <character> <character> <character>
#> 1 cpxR acrD +
#> 2 cpxR cpxR +
#> 3 cpxR aroG +
#> 4 cpxR cheA -
#> 5 cpxR cheA -
#> ... ... ... ...
#> 4401 bglJ,gadE,rcsA,rcsB yqhG +
#> 4402 bglJ,gadE,rcsA,rcsB ygiZ +
#> 4403 bglJ,gadE,rcsA,rcsB rseD +
#> 4404 NA accB -
#> 4405 NA accC -
## Retrieve TF-GENE network of AraC and display in Cytoscape
## Note that Cytospace needs to be open for this to work
cytoscape_present <- try(RCy3::cytoscapePing(), silent = TRUE)
if (!is(cytoscape_present, "try-error")) {
get_regulatory_network(
e_coli_regulondb,
regulator = "AraC",
type = "TF-GENE",
cytograph = TRUE
)
}