An r package that works as a wrapper to homologene
Available species are
homologene::taxData## tax_id name_txt
## 1 10090 Mus musculus
## 2 10116 Rattus norvegicus
## 3 28985 Kluyveromyces lactis
## 4 318829 Magnaporthe oryzae
## 5 33169 Eremothecium gossypii
## 6 3702 Arabidopsis thaliana
## 7 4530 Oryza sativa
## 8 4896 Schizosaccharomyces pombe
## 9 4932 Saccharomyces cerevisiae
## 10 5141 Neurospora crassa
## 11 6239 Caenorhabditis elegans
## 12 7165 Anopheles gambiae
## 13 7227 Drosophila melanogaster
## 14 7955 Danio rerio
## 15 8364 Xenopus (Silurana) tropicalis
## 16 9031 Gallus gallus
## 17 9544 Macaca mulatta
## 18 9598 Pan troglodytes
## 19 9606 Homo sapiens
## 20 9615 Canis lupus familiaris
## 21 9913 Bos taurus
install.packages('homologene')or
devtools::install_github('oganm/homologene')Basic homologene function requires a list of gene symbols or NCBI ids,
and an inTax and an outTax. In this example, inTax is the taxon id
of mus musculus while outTax is for humans.
homologene(c('Eno2','Mog'), inTax = 10090, outTax = 9606)## 10090 9606 10090_ID 9606_ID
## 1 Eno2 ENO2 13807 2026
## 2 Mog MOG 17441 4340
homologene(c('Eno2','17441'), inTax = 10090, outTax = 9606)## 10090 9606 10090_ID 9606_ID
## 1 Eno2 ENO2 13807 2026
## 2 Mog MOG 17441 4340
For mouse and humans two convenience functions exist that removes the
need to provide taxonomic identifiers. Note that the column names are
not the same as the homologene output.
mouse2human(c('Eno2','Mog'))## mouseGene humanGene mouseID humanID
## 1 Eno2 ENO2 13807 2026
## 2 Mog MOG 17441 4340
human2mouse(c('ENO2','MOG','GZMH'))## humanGene mouseGene humanID mouseID
## 1 ENO2 Eno2 2026 13807
## 2 MOG Mog 4340 17441
## 3 GZMH Gzmd 2999 14941
## 4 GZMH Gzme 2999 14942
## 5 GZMH Gzmg 2999 14944
## 6 GZMH Gzmf 2999 14943
Original homologene database has not been updated since 2014. This package also includes an updated version of the homologene database that replaces gene symbols and identifiers with the their latest version. For the procedure followed for updating, see this blog post and/or see the processing code.
Using the updated version can help you match genes that cannot matched due to out of date annotations.
mouse2human(c('Mesd',
'Trp53rka',
'Cstdc4',
'Ifit3b'))## [1] mouseGene humanGene mouseID humanID
## <0 rows> (or 0-length row.names)
mouse2human(c('Mesd',
'Trp53rka',
'Cstdc4',
'Ifit3b'),
db = homologeneData2)## mouseGene humanGene mouseID humanID
## 1 Mesd MESD 67943 23184
## 2 Trp53rka TP53RK 381406 112858
## 3 Cstdc4 CSTA 433016 1475
## 4 Ifit3b IFIT3 667370 3437
The homologeneData2 object that comes with the GitHub version of this
package is updated weekly but if you are using the CRAN version and want
the latest annotations, or if you want to keep a frozen version
homologene, you can use the updateHomologene function.
homologeneDataVeryNew = updateHomologene() # update the homologene database with the latest identifiers
mouse2human(c('Mesd',
'Trp53rka',
'Cstdc4',
'Ifit3b'),
db = homologeneDataVeryNew)The package also includes functions that were used to create the
homologeneData2, for updating outdated gene symbols and identifiers.
library(dplyr)
gene_history = getGeneHistory()
oldIds = c(4340964, 4349034, 4332470, 4334151, 4323831)
newIds = updateIDs(oldIds,gene_history)
print(newIds)## [1] "9267698" "4349033" "4332468" "4334150" "4324017"
# get the latest gene symbols for the ids
gene_info = getGeneInfo()
gene_info %>%
dplyr::filter(GeneID %in% as.integer(newIds)) # faster to match integers## # A tibble: 5 × 3
## tax_id GeneID Symbol
## <int> <int> <chr>
## 1 39947 4324017 LOC4324017
## 2 39947 4332468 SPO11-3
## 3 39947 4334150 LOC4334150
## 4 39947 4349033 LOC4349033
## 5 39947 9267698 LOC9267698
Instead of using just homologene, one can also make queries into the
DIOPT database.
