adding gene name correspond to gene id from Ensembl (Oryza sativa / rice)

Question

[Bioinfonext]

Hi,

I got multiple differential expressed gene list by using DESeq2, could you please suggest how I can add the gene name to this data correspond to gene ID: BGIOSGA000001 BGIOSGA000002

baseMeanAmanRootT1  baseMeanAmanRootT2  baseMean    log2FoldChange  lfcSE   stat    pvalue  padj
    BGIOSGA000001   429.9063436 437.2024577 1006.67217  -0.036725266    0.281814853 -0.129722119    0.896786282 1
    BGIOSGA000002   4050.739383 3536.980417 2456.48442  0.191799364 0.18717376  1.024621423 0.305541852 1

[GenoMax]

Looks like Rice. Check if Ensembl plants BioMart has the particular cultivar you are working with.

[Bioinfonext]

yes, I am working on rice. thanks for your help.

Answer 1

[Kevin Blighe]

Indeed, if this is the rice, Oryza sativa, then you can create a 'lookup' annotation table like this:

require(biomaRt)
mart <- useMart('plants_mart', host = 'plants.ensembl.org')
mart <- useDataset('oindica_eg_gene', mart)

annotLookup <- getBM(
  mart = mart,
  attributes = c(
    'ensembl_gene_id',
    'description',
    'external_gene_name',
    'external_gene_source',
    'external_synonym',
    'bgi_gene',
    'entrezgene_id'),
  uniqueRows=TRUE)

head(annotLookup)
  ensembl_gene_id
1   BGIOSGA039556
2   BGIOSGA038856
3   BGIOSGA039926
4   BGIOSGA013239
5   BGIOSGA028856
6   BGIOSGA017372
                                                                                       description
1 NAD(P)H-quinone oxidoreductase subunit 3, chloroplastic [Source:UniProtKB/Swiss-Prot;Acc:P0C321]
2                                                                                                 
3                                                                                                 
4                             3-isopropylmalate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:A2XK82]
5                                                                                                 
6                                                                                                 
  external_gene_name    external_gene_source      external_synonym         bgi_gene
1 ndhC                  UniProtKB Gene Name       ndh3                     LOC_Osp1g00390.1
2                                                 ndh5                     LOC_Osp1g00880.1
3                                                 ndh5                     LOC_Osp1g00880.1
4                                                                          LOC_Os03g45320.1
5                                                                          
6                                                                          
  entrezgene_id
1       4126869
2       4126907
3       4126907
4            NA
5            NA
6            NA

Understandably, the annotation is not as complete as other species. You can list all possible attributes via listAttributes(mart)

Kevin

PS - I edited your post title so that this will be easily found via search engines, i.e., by others who are also facing this issue

[Bioinfonext]

thank you so much Kevin!