gene GO ID

Question

[yingw7373]

Hi,

How can I find the gene GO ID? I only have a list of gene name.

Thank you!

kate

[Prasad]

What organism?? try biomart or ncbi gene database

Answer 1

[Guangchuang Yu]

see A: Collecting Genes with similar GO term, switch fromType and toType can map gene to GO.

> library(clusterProfiler)
> g = c("546",    "672",    "1786",   "1787")
> x = bitr(g, fromType="ENTREZID", toType="GOALL", OrgDb="org.Hs.eg.db")
> head(x)
  ENTREZID      GOALL EVIDENCEALL ONTOLOGYALL
1      546 GO:0000003         IEA          BP
2      546 GO:0000070         IMP          BP
3      546 GO:0000122         ISS          BP
4      546 GO:0000166         IEA          MF
5      546 GO:0000228         IDA          CC
6      546 GO:0000228         ISS          CC
> tail(x)
     ENTREZID      GOALL EVIDENCEALL ONTOLOGYALL
2402     1787 GO:0090304         TAS          BP
2403     1787 GO:0097159         IEA          MF
2404     1787 GO:1901360         IDA          BP
2405     1787 GO:1901360         TAS          BP
2406     1787 GO:1901363         IEA          MF
2407     1787 GO:1901698         IEA          BP
> head(subset(x, ONTOLOGYALL == 'BP'))
   ENTREZID      GOALL EVIDENCEALL ONTOLOGYALL
1       546 GO:0000003         IEA          BP
2       546 GO:0000070         IMP          BP
3       546 GO:0000122         ISS          BP
8       546 GO:0000278         IMP          BP
9       546 GO:0000280         IMP          BP
10      546 GO:0000723         ISS          BP
> head(subset(x, ONTOLOGYALL == 'MF'))
   ENTREZID      GOALL EVIDENCEALL ONTOLOGYALL
4       546 GO:0000166         IEA          MF
23      546 GO:0001882         IEA          MF
24      546 GO:0001883         IEA          MF
27      546 GO:0003674         IDA          MF
28      546 GO:0003674         IEA          MF
29      546 GO:0003674         IPI          MF
> head(subset(x, EVIDENCEALL != 'IEA'))
  ENTREZID      GOALL EVIDENCEALL ONTOLOGYALL
2      546 GO:0000070         IMP          BP
3      546 GO:0000122         ISS          BP
5      546 GO:0000228         IDA          CC
6      546 GO:0000228         ISS          CC
7      546 GO:0000228         TAS          CC
8      546 GO:0000278         IMP          BP

You can separate/filter the result by ontology and/or evidence.

Answer 2

[EagleEye]

Gene Set Clustering based on Functional annotation (GeneSCF)

A: Collecting Genes with similar GO term

Answer 3

[Lluís R.]

There isn't a unique Gene Ontology term that describes a gene. Each gene have a set of ontologies, from three different point of view: biological processes, cellular components and molecular functions in a species-independent manner. Ref

You can use Amigo to find the gene ontologies related to those genes.

Answer 4

[Persistent LABS]

Hi

GEne SeT AnaLysis Toolkit (http://www.webgestalt.org) is a web-based platform that you can explore. For a given organism, you can upload gene ids and perform gene ontology, pathway, enrichment studies etc. Worth exploring.

Thanks

Priyabrata Panigrahi

Persistent LABS