How to retreive all GO daughter terms of a particular Gene Ontology term (e.g. GO:0007275- Multicellular organism development)?

Hi,

I want to know How to retreive all GO child terms of a particular Gene Ontology term (e.g. GO:0007275- Multicellular organism development)? please provide me the details of databases(if any), or the methodology to follow.

Thanks in advance

gene ontology go amigo development

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updated 9.9 years ago by Guangchuang Yu

• written 9.9 years ago by debarunacharya •

2 answers

In R:

require(GO.db)
get("GO:0007275", GOBPCHILDREN)

Here is the output:

     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0009790" "GO:0007349" "GO:0007389" "GO:0007538" "GO:0007545" "GO:0007562"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0007566" "GO:0009791" "GO:0009835" "GO:0009838" "GO:0010259" "GO:0018992"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0018993" "GO:0030237" "GO:0030238" "GO:0035188" "GO:0035212" "GO:0035295"
     part_of      part_of      part_of      part_of      part_of         is_a
"GO:0042335" "GO:0043581" "GO:0045137" "GO:0046660" "GO:0046661" "GO:0048229"
     part_of      part_of      part_of    regulates
"GO:0048647" "GO:0048731" "GO:0048736" "GO:2000026"

• 1 views • link

written 9.9 years ago by Guangchuang Yu

even more, we can write a small function:

library(GO.db)
library(clusterProfiler)

go_children <- function(goid) {
  ont <- go2ont(goid)$Ontology
  GOCHILDREN <- switch(ont, 
                    BP = GOBPCHILDREN,
                    CC = GOCCCHILDREN,
                    MF = GOMFCHILDREN)
  get(goid, GOCHILDREN)
}

# Your case in Biological Process
> goid <- "GO:0007275"
> go_children(goid)
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0009790" "GO:0007349" "GO:0007389" "GO:0007538" "GO:0007545" "GO:0007562"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0007566" "GO:0009791" "GO:0009835" "GO:0009838" "GO:0010259" "GO:0018992"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0018993" "GO:0030237" "GO:0030238" "GO:0035188" "GO:0035212" "GO:0035295"
     part_of      part_of      part_of      part_of      part_of         is_a
"GO:0042335" "GO:0043581" "GO:0045137" "GO:0046660" "GO:0046661" "GO:0048229"
     part_of      part_of      part_of    regulates
"GO:0048647" "GO:0048731" "GO:0048736" "GO:2000026"

## Cellular Component term
> go_children("GO:0005886")
     part_of      part_of         is_a      part_of      part_of      part_of
"GO:0000222" "GO:0000223" "GO:0001533" "GO:0043190" "GO:0046658" "GO:0005887"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0009897" "GO:0009898" "GO:0016323" "GO:0016324" "GO:0016327" "GO:0019897"
     part_of      part_of      part_of      part_of      part_of         is_a
"GO:0030094" "GO:0031226" "GO:0031253" "GO:0031520" "GO:0033181" "GO:0042383"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0044214" "GO:0044459" "GO:0044853" "GO:0045258" "GO:0045260" "GO:0045262"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0045264" "GO:0045266" "GO:0045268" "GO:0045270" "GO:0045272" "GO:0045274"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:0045276" "GO:0045278" "GO:0045282" "GO:0045284" "GO:0060170" "GO:0060342"
        is_a      part_of      part_of      part_of      part_of      part_of
"GO:0097524" "GO:0098590" "GO:0098797" "GO:0098802" "GO:1990154" "GO:1990176"
     part_of      part_of      part_of      part_of      part_of      part_of
"GO:1990191" "GO:1990193" "GO:1990199" "GO:1990203" "GO:1990222" "GO:1990374"
     part_of      part_of
"GO:1990712" "GO:1990851"

• 1 views • link

written 9.9 years ago by Guangchuang Yu

Your answer is much better than mine ! I like it.

• 1 views • link

written 9.9 years ago by Carlo Yague

Go to the amigo page for the GO term, then go to the "neighborhood" tab, then look at the "Children of multicellular organism development (GO:0007275)"

• 1 views • link

written 9.9 years ago by Carlo Yague