Diopt uses multiple databases to find gene homolog/orthologues. Note
that this function has a delay parameter that is set to 10 seconds by
default. This was done to obey the robots.txt of their website.
diopt(c('GZMH'),inTax = 9606, outTax = 10090) %>%
knitr::kable()| Input Order | Search Term | Human GeneID | HGNCID | Human Symbol | Species 2 | Mouse GeneID | Mouse Species Gene ID | Mouse Symbol | Ensmbl ID (link HPA) | DIOPT Score | Weighted Score | Rank | Best Score | Best Score Reverse | Prediction Derived From | Alignment & Scores | Feedback | Gene Details |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14944 | 109253 | Gzmg | NA | 6 | 5.87 | high | Yes | Yes | eggNOG, Homologene, Isobase, OrthoDB, Panther, Phylome | NA | Add | G2F details (Gzmg) DRscDB Data: (Gzmg) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14939 | 109267 | Gzmb | NA | 6 | 5.85 | moderate | Yes | No | eggNOG, OrthoDB, orthoMCL, Panther, Phylome, RoundUp | NA | Add | G2F details (Gzmb) DRscDB Data: (Gzmb) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 245839 | 2675494 | Gzmn | NA | 5 | 4.93 | moderate | No | No | eggNOG, OMA, OrthoDB, Panther, Phylome | NA | Add | G2F details (Gzmn) DRscDB Data: (Gzmn) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14940 | 109256 | Gzmc | NA | 5 | 4.93 | moderate | No | No | eggNOG, OMA, OrthoDB, Panther, Phylome | NA | Add | G2F details (Gzmc) DRscDB Data: (Gzmc) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14941 | 109255 | Gzmd | NA | 5 | 4.92 | moderate | No | No | eggNOG, Homologene, OrthoDB, Panther, Phylome | NA | Add | G2F details (Gzmd) DRscDB Data: (Gzmd) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14943 | 109254 | Gzmf | NA | 5 | 4.92 | moderate | No | No | eggNOG, Homologene, OrthoDB, Panther, Phylome | NA | Add | G2F details (Gzmf) DRscDB Data: (Gzmf) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14942 | 109265 | Gzme | NA | 5 | 4.92 | moderate | No | No | eggNOG, Homologene, OrthoDB, Panther, Phylome | NA | Add | G2F details (Gzme) DRscDB Data: (Gzme) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 17231 | 1261780 | Mcpt8 | NA | 4 | 3.97 | moderate | No | No | eggNOG, OrthoDB, Panther, TreeFam | NA | Add | G2F details (Mcpt8) DRscDB Data: (Mcpt8) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 13035 | 88563 | Ctsg | NA | 2 | 1.91 | low | No | No | eggNOG, OrthoDB | NA | Add | G2F details (Ctsg) DRscDB Data: (Ctsg) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 17228 | 96941 | Cma1 | NA | 2 | 1.91 | low | No | No | eggNOG, OrthoDB | NA | Add | G2F details (Cma1) DRscDB Data: (Cma1) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 14938 | 109266 | Gzma | NA | 1 | 1.03 | low | No | No | RoundUp | NA | Add | G2F details (Gzma) DRscDB Data: (Gzma) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 17232 | 1194491 | Mcpt9 | NA | 1 | 1.01 | low | No | Yes | OrthoDB | NA | Add | G2F details (Mcpt9) DRscDB Data: (Mcpt9) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 17225 | 96938 | Mcpt2 | NA | 1 | 1.01 | low | No | Yes | OrthoDB | NA | Add | G2F details (Mcpt2) DRscDB Data: (Mcpt2) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 17224 | 96937 | Mcpt1 | NA | 1 | 1.01 | low | No | Yes | OrthoDB | NA | Add | G2F details (Mcpt1) DRscDB Data: (Mcpt1) |
