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InterPro Domains

Source: vignettes/articles/interpro_domains.Rmd
interpro_domains.Rmd

The MGI report MGI_InterProDomains.rpt provides associations between InterPro domains and MGI genetic markers.

To read this report using the key "interpro_domains", use the following code:

# To read all records (~ 120,000), use `read_report("interpro_domains")`.
(assoc_interpro_domains <- read_report(report_key = "interpro_domains", n_max = 10000L))
## # A tibble: 10,000 × 4
##    interpro_id interpro_domain marker_id   marker_symbol
##    <chr>       <chr>           <chr>       <chr>        
##  1 IPR000001   Kringle         MGI:1196378 Habp2        
##  2 IPR000001   Kringle         MGI:1347520 Ror1         
##  3 IPR000001   Kringle         MGI:1347521 Ror2         
##  4 IPR000001   Kringle         MGI:1859281 Hgfac        
##  5 IPR000001   Kringle         MGI:1891012 F12          
##  6 IPR000001   Kringle         MGI:1917016 Pik3ip1      
##  7 IPR000001   Kringle         MGI:1920266 Kremen2      
##  8 IPR000001   Kringle         MGI:1933988 Kremen1      
##  9 IPR000001   Kringle         MGI:88380   F2           
## 10 IPR000001   Kringle         MGI:96079   Hgf          
## # ℹ 9,990 more rows

Associated MGI markers

To find associated genetic markers with a specific InterPro domain, simply filter for that domain, e.g. the Retinoid X receptor/HNF4 domain (IPR000003):

assoc_interpro_domains |>
  dplyr::filter(interpro_id == "IPR000003")
## # A tibble: 4 × 4
##   interpro_id interpro_domain          marker_id  marker_symbol
##   <chr>       <chr>                    <chr>      <chr>        
## 1 IPR000003   Retinoid X receptor/HNF4 MGI:109128 Hnf4a        
## 2 IPR000003   Retinoid X receptor/HNF4 MGI:98214  Rxra         
## 3 IPR000003   Retinoid X receptor/HNF4 MGI:98215  Rxrb         
## 4 IPR000003   Retinoid X receptor/HNF4 MGI:98216  Rxrg

Associated InterPro domains

For the reverse operation, i.e. finding all associated domains with a genetic marker, e.g. the gene Rxra:

assoc_interpro_domains |>
  dplyr::filter(marker_symbol == "Rxra") |>
  dplyr::select("marker_id", "marker_symbol", "interpro_id", "interpro_domain")
## # A tibble: 2 × 4
##   marker_id marker_symbol interpro_id interpro_domain                           
##   <chr>     <chr>         <chr>       <chr>                                     
## 1 MGI:98214 Rxra          IPR000003   Retinoid X receptor/HNF4                  
## 2 MGI:98214 Rxra          IPR000536   Nuclear hormone receptor, ligand-binding …

Note that these results are not exhaustive because we selected the first 10,000 records when importing the report.

Variables

interpro_id

interpro_id: InterPro domain identifier.

interpro_domain

interpro_domain: InterPro domain name.

marker_id

marker_id: MGI accession identifier. A unique alphanumeric character string that is used to unambiguously identify a particular record in the Mouse Genome Informatics database. The format is MGI:nnnnnn, where n is a digit.

marker_symbol

marker_symbol: marker symbol is a unique abbreviation of the marker name.