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Official Genetic Markers

Source: vignettes/articles/marker_list2.Rmd
marker_list2.Rmd

The MGI report MRK_List2.rpt provides the list of official mouse genetic markers, i.e. excluding withdrawn marker symbols.

Read this report with key "marker_list2":

# To read all records: `read_report("marker_list2")`.
read_report(report_key = "marker_list2", n_max = 10L)
## # A tibble: 10 × 12
##    marker_status marker_type marker_id   marker_symbol  marker_name feature_type
##    <fct>         <fct>       <chr>       <chr>          <chr>       <fct>       
##  1 O             Gene        MGI:1918911 0610005C13Rik  RIKEN cDNA… lncRNA gene 
##  2 O             Gene        MGI:1923503 0610006L08Rik  RIKEN cDNA… lncRNA gene 
##  3 O             Gene        MGI:1925547 0610008J02Rik  RIKEN cDNA… lncRNA gene 
##  4 O             Gene        MGI:3698435 0610009E02Rik  RIKEN cDNA… lncRNA gene 
##  5 O             Gene        MGI:1918921 0610009F21Rik  RIKEN cDNA… lncRNA gene 
##  6 O             Gene        MGI:1918931 0610009K14Rik  RIKEN cDNA… lncRNA gene 
##  7 O             Gene        MGI:1914088 0610009L18Rik  RIKEN cDNA… lncRNA gene 
##  8 O             DNA Segment MGI:1337005 03.MMHAP34FRA… DNA segmen… DNA segment 
##  9 O             BAC/YAC end MGI:1341858 03B03F         DNA segmen… BAC/YAC end 
## 10 O             BAC/YAC end MGI:1341869 03B03R         DNA segmen… BAC/YAC end 
## # ℹ 6 more variables: chromosome <fct>, start <int>, end <int>, strand <fct>,
## #   genetic_map_pos <dbl>, synonyms <list>

Comparatively, the report MRK_List1.rpt is for the whole set of genetic markers, i.e. including withdrawn marker symbols, see vignette("marker_list1") for more details about this other report.

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marker_status: genetic marker status is a factor of two levels: 'O' for official, and 'W' for withdrawn. Official indicates a currently in-use genetic marker, whereas withdrawn means that the symbol or name was once approved but has since been replaced.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