ecolitk (version 1.44.0)

ecoligenome.operon: Known operon in E.coli - data.frame

Description

The known operon in the Escherichia coli genome.

Usage

data(ecoligenome.operon)

Format

A data frame with 932 observations (genes) on the following 4 variables.

gene.name

a character vector

gene.annotation

a character vector

operon.name

a factor with levels the names of the operons

operon.comments

a factor with levels the comments for the operons

Source

Built from the webpage: http://www.cib.nig.ac.jp/dda/backup/taitoh/ecoli.operon.html

Details

For some operons, the source of information specifies the existence of regulating elements such as promoter, terminator, box, etc... In those cases, the gene.name is set to "Regulation", and the gene.annotation gives what kind of regulating element it is. If volonteers, it would be neat to map those on the genome... Besides that, not much to add. The data structure is fairly straightforward.

Examples

library(Biobase)
data(ecoligenome.operon)
data(ecoligenomeSYMBOL2AFFY)

## something that might be useful when working with Affymetrix data:
## get the Affymetrix identifiers for the probe sets bundled in operons
## (see the vignette for more details)
ecoligenome.operon$affyid <-
unname(unlist(mget(ecoligenome.operon$gene.name,
                   ecoligenomeSYMBOL2AFFY, ifnotfound=NA)))