This function takes the output of get_gene_regulators() with
format multirow,
onerow or table, or a vector with genes and retrieves information about the
TFs and their regulated genes
get_regulatory_summary(regulondb, gene_regulators)A regulondb() object.
Result from get_gene_regulators() or vector of
genes
A data frame with the following columns:
The name or gene of TF
Regulated Genes per TF
Percent of regulated genes per TF
positive, negative or dual regulation
Name(s) of regulated genes
## 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"
)
## Get the araC regulators
araC_regulation <-
get_gene_regulators(
e_coli_regulondb,
genes = c("araC"),
format = "multirow",
output.type = "TF"
)
## Summarize the araC regulation
get_regulatory_summary(e_coli_regulondb, araC_regulation)
#> regulondb_result with 3 rows and 7 columns
#> TF Regulated_genes_per_TF Percent Activator Repressor
#> <character> <character> <character> <character> <character>
#> 1 AraC 1 33.3333333333333 0 0
#> 2 CRP 1 33.3333333333333 1 0
#> 3 XylR 1 33.3333333333333 0 1
#> Dual Regulated_genes
#> <character> <character>
#> 1 1 araC
#> 2 0 araC
#> 3 0 araC
## Retrieve summary of genes 'araC' and 'modB'
get_regulatory_summary(e_coli_regulondb,
gene_regulators = c("araC", "modB")
)
#> regulondb_result with 4 rows and 7 columns
#> TF Regulated_genes_per_TF Percent Activator Repressor
#> <character> <character> <character> <character> <character>
#> 1 AraC 1 20 0 0
#> 2 CRP 2 40 2 0
#> 3 ModE 1 20 0 1
#> 4 XylR 1 20 0 1
#> Dual Regulated_genes
#> <character> <character>
#> 1 1 araC
#> 2 0 modB, araC
#> 3 0 modB
#> 4 0 araC
## Obtain the summary for 'ECK120000050' and 'modB'
get_regulatory_summary(e_coli_regulondb,
gene_regulators = c("ECK120000050", "modB")
)
#> regulondb_result with 4 rows and 7 columns
#> TF Regulated_genes_per_TF Percent Activator Repressor
#> <character> <character> <character> <character> <character>
#> 1 AraC 1 20 0 0
#> 2 CRP 2 40 2 0
#> 3 ModE 1 20 0 1
#> 4 XylR 1 20 0 1
#> Dual Regulated_genes
#> <character> <character>
#> 1 1 araC
#> 2 0 modB, araC
#> 3 0 modB
#> 4 0 araC