Get TFs or genes that regulate the genes of interest

Given a list of genes (name, bnumber or GI), get all transcription factors or genes that regulate them. The effect of regulators over the gene of interest can be positive (+), negative (-) or dual (+/-)

get_gene_regulators(regulondb, genes, format = "multirow", output.type = "TF")

Arguments

regulondb

A regulondb class.

genes

Vector of genes (name, bnumber or GI).

format

Output format: multirow, onerow, table

output.type

How regulators will be represented: "TF"/"GENE"

Value

A regulondb_result object.

Author

Carmina Barberena Jonas, Jesús Emiliano Sotelo Fonseca, José Alquicira Hernández, Joselyn Chávez

Examples

## 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 Transcription factors that regulate araC in one row
get_gene_regulators(
    e_coli_regulondb,
    genes = c("araC"),
    output.type = "TF",
    format = "onerow"
)
#> regulondb_result with 1 row and 2 columns
#>         genes             regulators
#>   <character>            <character>
#> 1        araC CRP(+), AraC(+/-), X..

## Get genes that regulate araC in table format
get_gene_regulators(
    e_coli_regulondb,
    genes = c("araC"),
    output.type = "GENE",
    format = "table"
)
#> regulondb_result with 1 row and 3 columns
#>             araC         crp        xylR
#>      <character> <character> <character>
#> araC         +/-           +           -