Using R BioMart getting orthologus genes between two species
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@hemantcnaik-23771
Last seen 7 weeks ago
India

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

biomaRt • 219 views
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@kevin
Last seen 4 hours ago
Republic of Ireland

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

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Thanks you for the replay

I need a orthologus genes between mouse and chicken above mentioned method will it work

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Based on previous similar questions and answers, I would say that, yes, this biomaRt funciton retrieves orthologues, where possible. Tagging Mike Smith , biomaRt developer, to confirm this, though

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@Kevin Blighe Mike Smith Based on the previous thread 1 finding the orthologs method is different in a web based method we will get many attributes such as orthology type, similarity percentage between query, GOC in percentage option is available for filtering some genes to get more prominent ortholog so I was bit confused on above method.

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Those entries should be there:

mouse <- useMart('ensembl', dataset = 'mmusculus_gene_ensembl')
head(listAttributes(mouse)[grep('homol', listAttributes(mouse)[,1]),])
                                        name
239         cabingdonii_homolog_ensembl_gene
240 cabingdonii_homolog_associated_gene_name
241      cabingdonii_homolog_ensembl_peptide
242           cabingdonii_homolog_chromosome
243          cabingdonii_homolog_chrom_start
244            cabingdonii_homolog_chrom_end
                                                       description     page
239                  Abingdon island giant tortoise gene stable ID homologs
240                       Abingdon island giant tortoise gene name homologs
241 Abingdon island giant tortoise protein or transcript stable ID homologs
242        Abingdon island giant tortoise chromosome/scaffold name homologs
243  Abingdon island giant tortoise chromosome/scaffold start (bp) homologs
244    Abingdon island giant tortoise chromosome/scaffold end (bp) homologs
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Kevin Blighe Thank you for your help but this is not the method I am looking for.

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Then, I think that biomaRt may not be what you want, but you tagged it in your post (?) Take a look at the Ensembl REST APIs (in particular, final 2 of Comparative Genomics): https://rest.ensembl.org/

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