The MGI report MRK_GeneTrap.rpt provides associations
between MGI genetic markers and gene trap cell lines. For more details
about gene trapping, see MGI’s Gene
Trap Questions and Answers.
To read this report using the key "gene_trap_ids", use
the following code:
# To read all records (~ 17,000), use `read_report("gene_trap_ids")`.
(assoc_to_gene_trap_ids <- read_report(report_key = "gene_trap_ids", n_max = 150L))## # A tibble: 150 × 8
## marker_status marker_type marker_id marker_symbol marker_name chromosome
## <fct> <fct> <chr> <chr> <chr> <fct>
## 1 O Gene MGI:3698435 0610009E02Rik RIKEN cDNA 06… 2
## 2 O Gene MGI:1914088 0610009L18Rik RIKEN cDNA 06… 11
## 3 O Gene MGI:1915647 0610039H22Rik RIKEN cDNA 06… 11
## 4 O Gene MGI:1914922 0610040B10Rik RIKEN cDNA 06… 5
## 5 O Gene MGI:1922644 0610040F04Rik RIKEN cDNA 06… 6
## 6 O Gene MGI:1923511 0610040J01Rik RIKEN cDNA 06… 5
## 7 O Gene MGI:1915650 0610043K17Rik RIKEN cDNA 06… 4
## 8 O Gene MGI:1915738 1110002J07Rik RIKEN cDNA 11… 10
## 9 O Gene MGI:1915821 1110002L01Rik RIKEN cDNA 11… 12
## 10 O Gene MGI:1929274 1110004F10Rik RIKEN cDNA 11… 7
## # ℹ 140 more rows
## # ℹ 2 more variables: genetic_map_pos <dbl>, cell_line_id <list>Gene Trap Cell Lines
The list-column cell_line_id provides associated gene
trap cell lines. To unnest cell_line_id use:
assoc_to_gene_trap_ids |>
dplyr::select("marker_id", "marker_symbol","cell_line_id") |>
dplyr::filter(marker_id == "MGI:3698435") |>
tidyr::unnest("cell_line_id")## # A tibble: 9 × 3
## marker_id marker_symbol cell_line_id
## <chr> <chr> <chr>
## 1 MGI:3698435 0610009E02Rik EUCJ0179g02
## 2 MGI:3698435 0610009E02Rik IST11122B3
## 3 MGI:3698435 0610009E02Rik IST12077C2
## 4 MGI:3698435 0610009E02Rik IST12343D6
## 5 MGI:3698435 0610009E02Rik IST15046F3
## 6 MGI:3698435 0610009E02Rik OST106532
## 7 MGI:3698435 0610009E02Rik OST106540
## 8 MGI:3698435 0610009E02Rik OST206174
## 9 MGI:3698435 0610009E02Rik OST412537Variables
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withdrawn.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withdrawn means that the symbol or name was once approved but has since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_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_name
marker_name: marker name is a word or phrase that
uniquely identifies the genetic marker, e.g. a gene or allele name.
chromosome
chromosome: mouse chromosome name. Possible values are
names for the autosomal, sexual or mitochondrial chromosomes.
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.
cell_line_id
cell_line_id: a list-column of unique identifier(s)
assigned to each gene trap cell line. In gene trapping experiments, this
ID is crucial for tracking and cataloging the specific embryonic stem
(ES) cell lines that have undergone genome-wide insertional mutations.
Each cell_line_id corresponds to a mutant cell line in
which a gene has been disrupted by the integration of a selection gene,
potentially altering gene expression or protein production. The
identifier facilitates the retrieval of information regarding the
specific site of integration, which can be further characterized by
cloning, cDNA extension, or direct sequencing of the insertion site.