introduction to mouse genome informatics: module 1
TRANSCRIPT
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Module 1: The Mouse Genome
Informatics database
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Data in MGI comes via
multiple sources
Direct submission
by researchers
Curated from peer-
reviewed literature
by MGI scientists
Loaded* from large-scale
projects or other
databases*may involve additional
curation
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apoe
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Quick search ranks results by
best match
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ID & synonyms
Position
Vertebrate
homology
Diseases &
alleles
Function (GO)
Expression
Sequences &
polymorphisms
Protein links
References
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Alleles, phenotypes and
associated diseases
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Defining allele types in MGI
by Generation Type
Gene trapped
random cassette insertion site
allele may be:
null, hypomorphic or functional
reporter
1 2 3
SA cassette
1 SA cassette
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Defining allele types in MGI
by Generation Type
Gene trapped
Induced (chemical, radiation)
Spontaneous
random location of mutation
allele may be:
null, hypomorphic, functional,
gain-of-function
missense, nonsense,
rearrangement
1 2 3
1 2 3
**
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vector
germ line (post homologous recombination)
transcript
Defining allele types in MGI
by Generation Type
Gene trapped
Induced (chemical, radiation)
Spontaneous
Targeted
1 2 3
1 cassette 3
1 cassette 3
1 3
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vector
germ line (post homologous recombination)
transcript
Defining allele types in MGI
by Generation Type
Gene trapped
Induced (chemical, radiation)
Spontaneous
Targeted
specific locus
specific introduced variant
null/knockout, missense/
knock-in, conditional/floxed
1 2 3
1 cassette 3 1 2 3
1 cassette 3
1 3
1 2 3
1 3
or +cre
1 2 3 1 3
+cre
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Defining allele types in MGI
by Generation Type
Gene trapped
Induced (chemical, radiation)
Spontaneous
Targeted
Transgenic
introduces a foreign DNA
sequence for expression
may disrupt endogenous genes
or not
includes recombinases (cre, flp)
1 2 3
driver expressed seq
1 2 3seq
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Defining allele types in MGI
by Generation Type
Gene trapped
Induced (chemical, radiation)
Spontaneous
Targeted
Transgenic
Incidental mutations
induced germ-line variants from ENU
mutagenesis
unknown significance, not
characterized or thought not to
contribute to the studied phenotype
1 2 3
*
*
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Alleles, phenotypes and
associated diseases
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Phenotypic allele summary
Allele nomenclature:
(Gene Symbol)alleleID :
Apoeshl
(Gene Symbol)tm(serial number)(lab code) : Apoetm1Bres
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Phenotype tables annotate
observations to genotypes
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Summary
MGI provides data and tools for the research
community in a relational database
Genes, alleles and phenotypes are described
using searchable, structured terms as well as
more detailed free text
each piece of information is cited with a J:# referring
back to the source of the information
contact [email protected] with any questions