Module 1: The Mouse Genome

Informatics database

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

apoe

Quick search ranks results by

best match

ID & synonyms

Position

Vertebrate

homology

Diseases &

alleles

Function (GO)

Expression

Sequences &

polymorphisms

Protein links

References

Alleles, phenotypes and

associated diseases

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

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

**

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

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

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

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

*

*

Alleles, phenotypes and

associated diseases

Phenotypic allele summary

Allele nomenclature:

(Gene Symbol)alleleID :

Apoeshl

(Gene Symbol)tm(serial number)(lab code) : Apoetm1Bres

Phenotype tables annotate

observations to genotypes

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 mgi-help@jax.org with any questions