All Genetic Markers

The MGI report MRK_List1.rpt provides the complete list of mouse genetic markers, including withdrawn marker symbols.

Read this report with key "marker_list1":

# To read all records: `read_report("marker_list1")`.
(all_markers <- read_report(report_key = "marker_list1", n_max = 10L))

## # A tibble: 10 × 15
##    marker_status marker_type marker_id   marker_symbol  marker_name feature_type
##    <fct>         <fct>       <chr>       <chr>          <chr>       <fct>       
##  1 O             BAC/YAC end MGI:1341858 03B03F         DNA segmen… BAC/YAC end 
##  2 O             BAC/YAC end MGI:1341869 03B03R         DNA segmen… BAC/YAC end 
##  3 O             DNA Segment MGI:1337005 03.MMHAP34FRA… DNA segmen… DNA segment 
##  4 W             Gene        NA          0610005A07Rik  NA          NA          
##  5 O             Gene        MGI:1918911 0610005C13Rik  RIKEN cDNA… lncRNA gene 
##  6 W             Gene        NA          0610005K03Rik  NA          NA          
##  7 W             Gene        NA          0610005M07Rik  NA          NA          
##  8 W             Gene        NA          0610006A03Rik  NA          NA          
##  9 W             Gene        NA          0610006A11Rik  NA          NA          
## 10 W             Gene        NA          0610006C01Rik  NA          NA          
## # ℹ 9 more variables: chromosome <fct>, start <int>, end <int>, strand <fct>,
## #   genetic_map_pos <dbl>, synonyms <list>, marker_id_now <chr>,
## #   marker_symbol_now <chr>, note <chr>

Official, in-use symbols are indicated by the marker_status value "O", whereas withdrawn symbols are indicated with "W".

Comparatively, the report MRK_List2.rpt is only for the official genetic markers, see vignette("marker_list2") for more details.

Old to new marker symbols

If a symbol was withdrawn it is very likely (but not guaranteed) that it is now replaced by a new MGI identifier and symbol. The variables marker_id_now and marker_symbol_now provide these up-to-date values.

all_markers |>
  dplyr::select(
    "marker_status",
    "marker_id",
    "marker_id_now",
    "marker_symbol",
    "marker_symbol_now"
  )

## # A tibble: 10 × 5
##    marker_status marker_id   marker_id_now marker_symbol     marker_symbol_now
##    <fct>         <chr>       <chr>         <chr>             <chr>            
##  1 O             MGI:1341858 MGI:1341858   03B03F            03B03F           
##  2 O             MGI:1341869 MGI:1341869   03B03R            03B03R           
##  3 O             MGI:1337005 MGI:1337005   03.MMHAP34FRA.seq 03.MMHAP34FRA.seq
##  4 W             NA          MGI:1915562   0610005A07Rik     Gstm7            
##  5 O             MGI:1918911 MGI:1918911   0610005C13Rik     0610005C13Rik    
##  6 W             NA          MGI:1915561   0610005K03Rik     Lypd2            
##  7 W             NA          MGI:1913288   0610005M07Rik     Sdhaf3           
##  8 W             NA          MGI:95593     0610006A03Rik     Fuca1            
##  9 W             NA          MGI:88170     0610006A11Rik     Blvra            
## 10 W             NA          MGI:1917706   0610006C01Rik     Mpc2

Variables

marker_status

marker_status: genetic marker status is a factor of two levels: 'O' for official, and 'W' for withdrawn. Official indicates a currently in-use genetic marker, whereas withdrawn means that the symbol or name was once approved but has since been replaced.

marker_type

marker_type: genetic marker type is a factor of 10 levels: Gene, GeneModel, Pseudogene, DNA Segment, Transgene, QTL, Cytogenetic Marker, BAC/YAC end, Complex/Cluster/Region, Other Genome Feature. See ?marker_type_definitions for the meaning of each type.

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.

marker_name

marker_name: marker name is a word or phrase that uniquely identifies the genetic marker, e.g. a gene or allele name.

feature_type

feature_type: an attribute of a portion of a genomic sequence. See the dataset ?feature_type_definitions for details.

chromosome

chromosome: mouse chromosome name. Possible values are names for the autosomal, sexual or mitochondrial chromosomes.

start

start: genomic start position (one-offset).

end

end: genomic end position (one-offset).

strand

strand: DNA strand, ‘+’ for sense, and ‘-’ for antisense.

genetic_map_pos

genetic_map_pos: genetic map position in centiMorgan (cM): a unit of length in a genetic map. Two loci are 1 cM apart if recombination is detected between them in 1% of meioses.

synonyms

synonyms: alternative marker symbols. These alternatives can be either an unofficial symbol that has appeared in the scientific literature or in public databases such as GenBank, or a formerly official symbol, withdrawn due to gene family revisions or to conform to the human ortholog symbol.

marker_id_now

marker_id_now: genetic marker identifier replacement. If the record pertains a marker_symbol that was withdrawn, then marker_id_now indicates the most recent in-use marker identifier that replaced it.

marker_symbol_now

marker_symbol_now: genetic marker symbol replacement. If the record pertains a marker_symbol that was withdrawn, then marker_symbol_now indicates the most recent in-use marker symbol that replaced it.

note

note: message about marker symbol withdrawal. When a symbol is withdrawn, the note includes a brief message indicating the reason for withdrawal. Most messages are of the form: 'withdrawn, = <gene symbol>'. In many cases, the gene symbol indicated in the message will correspond to marker_symbol_now, but this is not always the case. Some withdrawn symbols have been remapped to other symbols, which may have subsequently been remapped again. Therefore, the note message will only indicate the first symbol remapping, while marker_symbol_now holds the most up-to-date marker symbol, if applicable.