| 1 | GZMH | 2999 | 4710 | GZMH | Mouse | 545055 | 88426 | Cma2 | NA | 1 | 1.01 | low | No | Yes | OrthoDB | NA | Add | G2F details (Cma2) DRscDB Data: (Cma2) |
diopt(c('Eno2','Mog'),inTax = 10090, outTax =9606) %>%
knitr::kable()| Input Order | Search Term | Mouse GeneID | MGIID | Mouse Symbol | Species 2 | Human GeneID | Human Species Gene ID | Human Symbol | Ensmbl ID (link HPA) | DIOPT Score | Weighted Score | Rank | Best Score | Best Score Reverse | Prediction Derived From | Alignment & Scores | Feedback | Gene Details |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | Eno2 | 13807 | 95394 | Eno2 | Human | 2026 | 3353 | ENO2 | ENSG00000111674 | 14 | 14.29 | high | Yes | Yes | Compara, eggNOG, HGNC, Hieranoid, Homologene, Inparanoid, OMA, OrthoFinder, OrthoInspector, orthoMCL, Panther, Phylome, RoundUp, TreeFam | NA | Add | G2F details (ENO2) DRscDB Data: (ENO2) |
| Human Protein Atlas (HPA) | ||||||||||||||||||
| 1 | Eno2 | 13807 | 95394 | Eno2 | Human | 2023 | 3350 | ENO1 | ENSG00000074800 | 5 | 4.84 | moderate | No | No | eggNOG, OrthoDB, OrthoFinder, orthoMCL, RoundUp | NA | Add | G2F details (ENO1) DRscDB Data: (ENO1) |
| Human Protein Atlas (HPA) | ||||||||||||||||||
| 1 | Eno2 | 13807 | 95394 | Eno2 | Human | 2027 | 3354 | ENO3 | ENSG00000108515 | 4 | 3.83 | moderate | No | No | eggNOG, OrthoFinder, orthoMCL, RoundUp | NA | Add | G2F details (ENO3) DRscDB Data: (ENO3) |
| Human Protein Atlas (HPA) | ||||||||||||||||||
| 1 | Eno2 | 13807 | 95394 | Eno2 | Human | 2580 | 4113 | GAK | ENSG00000178950 | 1 | 1.01 | low | No | No | OrthoDB | NA | Add | G2F details (GAK) DRscDB Data: (GAK) |
| Human Protein Atlas (HPA) | ||||||||||||||||||
| 1 | Eno2 | 13807 | 95394 | Eno2 | Human | 2534 | 4037 | FYN | ENSG00000010810 | 1 | 1.01 | low | No | No | OrthoDB | NA | Add | G2F details (FYN) DRscDB Data: (FYN) |
| Human Protein Atlas (HPA) | ||||||||||||||||||
| 1 | Eno2 | 13807 | 95394 | Eno2 | Human | 387712 | 31670 | ENO4 | ENSG00000188316 | 1 | 0.90 | low | No | No | eggNOG | NA | Add | G2F details (ENO4) DRscDB Data: (ENO4) |
| Human Protein Atlas (HPA) | ||||||||||||||||||
| 2 | Mog | 17441 | 97435 | Mog | Human | 4340 | 7197 | MOG | ENSG00000204655 | 15 | 15.30 | high | Yes | Yes | Compara, eggNOG, HGNC, Hieranoid, Homologene, Inparanoid, OMA, OrthoDB, OrthoFinder, OrthoInspector, orthoMCL, Panther, Phylome, RoundUp, TreeFam | NA | Add | G2F details (MOG) DRscDB Data: (MOG) |
| Human Protein Atlas (HPA) |
As of version version 1.1.68, the output now includes NCBI ids. Since it doesn’t change any of the existing column names or their order, this shouldn’t cause problems in most use cases.
If a you can’t find a gene you are looking for it may have synonyms. See geneSynonym package to find them. If you have other problems open an issue or send a mail.