Category Archives: KEGG

Search KEGG Pathway Maps by Keyword in R

I was recently asked about how to list KEGG pathways not specific to any organism, which was not addressed in my previous post on accessing KEGG pathway from R.  Here, I post one example that shows you how to search KEGG pathway by keyword from R.

First, let’s define the function getKeggPathwayTable:

getKeggPathwayTable <- function(){
  pathway_link_REST_url <- "http://rest.kegg.jp/list/pathway/"
  kegg_pathways<- data.frame()

  current_row = 1
  for (line in readLines(pathway_link_REST_url)) {
    tmp <- strsplit(line, "\t")[[1]]
    map <- tmp[1]
    map <- strsplit(map, ":")[[1]][2]  
    pathway_name<- tmp[2]
    kegg_pathways[current_row, 1]=map
    kegg_pathways[current_row, 2]=pathway_name
    current_row = current_row + 1
  }
  names(kegg_pathways) <- c("map_id","name")
  kegg_pathways
}

Running the above function will give a data frame that lists all the current KEGG pathway IDs and names.

Next, lets define a function to search the data frame returned by getKeggPathwayTable by keyword.

searchKeggPathwayByKeyword <- function(keyword) {
  kegg_pathways <- getKeggPathwayTable()
  hits <- grep(keyword, kegg_pathways$name, ignore.case=TRUE)
  kegg_pathways[hits,]
}

Note that I use “ignore.case=TRUE” to make sure that the search is not case sensitive. Now let’s try it with the keyword “vitamin” and “sucrose.”

> searchKeggPathwayByKeyword("vitamin")
      map_id                             name
110 map00750            Vitamin B6 metabolism
303 map04977 Vitamin digestion and absorption

> searchKeggPathwayByKeyword("sucrose")
     map_id                          name
60 map00500 Starch and sucrose metabolism
Advertisements

Merge pathway name and pathway ID from KEGG database

 If an organism is listed in KEGG database, one can easily get a list of its pathways and map a list of genes to the pathways (see here for an example about how to do it in R/bioconductor).

However, the pathway mapping result only provides the pathway IDs and not pathway names. To merge pathway IDs with pathway names, we only need to add  one more column of pathway names for each pathway ID listed in the same row of the mapping result dataframe. The R code below provides an example.

my_organism.gene_pathway <- mapGeneToPathway(organism) # map each gene to pathway ID.
my_organism.pathway_id_name <- mapPathwayToName(organism) # get the pathway name for each pathway ID.

# adding pathway names to mapped pathway IDs.
for (gene in row.names(my_orgranism.gene_pathway)) { 
  pathway_id <- my_orgranism.gene_pathway[gene, 'pathway_id']
  pathway_id <- strsplit(pathway_id, ";")[[1]]
  
  if (length(pathway_id) == 1) {        # if a gene maps to a single pathway
    pathway_name <- my_orgranism.pathway_id_name[pathway_id, "pathway_name"]
    my_orgranism.gene_pathway[gene,"pathway_name"] = pathway_name
  } else {                              # if a gene mapes to multiple pathways
    for (a_id in pathway_id) {
      if (is.null(my_orgranism.gene_pathway[gene, "pathway_name"])) {
        my_orgranism.gene_pathway[gene, "pathway_name"] = my_orgranism.pathway_id_name[a_id, "pathway_name"]
      } else {
        name <- my_orgranism.gene_pathway[gene, "pathway_name"]
        if (is.na(name)) {
          name <- my_orgranism.pathway_id_name[a_id, "pathway_name"]
        } else {
          name <- paste(name, my_orgranism.pathway_id_name[a_id, "pathway_name"], sep=";")
        }
        my_orgranism.gene_pathway[gene, "pathway_name"] <- name
      }
    }
  }
}

Find organism code used in KEGG reference pathways

In my recent blog on accessing KEGG database from R/bioconductor, I used examples from human data, which is identified as “hsa” in KEGG. One has to know the organism code to retrieve information from KEGG for that specified organism. The table below lists the first three codes used in KEGG.

eco Escherichia coli K-12 MG1655
ecj Escherichia coli K-12 W3110
ecd Escherichia coli K-12 DH10B

The first text string of 3 or 4 characters in the table are the code, followed by the organism name.

This table generated from the source code of a pathway page in KEGG, which lists organism code for the organism name table.

</pre>
<form method="get" name="selmenu"><select name="org_name"><option value="map">Reference pathway</option><option value="ko">Reference pathway (KO)</option><option value="set_cookie">-----< Set personalized menu >-----</option><option value="has.sort_alp">-----< Sort below by alphabet >-----</option><option value="eco">Escherichia coli K-12 MG1655</option><option value="ecj">Escherichia coli K-12 W3110</option><option value="ecd">Escherichia coli K-12 DH10B</option></select>
<select name="org_name">...</select>
<select name="org_name">