Get genus specific pathways from KEGG

Question

[BioStarUser99]

Can you use bioconductor to search kegg pathways (only in a specific genus like Candida) and return the gene names for each pathway?

If so, can you please paste the script that does this? I would like all pathways and members:

pathway1, member1, member2, ...
pathway2, member1,....
.....

Thanks!

Answer 1

[Felix Francis]

Given a KEGG pathway id and a set of KEGG gene ids, the functions return the URL of a KEGG pathway diagram with the elements corresponding to the genes marked by red or specified color

• mark.pathway.by.objects(pathway.id, object.id.list)
• color.pathway.by.objects(pathway.id, object.id.list, fg.color.list, bg.color.list)

Examples

listDatabases()
keggList("organism") ## list all organisms
keggList("hsa") ## list all human genes
keggList("genome") ## list all genome identifiers
keggList("T01001") ## list all human genes

pathway.id: a character string for a KEGG pathway id. KEGG pathway ids consist of the string path followed by a colon, a three-letter code for the organism of concern, and then a number (e. g. "path:eco00020"). The three-letter organism code consists of the first letter of the genus name and the first two letters of the species name of the scientific name of the organism of concern

object.id.list: a vector of character strings for KEGG gene ids. KEGG gene ids normally consist of three letters followed by a column and then several numeric numbers. The three letters are from the first letter of the genus name and the first two letters of the species name of the scientific name of the organism of concern (e. g. hsa:111 for Homo Sapiens)

fg.color.list: a vector of two character strings to indicate the color for the text and border, respectively, of the objects in a pathway diagram. The strings can either be a color code linke #ff0000 or letter link yellow

bg.color.list: a vector of character strings of the same length of object.id.list to indicate the background color of the objects in a pathway diagram. The strings can either be a color code like #ff0000 or letter like yellow

[BioStarUser99]

Hi Felix,

I'm actually not looking for the diagrams, just a list of genes, by pathway for all pathways in candida genus. How would you go about doing that?