homologene

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

Installation

install.packages('homologene')

or

devtools::install_github('oganm/homologene')

Usage

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

homologeneData2

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)

Gene ID syncronization

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

Querying DIOPT

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()

diopt(c('Eno2','Mog'),inTax = 10090, outTax =9606) %>%
    knitr::kable()

Mishaps

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.