My objective is to get orthologus genes between Mouse and Chiken I have tried to get this using the BioMart GUI. I need try same with R because I was missing some attributes columns on web GUI I need a information gene order conservation score (GOC) and whole genome alignment coverage (WGA). In GUI I was getting only GOC info not WGA is it possible to get WGA here please help me I am new to R and biomaRt.

library(biomaRt)

mouse = useMart("ensembl", dataset = "mmusculus_gene_ensembl")
searchAttributes(mart = mouse, pattern = "ggallus")

searchAttributes(mart = mouse, pattern = "ptroglodytes")

when I see the above attributes search for ptroglodytes(Chimpanzee) I am getting wga attributes why its not given in chiken(gallus gallus)

Thank you

Hi,

The problem is that you are first creating a 'mouse mart', and then searching for the homology attributes in this - they don't exist there, from what I know.

If you want to map between, e.g., Chicken and Chimpanzee, then this is how we would do it (taken from my previous answer: Convert mouse gene ids to hamster gene ids):

[see further below for Mouse-to-Chicken]

Set-up

require(biomaRt)
listDatasets(useMart('ensembl'))

datasets[grep('gallus', datasets[,1]),]
                dataset            description version
73 ggallus_gene_ensembl Chicken genes (GRCg6a)  GRCg6a

datasets[grep('troglodytes', datasets[,1]),]
                      dataset                    description     version
162 ptroglodytes_gene_ensembl Chimpanzee genes (Pan_tro_3.0) Pan_tro_3.0

chicken <- useMart('ensembl', dataset = 'ggallus_gene_ensembl')
chimpz<- useMart('ensembl', dataset = 'ptroglodytes_gene_ensembl')

Create annotation lookup table

annot_table <- getLDS(
  mart = chicken,
  attributes = c('ensembl_gene_id','external_gene_name','chromosome_name'),
  martL = chimpz,
  attributesL = c('ensembl_gene_id','external_gene_name','chromosome_name','gene_biotype'))

head(annot_table)

      Gene.stable.ID Gene.name Chromosome.scaffold.name   Gene.stable.ID.1
1 ENSGALG00000048563                                  Z ENSPTRG00000016810
2 ENSGALG00000031424      SDC2                        2 ENSPTRG00000020443
3 ENSGALG00000012395   PLEKHG1                        3 ENSPTRG00000018709
4 ENSGALG00000029500       ND5                       MT ENSPTRG00000042651
5 ENSGALG00000041163   ABHD17A                       28 ENSPTRG00000042737
6 ENSGALG00000033404      RARG                       33 ENSPTRG00000005007
  Gene.name.1 Chromosome.scaffold.name.1      Gene.type
1        OSMR                          5 protein_coding
2        SDC2                          8 protein_coding
3     PLEKHG1                          6 protein_coding
4      MT-ND5                         MT protein_coding
5                                      1 protein_coding
6        RARG                         12 protein_coding

Do a specific lookup

getLDS(
  mart = chicken,
  attributes = c('ensembl_gene_id','external_gene_name','chromosome_name'),
  martL = chimpz,
  attributesL = c('ensembl_gene_id','external_gene_name','chromosome_name','gene_biotype'),
  filters = 'external_gene_name',
  values = c('BRCA1', 'RAD21'))

      Gene.stable.ID Gene.name Chromosome.scaffold.name   Gene.stable.ID.1
1 ENSGALG00000029523     RAD21                        2 ENSPTRG00000020522
2 ENSGALG00000002781     BRCA1                       27 ENSPTRG00000009236
  Gene.name.1 Chromosome.scaffold.name.1      Gene.type
1       RAD21                          8 protein_coding
2       BRCA1                         17 protein_coding

For Mouse and Chicken:

require(biomaRt)
chicken <- useMart('ensembl', dataset = 'ggallus_gene_ensembl')
mouse <- useMart('ensembl', dataset = 'mmusculus_gene_ensembl')
annot_table <- getLDS(
  mart = mouse,
  attributes = c('ensembl_gene_id','mgi_symbol','external_gene_name','chromosome_name'),
  martL = chicken,
  attributesL = c('ensembl_gene_id','external_gene_name','chromosome_name','gene_biotype'))

head(annot_table)
      Gene.stable.ID MGI.symbol Gene.name Chromosome.scaffold.name
1 ENSMUSG00000026750      Psmb7     Psmb7                        2
2 ENSMUSG00000064341     mt-Nd1    mt-Nd1                       MT
3 ENSMUSG00000033075      Senp1     Senp1                       15
4 ENSMUSG00000025855    Prkar1b   Prkar1b                        5
5 ENSMUSG00000004455     Ppp1cc    Ppp1cc                        5
6 ENSMUSG00000064351     mt-Co1    mt-Co1                       MT
    Gene.stable.ID.1 Gene.name.1 Chromosome.scaffold.name.1      Gene.type
1 ENSGALG00000001103       PSMB7                         17 protein_coding
2 ENSGALG00000042750         ND1                         MT protein_coding
3 ENSGALG00000034421       SENP1                         33 protein_coding
4 ENSGALG00000003675     PRKAR1B                         14 protein_coding
5 ENSGALG00000004571      PPP1CC                         15 protein_coding
6 ENSGALG00000032142      MT-CO1                         MT protein_coding

Keviin