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| File | Version | Author | Date | Message |
|---|---|---|---|---|
| Rmd | bfebc82 | Dave Tang | 2025-09-05 | All human mouse homologues for Ensembl 113 |
| html | 2d0dd8f | Dave Tang | 2025-09-04 | Build site. |
| Rmd | 87b461f | Dave Tang | 2025-09-04 | Using biomaRt to get homologues |
To begin, install the {biomaRt} package.
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("biomaRt")Load package.
suppressPackageStartupMessages(library(biomaRt))
packageVersion("biomaRt")[1] '2.64.0'List the available BioMart databases.
listMarts() biomart version
1 ENSEMBL_MART_ENSEMBL Ensembl Genes 115
2 ENSEMBL_MART_MOUSE Mouse strains 115
3 ENSEMBL_MART_SNP Ensembl Variation 115
4 ENSEMBL_MART_FUNCGEN Ensembl Regulation 115Connect to the selected BioMart database by using
useMart().
ensembl <- useMart("ENSEMBL_MART_ENSEMBL")
avail_datasets <- listDatasets(ensembl)
head(avail_datasets) dataset description
1 abrachyrhynchus_gene_ensembl Pink-footed goose genes (ASM259213v1)
2 acalliptera_gene_ensembl Eastern happy genes (fAstCal1.3)
3 acarolinensis_gene_ensembl Green anole genes (AnoCar2.0v2)
4 acchrysaetos_gene_ensembl Golden eagle genes (bAquChr1.2)
5 acitrinellus_gene_ensembl Midas cichlid genes (Midas_v5)
6 amelanoleuca_gene_ensembl Giant panda genes (ASM200744v2)
version
1 ASM259213v1
2 fAstCal1.3
3 AnoCar2.0v2
4 bAquChr1.2
5 Midas_v5
6 ASM200744v2Look for human datasets by searching the description column.
idx <- grep('human', avail_datasets$description, ignore.case = TRUE)
avail_datasets[idx, ] dataset description version
80 hsapiens_gene_ensembl Human genes (GRCh38.p14) GRCh38.p14Connect to the selected BioMart database and human dataset.
ensembl <- useMart("ensembl", dataset=avail_datasets[idx, 'dataset'])
ensemblObject of class 'Mart':
Using the ENSEMBL_MART_ENSEMBL BioMart database
Using the hsapiens_gene_ensembl datasetBuilding a query, requires three things:
Use listFilters() to show available filters.
avail_filters <- listFilters(ensembl)
head(avail_filters) name description
1 chromosome_name Chromosome/scaffold name
2 start Start
3 end End
4 band_start Band Start
5 band_end Band End
6 marker_start Marker StartUse listAttributes() to show available attributes.
avail_attributes <- listAttributes(ensembl)
head(avail_attributes) name description page
1 ensembl_gene_id Gene stable ID feature_page
2 ensembl_gene_id_version Gene stable ID version feature_page
3 ensembl_transcript_id Transcript stable ID feature_page
4 ensembl_transcript_id_version Transcript stable ID version feature_page
5 ensembl_peptide_id Protein stable ID feature_page
6 ensembl_peptide_id_version Protein stable ID version feature_pageLook for mouse homologues.
grep('homolog', avail_attributes$name, ignore.case = TRUE, value = TRUE) |>
grep('mmus', x = _, ignore.case = TRUE, value = TRUE) -> wanted_attr
wanted_attr <- c('ensembl_gene_id', wanted_attr)
wanted_attr [1] "ensembl_gene_id"
[2] "mmusculus_homolog_ensembl_gene"
[3] "mmusculus_homolog_associated_gene_name"
[4] "mmusculus_homolog_ensembl_peptide"
[5] "mmusculus_homolog_chromosome"
[6] "mmusculus_homolog_chrom_start"
[7] "mmusculus_homolog_chrom_end"
[8] "mmusculus_homolog_canonical_transcript_protein"
[9] "mmusculus_homolog_subtype"
[10] "mmusculus_homolog_orthology_type"
[11] "mmusculus_homolog_perc_id"
[12] "mmusculus_homolog_perc_id_r1"
[13] "mmusculus_homolog_goc_score"
[14] "mmusculus_homolog_wga_coverage"
[15] "mmusculus_homolog_orthology_confidence" ENSG00000206172 (HBA1).
