kegg orthology entry to pathway ko
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alaihd ▴ 10
@luyang1005-13391
Last seen 10 months ago
United States

Hi, community,

I have used EggNOG produce a table(as shown below) which contains the kegg orthlogy entry. May I know how to get the pathway name based on the list column? 

Thanks in advance.

query list
k119_1151408_63 K00864
k119_1151408_78 K13963
k119_1151433_12 K00873

 

kegg • 589 views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

You could use the KEGGREST package:

> library(KEGGREST)

> keggLink("pathway", c("K00864","K13963","K00873"))
      ko:K00864       ko:K00864       ko:K00864       ko:K00864       ko:K00864
"path:map00561"  "path:ko00561" "path:map01100"  "path:ko01100" "path:map03320"
      ko:K00864       ko:K00864       ko:K00864       ko:K13963       ko:K13963
 "path:ko03320" "path:map04626"  "path:ko04626" "path:map05146"  "path:ko05146"
      ko:K00873       ko:K00873       ko:K00873       ko:K00873       ko:K00873
"path:map00010"  "path:ko00010" "path:map00230"  "path:ko00230" "path:map00620"
      ko:K00873       ko:K00873       ko:K00873       ko:K00873       ko:K00873
 "path:ko00620" "path:map01100"  "path:ko01100" "path:map01110"  "path:ko01110"
      ko:K00873       ko:K00873       ko:K00873       ko:K00873       ko:K00873
"path:map01120"  "path:ko01120" "path:map01130"  "path:ko01130" "path:map01200"
      ko:K00873       ko:K00873       ko:K00873       ko:K00873       ko:K00873
 "path:ko01200" "path:map01230"  "path:ko01230" "path:map04922"  "path:ko04922"
      ko:K00873       ko:K00873       ko:K00873       ko:K00873       ko:K00873
"path:map04930"  "path:ko04930" "path:map05165"  "path:ko05165" "path:map05203"
      ko:K00873       ko:K00873       ko:K00873
 "path:ko05203" "path:map05230"  "path:ko05230"

Or maybe a bit clearer:

> z <- keggLink("pathway", c("K00864","K13963","K00873"))

> lapply(split(z, names(z)), unique)
$`ko:K00864`
[1] "path:map00561" "path:ko00561"  "path:map01100" "path:ko01100"
[5] "path:map03320" "path:ko03320"  "path:map04626" "path:ko04626"

$`ko:K00873`
 [1] "path:map00010" "path:ko00010"  "path:map00230" "path:ko00230"
 [5] "path:map00620" "path:ko00620"  "path:map01100" "path:ko01100"
 [9] "path:map01110" "path:ko01110"  "path:map01120" "path:ko01120"
[13] "path:map01130" "path:ko01130"  "path:map01200" "path:ko01200"
[17] "path:map01230" "path:ko01230"  "path:map04922" "path:ko04922"
[21] "path:map04930" "path:ko04930"  "path:map05165" "path:ko05165"
[25] "path:map05203" "path:ko05203"  "path:map05230" "path:ko05230"

$`ko:K13963`
[1] "path:map05146" "path:ko05146"
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