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Mouse Genome Informatics
Mouse Genome Informatics (MGI) is the international database for genetic, genomic,
phenotypic and expression data in the laboratory mouse. The database has existed
online at www.informatics.jax.org for 25 years, providing free access to information
for researchers, and developing tools and structures to explore, manipulate and
connect data in order to answer many kinds of biological questions.
This worksheet is intended to cover a basic introduction (Intro module 1), a brief
overview of cre-‐lox and recombinase tools (Cre module 2), a new clinical and
translational tool (Human-‐Mouse: Disease Connection module 3) and a new
computational access platform for MGI data access (MouseMine module 4).
Each section has an accompanying video walkthrough and then users are invited to
explore the website sections in order to answer the following questions. Additional
online tutorial documentation can be found:
An introduction to mouse genetics:
How to use MGI overview:
A tour of the Human-‐Mouse: Disease Connection (http://diseasemodel.org/):
MouseMine basic tools and navigation (http://www.mousemine.org/):
The data and tools referred to in this worksheet are accurate as of May 19, 2014,
though ongoing curation may cause some numbers to shift slightly as data is
constantly added. As well, MGI will be releasing an infrastructure update on May 22,
2014 which will change some of the allele displays, specifically the way alleles are
categorized to reflect both generation method and allele attributes.
Answers to the multiple choice questions follow at the bottom of this document, and
additional walkthroughs and explanations are provided in a separate Worksheet
1. On which mouse chromosome would you find the vang-‐like 2 gene (Vangl2)?
a) Chr 1
b) Chr 4
c) Chr 10
d) Chr 19
2. How many phenotypic alleles have been described for this gene?
3. Has a mouse mutant of this gene been used to model a human disease? If yes,
b) Yes, neural tube defects
c) Yes, cancer
d) Yes, Alzheimer disease
e) Yes, polydactyly
4. What category of allele is Vangl2Lp-‐m1Jus?
b) Gene trap
d) Chemically induced (ENU)
e) Targeted (null/knockout)
5. What are the mutation details of Vangl2Lp-‐m1Jus?
a) Exon 1 is floxed
b) Exon 4 was targeted and replaced by a neomycin cassette
c) A transversion mutation occurred, changing Asp255 to Glu
d) A stop codon mutation truncating the protein at amino acid 410
e) The entire gene was deleted
6. Which of the following nervous system phenotypes have been observed in mice
homozygous for Vangl2Lp-‐m1Jus?
b) abnormal synapse morphology
c) abnormal kidney morphology
d) decreased Purkinje cell number
e) no observed nervous system phenotypes
7. Using the Phenotypes, Alleles and Diseases query form, how many targeted alleles
have been annotated to craniorachischisis?
Hint: prior to May 22nd “Categories: targeted (all)” or after May 22nd “Categories:
Generation Method: Targeted”.
You want to design an experiment where you study the effects of removing
cadherin 2 (Cdh2) from mouse stomach glandular epithelium, but NOT
To do this requires use of a cre-‐lox strategy, where you have (1) a mouse with a
targeted conditional allele of Cdh2, with loxP recombinase recognition sites used to
flank some portion of the Cdh2 gene, and (2) a mouse carrying a cre transgene with
recombinase activity detected in the stomach glandular epithelium along with no
activity in the respiratory system.
8. Of the following, which allele of Cdh2 would be most appropriate?
e) None of the above
9. Which exon(s) of the Cdh2 gene are flanked by LoxP sites (floxed) in Cdh2tm1Glr?
a) The entire gene
b) Exon 1 and upstream transcriptional regulatory sequences
c) Exon 3
d) Exons 4&5
e) It is not specified
10. How many cre transgenes have recombinase activity results annotated to
“stomach glandular epithelium”?
e) It is impossible to tell
11. Of the following, which transgene best matches recombinase activity “detected
in: alimentary system” (which contains stomach glandular epithelium) and
recombinase activity known to be “not detected in: respiratory system”
d) Any/all of the above
e) None of the above
12. Which is the driver of the cre recombinase transgene Tg(Atp4b-‐cre)1Jig?
e) There is no driver
13. Which tissues, structures or substructures of the renal and urinary system were
examined for cre recominbase activity in Tg(Atp4b-‐cre)1Jig? Was recombinase
activity noted as detected (√) or not detected (-‐)?