my_gene <- 'ENSG00000206172'
getBM(
attributes = wanted_attr,
filters = "ensembl_gene_id",
values = my_gene,
mart = ensembl
) -> my_res
t(my_res) [,1]
ensembl_gene_id "ENSG00000206172"
mmusculus_homolog_ensembl_gene "ENSMUSG00000069919"
mmusculus_homolog_associated_gene_name "Hba-a1"
mmusculus_homolog_ensembl_peptide "ENSMUSP00000090897"
mmusculus_homolog_chromosome "11"
mmusculus_homolog_chrom_start "32233511"
mmusculus_homolog_chrom_end "32234465"
mmusculus_homolog_canonical_transcript_protein "ENSP00000322421"
mmusculus_homolog_subtype "Boreoeutheria"
mmusculus_homolog_orthology_type "ortholog_many2many"
mmusculus_homolog_perc_id "86.6197"
mmusculus_homolog_perc_id_r1 "86.6197"
mmusculus_homolog_goc_score "75"
mmusculus_homolog_wga_coverage "0"
mmusculus_homolog_orthology_confidence "1"
[,2]
ensembl_gene_id "ENSG00000206172"
mmusculus_homolog_ensembl_gene "ENSMUSG00000069917"
mmusculus_homolog_associated_gene_name "Hba-a2"
mmusculus_homolog_ensembl_peptide "ENSMUSP00000090895"
mmusculus_homolog_chromosome "11"
mmusculus_homolog_chrom_start "32246489"
mmusculus_homolog_chrom_end "32247298"
mmusculus_homolog_canonical_transcript_protein "ENSP00000322421"
mmusculus_homolog_subtype "Boreoeutheria"
mmusculus_homolog_orthology_type "ortholog_many2many"
mmusculus_homolog_perc_id "86.6197"
mmusculus_homolog_perc_id_r1 "86.6197"
mmusculus_homolog_goc_score "25"
mmusculus_homolog_wga_coverage "0"
mmusculus_homolog_orthology_confidence "0" I manually slugged through the Compara database and found that ENSG00000207721 (MIR186) should have a one-to-one ortholog with ENSMUSG00000065431 (Mir186).
my_gene <- 'ENSG00000207721'
getBM(
attributes = wanted_attr,
filters = "ensembl_gene_id",
values = my_gene,
mart = ensembl
) -> my_res
t(my_res) [,1]
ensembl_gene_id "ENSG00000207721"
mmusculus_homolog_ensembl_gene "ENSMUSG00000065431"
mmusculus_homolog_associated_gene_name "Mir186"
mmusculus_homolog_ensembl_peptide "ENSMUST00000083497"
mmusculus_homolog_chromosome "3"
mmusculus_homolog_chrom_start "157249916"
mmusculus_homolog_chrom_end "157249986"
mmusculus_homolog_canonical_transcript_protein "ENST00000384988"
mmusculus_homolog_subtype "Eutheria"
mmusculus_homolog_orthology_type "ortholog_one2one"
mmusculus_homolog_perc_id "79.0698"
mmusculus_homolog_perc_id_r1 "95.7747"
mmusculus_homolog_goc_score NA
mmusculus_homolog_wga_coverage "100"
mmusculus_homolog_orthology_confidence "1" List releases.
