Tag 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
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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">

Accessing KEGG database from R/Bioconductor

KEGG database is a great resource for biological pathway information, which is an essential part of genome/transcriptome analysis where biological interpretation are formed.

For high throughput studies, it is preferred to access KEGG database programmatically. KEGG recently released the REST service to accomodate such needs. More information about REST service in KEGG can be found from here.

There is also a KEGGREST Bioconductor package available. Since KEGGREST is not working well under my computing environment, I wrote my own code. Below are some examples.

First, a simple example of getting an organism’s basic information.

getOrganismInfo <- function(organism){
  KEGG_INFO_BASE <- "http://rest.kegg.jp/info/"
  info_REST_url <- paste(KEGG_INFO_BASE, organism, sep="")
  info <- readLines(info_REST_url)
  info
}

Calling the above function for human (“hsa” as the organism code), you will get the following:

> getOrganismInfo(“hsa”)
[1] “T01001 Homo sapiens (human) KEGG Genes Database”
[2] “hsa Release 65.0+/02-21, Feb 13″
[3] ” Kanehisa Laboratories”
[4] ” 26,241 entries”

The second example demonstrate how to list KEGG pathway ids and names for a specified organism:

mapPathwayToName <- function(organism) {
  KEGG_PATHWAY_LIST_BASE <- "http://rest.kegg.jp/list/pathway/"
  pathway_list_REST_url <- paste(KEGG_PATHWAY_LIST_BASE, organism, sep="")

  pathway_id_name <- data.frame()

  for (line in readLines(pathway_list_REST_url)) {
    tmp <- strsplit(line, "\t")[[1]]
    pathway_id <- strsplit(tmp[1], organism)[[1]][2]
    pathway_name <- tmp[2]
    pathway_name <- strsplit(pathway_name, "\\s+-\\s+")[[1]][1]
    pathway_id_name[pathway_id, 1] = pathway_name

  }

  names(pathway_id_name) <- "pathway_name"
  pathway_id_name
}

Running this code with “hsa” lists all the human pathways stored in KEGG.

> human_pathways head(human_pathways)
pathway_name
00010 Glycolysis / Gluconeogenesis
00020 Citrate cycle (TCA cycle)
00030 Pentose phosphate pathway
00040 Pentose and glucuronate interconversions
00051 Fructose and mannose metabolism
00052 Galactose metabolism

The third example shows how to map a list of genes to pathways. Note since not all the genes have functions assigned, we’ll only get pathways for some of the genes.

mapGeneToPathway <- function(organism) {
  KEGG_PATHWAY_LINK_BASE <- "http://rest.kegg.jp/link/pathway/"
  pathway_link_REST_url <- paste(KEGG_PATHWAY_LINK_BASE, organism, sep="")
  
  gene_pathway <- data.frame()

  for (line in readLines(pathway_link_REST_url)) {
    tmp <- strsplit(line, "\t")[[1]]
    gene <- tmp[1]
    gene <- strsplit(gene, ":")[[1]][2]  
    pathway_id<- strsplit(tmp[2], organism)[[1]][2]

    if (is.null(gene_pathway[gene, 1])) {
      gene_pathway[gene,1] = pathway_id
    } else {
      if (is.na(gene_pathway[gene,1])) {
        gene_pathway[gene,1] = pathway_id
      } else {
        gene_pathway[gene,1] = paste(gene_pathway[gene, 1], pathway_id, sep=";")
      }
    }
  }
  names(gene_pathway) <- "pathway_id"
  gene_pathway
}

Try it with “hsa”:

> gene_to_pathway <- mapGeneToPathway("hsa")
> head(gene_to_pathway, n=3)
pathway_id
10 00232;00983;01100;05204
100 00230;01100;05340
1000 04514;05412

Note that some gene (10) are mapped to 4 pathway id. Combine this function with the second example, you will be able to add pathway names to the table.