Molecular Function from ENSEMBL ID

Question

[Scott McKay]

Is there an attribute in biomaRt that will allow me to see the BASIC function of a gene given its ENEMBL ID? I have been searching for a while but 'description' is not desired and I cannot find a 'function' or 'molecular' attribute.

I want to get the following: TGIF1......Transcription Factor XIST.......Chromatin Modifier

Answer 1

[Kevin Blighe]

Hey again Scott, all good?

You could try something like this:

require('biomaRt')
mart <- useMart("ENSEMBL_MART_ENSEMBL")
mart <- useDataset("hsapiens_gene_ensembl", mart)

ens_ids <- c('ENSG00000283726','ENSG00000126351',
  'ENSG00000169609','ENSG00000250565',
  'ENSG00000139133','ENSG00000070778',
  'ENSG00000073060')

annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'ensembl_gene_id',
    'external_gene_name',
    'gene_biotype',
    'go_id',
    'name_1006',
    'definition_1006',
    'go_linkage_type',
    'namespace_1003',
    'goslim_goa_accession',
    'goslim_goa_description',
    'wikigene_description',
    'description'),
  filter = 'ensembl_gene_id',
  values = ens_ids,
  uniqueRows = TRUE)

head(annotLookup)
  ensembl_gene_id external_gene_name   gene_biotype      go_id name_1006
1 ENSG00000070778             PTPN21 protein_coding GO:0005737 cytoplasm
2 ENSG00000070778             PTPN21 protein_coding GO:0005737 cytoplasm
3 ENSG00000070778             PTPN21 protein_coding GO:0005737 cytoplasm
4 ENSG00000070778             PTPN21 protein_coding GO:0005737 cytoplasm
5 ENSG00000070778             PTPN21 protein_coding GO:0005737 cytoplasm
6 ENSG00000070778             PTPN21 protein_coding GO:0005737 cytoplasm
                                                                                                       definition_1006
1 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
2 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
3 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
4 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
5 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
6 All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
  go_linkage_type     namespace_1003 goslim_goa_accession
1             IEA cellular_component           GO:0005575
2             IEA cellular_component           GO:0005623
3             IEA cellular_component           GO:0005622
4             IEA cellular_component           GO:0005737
5             IEA cellular_component           GO:0003674
6             IEA cellular_component           GO:0008150
  goslim_goa_description                              wikigene_description
1     cellular_component protein tyrosine phosphatase non-receptor type 21
2                   cell protein tyrosine phosphatase non-receptor type 21
3          intracellular protein tyrosine phosphatase non-receptor type 21
4              cytoplasm protein tyrosine phosphatase non-receptor type 21
5     molecular_function protein tyrosine phosphatase non-receptor type 21
6     biological_process protein tyrosine phosphatase non-receptor type 21
                                                                           description
1 protein tyrosine phosphatase non-receptor type 21 [Source:HGNC Symbol;Acc:HGNC:9651]
2 protein tyrosine phosphatase non-receptor type 21 [Source:HGNC Symbol;Acc:HGNC:9651]
3 protein tyrosine phosphatase non-receptor type 21 [Source:HGNC Symbol;Acc:HGNC:9651]
4 protein tyrosine phosphatase non-receptor type 21 [Source:HGNC Symbol;Acc:HGNC:9651]
5 protein tyrosine phosphatase non-receptor type 21 [Source:HGNC Symbol;Acc:HGNC:9651]
6 protein tyrosine phosphatase non-receptor type 21 [Source:HGNC Symbol;Acc:HGNC:9651]

To see all of the fields that can be returned by the mart to which you have connected, just type:

listAttributes(mart)

Kevin

[Scott McKay]

Hey Kevin,

Thanks man! Really appreciate your insight!

[Kevin Blighe]

Just re-reading what you wrote, you may have to parse what you need out of the various description fields. It will be virtually impossible to find the exact terms that you want, so, you may have to define a set of key terms and then search for these, and/or use a non-biomaRt solution.