listEnsemblArchives() name date url version
1 Ensembl GRCh37 Feb 2014 https://grch37.ensembl.org GRCh37
2 Ensembl 115 Sep 2025 https://sep2025.archive.ensembl.org 115
3 Ensembl 114 May 2025 https://may2025.archive.ensembl.org 114
4 Ensembl 113 Oct 2024 https://oct2024.archive.ensembl.org 113
5 Ensembl 112 May 2024 https://may2024.archive.ensembl.org 112
6 Ensembl 111 Jan 2024 https://jan2024.archive.ensembl.org 111
7 Ensembl 110 Jul 2023 https://jul2023.archive.ensembl.org 110
8 Ensembl 109 Feb 2023 https://feb2023.archive.ensembl.org 109
9 Ensembl 108 Oct 2022 https://oct2022.archive.ensembl.org 108
10 Ensembl 107 Jul 2022 https://jul2022.archive.ensembl.org 107
11 Ensembl 106 Apr 2022 https://apr2022.archive.ensembl.org 106
12 Ensembl 105 Dec 2021 https://dec2021.archive.ensembl.org 105
13 Ensembl 104 May 2021 https://may2021.archive.ensembl.org 104
14 Ensembl 103 Feb 2021 https://feb2021.archive.ensembl.org 103
15 Ensembl 102 Nov 2020 https://nov2020.archive.ensembl.org 102
16 Ensembl 101 Aug 2020 https://aug2020.archive.ensembl.org 101
17 Ensembl 100 Apr 2020 https://apr2020.archive.ensembl.org 100
18 Ensembl 80 May 2015 https://may2015.archive.ensembl.org 80
19 Ensembl 77 Oct 2014 https://oct2014.archive.ensembl.org 77
20 Ensembl 75 Feb 2014 https://feb2014.archive.ensembl.org 75
21 Ensembl 54 May 2009 https://may2009.archive.ensembl.org 54
current_release
1
2 *
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21 Use Ensembl 113.
ensembl <- useMart(
"ENSEMBL_MART_ENSEMBL",
dataset=avail_datasets[idx, 'dataset'],
host = "https://oct2024.archive.ensembl.org"
)Check again.
my_gene <- 'ENSG00000207721'
getBM(
attributes = wanted_attr,
filters = "ensembl_gene_id",
values = my_gene,
mart = ensembl
) -> my_res
t(my_res) [,1]
ensembl_gene_id "ENSG00000207721"
mmusculus_homolog_ensembl_gene "ENSMUSG00000065431"
mmusculus_homolog_associated_gene_name "Mir186"
mmusculus_homolog_ensembl_peptide "ENSMUST00000083497"
mmusculus_homolog_chromosome "3"
mmusculus_homolog_chrom_start "157249916"
mmusculus_homolog_chrom_end "157249986"
mmusculus_homolog_canonical_transcript_protein "ENST00000384988"
mmusculus_homolog_subtype "Eutheria"
mmusculus_homolog_orthology_type "ortholog_one2one"
mmusculus_homolog_perc_id "79.0698"
mmusculus_homolog_perc_id_r1 "95.7747"
mmusculus_homolog_goc_score NA
mmusculus_homolog_wga_coverage "100"
mmusculus_homolog_orthology_confidence "1" Get all human genes for Ensembl 113.
all_genes_113 <- getBM(
attributes = "ensembl_gene_id",
mart = ensembl
)
length(unique(all_genes_113$ensembl_gene_id))[1] 86402Get all homologues.
getBM(
attributes = wanted_attr,
filters = "ensembl_gene_id",
values = all_genes_113$ensembl_gene_id,
mart = ensembl
) -> human_mouse_homologues
dim(human_mouse_homologues)[1] 92787 15Check out the results!
