Mouse Genetic Markers

Introduction

The MGI (Mouse Genome Informatics) provides three reports under Mouse Genetic Markers:

Name	File
List of Mouse Genetic Markers (including withdrawn marker symbols)	MRK_List1.rpt
List of Mouse Genetic Markers (excluding withdrawn marker symbols)	MRK_List2.rpt
MGI Marker Coordinates	MGI_MRK_Coord.rpt

To read any of these reports into R, you can use the helper read_report(), see the examples below.

Reports

Including withdrawn marker symbols:

(base_url <- "https://www.informatics.jax.org/downloads/reports")
#> [1] "https://www.informatics.jax.org/downloads/reports"

(mrk_symbols1 <- read_report(file.path(base_url, "MRK_List1.rpt"), "MRK_List1", n_max = 30L))
#> # A tibble: 30 × 12
#>    marker_id   marker_symbol marker_name marker_type status cM_pos chr     start
#>    <chr>       <chr>         <chr>       <fct>       <fct>   <dbl> <fct>   <int>
#>  1 MGI:1341858 03B03F        DNA segmen… BAC/YAC end O        NA   5     NA     
#>  2 MGI:1341869 03B03R        DNA segmen… BAC/YAC end O        NA   5     NA     
#>  3 MGI:1337005 03.MMHAP34FR… DNA segmen… DNA Segment O        NA   11    NA     
#>  4 NA          0610005A07Rik withdrawn,… Gene        W        NA   3     NA     
#>  5 MGI:1918911 0610005C13Rik RIKEN cDNA… Gene        O        29.4 7      4.52e7
#>  6 NA          0610005K03Rik withdrawn,… Gene        W        NA   15    NA     
#>  7 NA          0610005M07Rik withdrawn,… Gene        W        NA   6     NA     
#>  8 NA          0610006A03Rik withdrawn,… Gene        W        NA   4     NA     
#>  9 NA          0610006A11Rik withdrawn,… Gene        W        NA   NA    NA     
#> 10 NA          0610006C01Rik withdrawn,… Gene        W        NA   NA    NA     
#> # ℹ 20 more rows
#> # ℹ 4 more variables: end <int>, strand <fct>, feature_type <fct>,
#> #   synonyms <list>

Note that withdrawn genetic markers are indicated by their status being "W" (withdrawn), and marker_name typically reads as "withdrawn, = 2610205H19Rik" if there is a more up-to-date symbol.

mrk_symbols1 |>
  dplyr::filter(status == "W") |>
  dplyr::select(c("marker_symbol", "marker_name", "marker_type", "status"))
#> # A tibble: 25 × 4
#>    marker_symbol marker_name                marker_type status
#>    <chr>         <chr>                      <fct>       <fct> 
#>  1 0610005A07Rik withdrawn, = Gstm7         Gene        W     
#>  2 0610005K03Rik withdrawn, = Lypdc2        Gene        W     
#>  3 0610005M07Rik withdrawn, = Acn9          Gene        W     
#>  4 0610006A03Rik withdrawn, = Fuca          Gene        W     
#>  5 0610006A11Rik withdrawn, = Blvra         Gene        W     
#>  6 0610006C01Rik withdrawn, = 2610205H19Rik Gene        W     
#>  7 0610006F02Rik withdrawn, = Mettl7b       Gene        W     
#>  8 0610006G05Rik withdrawn, = Sostl         Gene        W     
#>  9 0610006G08Rik withdrawn, = Brp44l        Gene        W     
#> 10 0610006G17Rik withdrawn, = Hirip5        Gene        W     
#> # ℹ 15 more rows

Excluding withdrawn marker symbols:

(mrk_symbols2 <- read_report(file.path(base_url, "MRK_List2.rpt"), "MRK_List2", n_max = 10L))
#> # A tibble: 10 × 12
#>    marker_id   marker_symbol marker_name marker_type status cM_pos chr     start
#>    <chr>       <chr>         <chr>       <fct>       <fct>   <dbl> <fct>   <int>
#>  1 MGI:1341858 03B03F        DNA segmen… BAC/YAC end O        NA   5     NA     
#>  2 MGI:1341869 03B03R        DNA segmen… BAC/YAC end O        NA   5     NA     
#>  3 MGI:1337005 03.MMHAP34FR… DNA segmen… DNA Segment O        NA   11    NA     
#>  4 MGI:1918911 0610005C13Rik RIKEN cDNA… Gene        O        29.4 7      4.52e7
#>  5 MGI:1923503 0610006L08Rik RIKEN cDNA… Gene        O        NA   7      7.45e7
#>  6 MGI:1925547 0610008J02Rik RIKEN cDNA… Gene        O        NA   NA    NA     
#>  7 MGI:3698435 0610009E02Rik RIKEN cDNA… Gene        O        18.9 2      2.63e7
#>  8 MGI:1918921 0610009F21Rik RIKEN cDNA… Gene        O        NA   16     9.17e7
#>  9 MGI:1918931 0610009K14Rik RIKEN cDNA… Gene        O        NA   4      1.36e7
#> 10 MGI:1914088 0610009L18Rik RIKEN cDNA… Gene        O        84.1 11     1.20e8
#> # ℹ 4 more variables: end <int>, strand <fct>, feature_type <fct>,
#> #   synonyms <list>

MGI Marker Coordinates

(mrk_coordinates <- read_report(file.path(base_url, "MGI_MRK_Coord.rpt"), "MGI_MRK_Coord", n_max = 10L))
#> # A tibble: 10 × 12
#>    marker_id marker_type marker_symbol marker_name  genome_assembly chr    start
#>    <chr>     <fct>       <chr>         <chr>        <fct>           <fct>  <int>
#>  1 MGI:87853 Gene        a             nonagouti    GRCm39          2     1.55e8
#>  2 MGI:87854 Gene        Pzp           PZP, alpha-… GRCm39          6     1.28e8
#>  3 MGI:87881 Gene        Acp1          acid phosph… GRCm39          12    3.09e7
#>  4 MGI:87926 Gene        Adh7          alcohol deh… GRCm39          3     1.38e8
#>  5 MGI:87929 Gene        Adh5          alcohol deh… GRCm39          3     1.38e8
#>  6 MGI:87859 Gene        Abl1          c-abl oncog… GRCm39          2     3.16e7
#>  7 MGI:87882 Gene        Acp2          acid phosph… GRCm39          2     9.10e7
#>  8 MGI:87862 Gene        Scgb1b27      secretoglob… GRCm39          7     3.37e7
#>  9 MGI:87883 Gene        Acp5          acid phosph… GRCm39          9     2.20e7
#> 10 MGI:87930 Gene        Adk           adenosine k… GRCm39          14    2.11e7
#> # ℹ 5 more variables: end <int>, strand <fct>, feature_type <fct>,
#> #   provider <fct>, provider_display <fct>

Mouse Genetic Markers

27 June, 2024

Introduction

Reports

Mouse Genetic Markers

MGI Marker Coordinates