Question

How to retrieve gene ontology GO class from gene list?

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bandconductor • 0

@7c443214

Last seen 4 weeks ago

Canada

Hi all,

Does any one know how to obtain the information under GO class (direct) given a gene list? Ideally I would like to be able to retrieve it with R / API. I have tested several packages but none are able to retrieve this information... Any help would be greatly appreciated!

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edit: this screenshot is taken from AmiGO Annotations edit2: title updated for clarity

GO.db goTools • 572 views

ADD COMMENT • link updated 7 months ago by James W. MacDonald 67k • written 7 months ago by bandconductor • 0

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What do you mean by 'the information'? Do you have things in particular that you want?

ADD REPLY • link 7 months ago James W. MacDonald 67k

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Sorry I wasn't clear before. What I mean is the all the information associated with the go term, such as description and evidence.

I have since realized that most of this can be done via BiomaRt (under some confusingly named attributes). Included below in case it may help others. e.g.

ensembl = useMart("ensembl",dataset="hsapiens_gene_ensembl")
gene.data  <- getBM(attributes = c('hgnc_symbol','go_id','name_1006','definition_1006','go_linkage_type','namespace_1003'),
                    filters = 'hgnc_symbol',
                    values = "TOX3", 
                    mart = ensembl,
                    uniqueRows = TRUE)
head(gene.data,n=2)

  hgnc_symbol      go_id   name_1006                                                                                                                        definition_1006 go_linkage_type     namespace_1003
2        TOX3 GO:0005654 nucleoplasm                                                          That part of the nuclear content other than the chromosomes or the nucleolus.             IDA cellular_component
3        TOX3 GO:0005829     cytosol The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.             IDA cellular_component

ADD REPLY • link 7 months ago bandconductor • 0

score 2 · Accepted Answer · 2024-04-24

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James W. MacDonald 67k

@james-w-macdonald-5106

Last seen 17 hours ago

United States

You can also use a combination of the org.Hs.eg.db and GO.db packages.

> library(GO.db)

> library(org.Hs.eg.db)

> go <- mapIds(org.Hs.eg.db, "TOX3", "GO","SYMBOL")
'select()' returned 1:many
mapping between keys and columns

> go
        TOX3 
"GO:0003682" 

> info <- select(GO.db, go, c("TERM","DEFINITION"), "GOID")
'select()' returned 1:1 mapping
between keys and columns
> info
        GOID              TERM
1 GO:0003682 chromatin binding
                                                                                                                                                 DEFINITION
1 Binding to chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.

ADD COMMENT • link 7 months ago James W. MacDonald 67k

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Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a few more), is there anyway to make it show all the associated ones? Secondly, is it also possible to retrieve the genomic coordinates from org.Hs.eg.db?

ADD REPLY • link 7 months ago bandconductor • 0

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Yes. The keys argument to both select and mapIds will accept a vector (see ?select for more information). Also, the vignette for AnnotationDbi has lots of examples that you can emulate. The best way to improve with R is to learn how to figure things out, and reading both the help pages and vignettes is a good start.

You can no longer get positional information (except for the karyotype info) from the OrgDb packages. Instead you should use a TxDb package, which is a different subject entirely. You can read the relevant vignette for that sort of thing as well.

ADD REPLY • link 7 months ago James W. MacDonald 67k