head(human_mouse_homologues) ensembl_gene_id mmusculus_homolog_ensembl_gene
1 ENSG00000000003 ENSMUSG00000067377
2 ENSG00000000005 ENSMUSG00000031250
3 ENSG00000000419 ENSMUSG00000078919
4 ENSG00000000457 ENSMUSG00000026584
5 ENSG00000000460 ENSMUSG00000041406
6 ENSG00000000938 ENSMUSG00000028874
mmusculus_homolog_associated_gene_name mmusculus_homolog_ensembl_peptide
1 Tspan6 ENSMUSP00000084838
2 Tnmd ENSMUSP00000033602
3 Dpm1 ENSMUSP00000118776
4 Scyl3 ENSMUSP00000027876
5 Firrm ENSMUSP00000095101
6 Fgr ENSMUSP00000030693
mmusculus_homolog_chromosome mmusculus_homolog_chrom_start
1 X 132791817
2 X 132751729
3 2 168050968
4 1 163756669
5 1 163773562
6 4 132701406
mmusculus_homolog_chrom_end mmusculus_homolog_canonical_transcript_protein
1 132799178 ENSP00000362111
2 132766326 ENSP00000362122
3 168072511 ENSP00000360644
4 163782695 ENSP00000356745
5 163822365 ENSP00000352276
6 132729221 ENSP00000363117
mmusculus_homolog_subtype mmusculus_homolog_orthology_type
1 Euarchontoglires ortholog_one2one
2 Euarchontoglires ortholog_one2one
3 Eutheria ortholog_one2one
4 Euarchontoglires ortholog_one2one
5 Euarchontoglires ortholog_one2one
6 Euarchontoglires ortholog_one2one
mmusculus_homolog_perc_id mmusculus_homolog_perc_id_r1
1 93.0612 93.0612
2 96.2145 96.2145
3 91.1538 91.1538
4 82.8488 77.5510
5 72.0985 66.3430
6 83.9319 85.8801
mmusculus_homolog_goc_score mmusculus_homolog_wga_coverage
1 100 100.00
2 100 100.00
3 100 100.00
4 100 100.00
5 0 99.21
6 100 100.00
mmusculus_homolog_orthology_confidence
1 1
2 1
3 1
4 1
5 1
6 1
sessionInfo()R version 4.5.0 (2025-04-11)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 24.04.2 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: Etc/UTC
tzcode source: system (glibc)
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] biomaRt_2.64.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] KEGGREST_1.48.1 xfun_0.52 bslib_0.9.0
[4] httr2_1.2.1 processx_3.8.6 Biobase_2.68.0
[7] callr_3.7.6 vctrs_0.6.5 tools_4.5.0
[10] ps_1.9.1 generics_0.1.4 curl_6.4.0
[13] stats4_4.5.0 tibble_3.2.1 AnnotationDbi_1.70.0
[16] RSQLite_2.4.2 blob_1.2.4 pkgconfig_2.0.3
[19] dbplyr_2.5.0 S4Vectors_0.46.0 lifecycle_1.0.4
[22] GenomeInfoDbData_1.2.14 compiler_4.5.0 stringr_1.5.1
[25] git2r_0.36.2 Biostrings_2.76.0 progress_1.2.3
[28] getPass_0.2-4 httpuv_1.6.16 GenomeInfoDb_1.44.1
[31] htmltools_0.5.8.1 sass_0.4.10 yaml_2.3.10
[34] later_1.4.2 pillar_1.10.2 crayon_1.5.3
[37] jquerylib_0.1.4 whisker_0.4.1 cachem_1.1.0
[40] tidyselect_1.2.1 digest_0.6.37 stringi_1.8.7
[43] purrr_1.0.4 dplyr_1.1.4 rprojroot_2.0.4
[46] fastmap_1.2.0 cli_3.6.5 magrittr_2.0.3
[49] withr_3.0.2 filelock_1.0.3 prettyunits_1.2.0
[52] UCSC.utils_1.4.0 promises_1.3.2 rappdirs_0.3.3
[55] bit64_4.6.0-1 rmarkdown_2.29 XVector_0.48.0
[58] httr_1.4.7 bit_4.6.0 png_0.1-8
[61] hms_1.1.3 memoise_2.0.1 evaluate_1.0.3
[64] knitr_1.50 IRanges_2.42.0 BiocFileCache_2.16.1
[67] rlang_1.1.6 Rcpp_1.0.14 glue_1.8.0
[70] DBI_1.2.3 xml2_1.3.8 BiocGenerics_0.54.0
[73] rstudioapi_0.17.1 jsonlite_2.0.0 R6_2.6.1
[76] fs_1.6.6