a) bladder (-‐)
b) renal tubule (√) and renal corpuscle (-‐)
c) kidney (√)
d) kidney (-‐)
e) metanephros (-‐)
14. What is the level (present/absent) and pattern of cre recombinase activity
detected in the stomach of mice aged post-‐natal week 7 (adult)?
a) Not reported
b) absent, not applicable
c) present, not specified
d) present, strong
e) present, regionally restricted
You have an exome sequencing result come back for a patient who as a familial
susceptibility to glomerulonephritis (renal/urinary system phenotype), vasuculitis
(cardiovascular system phenotype), and leukemia (tumorigenesis phenotype), which
appears to be inherited as a monogenic trait. The genes with predicted pathogenic
variants are: CHAT, ACOX1, SH2D3C, TUSC2 and ZYX.
For the following problems, use the Human-‐Mouse: Disease Connection, which
has a link from MGI’s homepage, or can be accessed directly at:
15. Based on mouse phenotypic annotations, which of these genes is the most likely
candidate for your observations?
16. Which of these genes would be expected to be associated with infertility (a
reproductive system phenotype)?
17. Which of these genes has variants associated with Myasthenic Syndrome,
Congenital, Associated with Episodic Apnea in human patients?
18. What is the Disease Relevant publication that describes the association of mouse
Acox1 in Peroxisomal Acyl-‐Coa Oxidase Deficiency?
a) Abbott BD et al. (2012) Reprod. Toxicol.
b) Huang J et al. (2011) Am. J. Pathol.
c) Fan CY et al. (1996) J. Biol. Chem.
d) Suzuki et al. (1994) J. Pediat.
e) this association was made by Mouse Genome Informatics curators
For these problems, please access MouseMine either from MGI (homepage>Batch
Data and Analysis Tools, or dropdown menu Search>MouseMine) or direct, at
You are a researcher working on DNA repair and have generated a list of 321 mouse
genes based on functional annotations. This list is pre-‐loaded into MouseMine – go
to the “Lists” tab, “View” and click on “Mouse DNA repair genes 2013-‐01-‐06”.
Be sure to scroll down the page to find Enrichment widgets and Template queries.
** Please note that the content in these worksheets is accurate as of 16 May 2014.
Updates to the data may cause some numbers to shift slightly. **
19. At the top of the page in list analysis tools, use Manage Columns (may compress
to “Columns” in smaller windows) to add a column for “NCBI Gene Number” to the
list of 321 DNA repair genes. What are the positional coordinates for Hmga2?
20. In the Human Disease Enrichment widget, using the default of Holm-‐Bonferroni
test correction, what is the associated p-‐value for the MEDIC term: “DNA Repair-‐
a) 2.641253e-‐84 with 62 genes matched
b) 5.148577e-‐27 with 23 genes matched
c) 0.001798 with 5 genes matched
e) There is no significant enrichment for this term
21. Scroll further down the page below the Enrichment Widgets to the Template
Results for this list. Locate the table for Function: “Mouse Features à Functions
(GO terms)”. Expand, if necessary, by clicking on the name of the template.
According to the column summary for “Code”, how many functional annotations
have the evidence code “IMP” which corresponds to “Inferred from Mutant
22. Exit the list analysis tools and return to MouseMine Home. Find the template for
Homology: “Genes -‐> Homologs”. Enter “pxn” into the search box, leaving the
Organism dropdown menu at the default M. musculus.
What is the Homolog symbol corresponding to the Homolog Organism:
e) there is no homolog in S. cerevisiae
1. a) Chr 1
2. e) 22
3. b) Yes, neural tube defects
4. d) Chemically induced (ENU)
5. c) A transversion mutation changing Asp 255 to Glu
6. a) craniorachischisis
7. d) 15
8. b) Cdh2tm1Glr
9. b) Exon 1 and upstream transcriptional regulatory sequences
10. b) 6 recombinase alleles
11. a) Tg(Atp4b-‐cre)1Jig
12. d) Atp4b
13. d) kidney (-‐)
14. e) present, regionally restricted
15. d) Tusc2
16. a) Acox1
17. b) CHAT
18. c) Fan CY et al. (1996) J. Biol. Chem
MOUSE MINE MODULE
19. a) 5.148577e-‐27 with 23 genes matched
20. b) 1214
21. c) 10:120361275-‐120476469
22. c) PXL1