The Mouse Metabolic Phenotyping Centers (MMPC) is a National Institutes of Health-Sponsored resource that provides experimental testing services to scientists studying diabetes, obesity, diabetic complications, and other metabolic diseases in mice. Dr. Richard McIndoe will introduce resources and tools that are available at MMPC. Abstract A common strategy to dissect the etiology, genetics and underlying physiology of a disease is to create mouse models using gene targeting and manipulation techniques. These mouse models were developed by targeting one or more candidate genes or by using a whole genome mutagenesis strategy. The careful and reproducible characterization of these animal models is important for the advancement of biomedical research. The expense, expertise and time required to develop state-of-the-art phenotyping technologies is beyond the reach of many investigators. The Mouse Metabolic Phenotyping Centers (MMPC) were created to provide the scientific community with cost effective, high quality, standardized metabolic and phenotyping services. The focus of the MMPC is on experiments that characterize living animals as well as providing technologies that are important for understanding metabolism and physiology. The MMPC provides state-of-the-art technologies to investigators for a fee, with their services including characterization of mouse metabolism, blood composition (including hormones), energy balance, eating and exercise, organ function and morphology, physiology and histology. There are currently five MMPC Centers located at Vanderbilt University, University of California Davis, University of Cincinnati, University of Massachusetts and the University of Michigan. Investigators using the MMPC services agree to release the data generated by the MMPC to the general public via the national website database. This talk will review the structure of the MMPC, the services it provides and the data generated by the consortium for public use. Presenter: Dr. Richard McIndoe, Professor, College of Graduate Studies and the College of Allied Health Sciences, Medical College of Georgia. More information: https://dknet.org/about/webinar

1. Mouse Metabolic Phenotyping Centers:
Services and Data
Richard A. McIndoe, Ph.D.
Director, Coordinating Unit MMPC
Associate Director, Center for Biotechnology and Genomic Medicine
Regents’ Professor
Augusta University, Augusta GA
rmcindoe@augusta.edu

2. Seminar Agenda
1. MMPC Organization
2. MMPC Services
3. MMPC Order Process
4. MMPC Data Curation / Data
5. MMPC Data Search
6. Future MMPC Integrations

3. MMPC CU

4. MMPC CU Organization
Dr. Richard McIndoe
Director
Mike Aufiero
Web
Development
Danilo Guesela
Network
Management
Colby Williams
Data
Curation
Dr. Ashok Sharma
Bioinformatics
Dr. Nathan Xu
Biostatistics
Sarah Gross
Administrator

5. MMPC Coordinating Unit
1) Create data schemas to store animal model and phenotype
information as well as links to outside sources.
2) Provide an API to access the underlying data structures
5) Provide organizational infrastructure to facilitate the coordination
of the consortium’s efforts.
4) Provide website for consortium members, MMPC clients, and the public.
3) Organize data curation and data visualization tools

6. 6) Provide support and fiscal oversight for awarding MICROMouse
subcontracts
7) Provide support and fiscal oversight for the distribution of funds as
dictated by the NIH
8) Development of reports to track business activities and core
utilization of the MMPC
9) Integrate and coordinate with external resources (e.g. dkNET, IMPC)
that would provide value to the MMPC.

7. MMPC Center Cores
1) Lipid, Lipoprotein and
Glucose Metabolism Core
2) Energy Metabolism, Food
Intake & Body Weight
Regulation Core
3) Behavioral and Cognitive
Core
1) Metabolism Core
2) Analytical Core
3) Animal Care Core
4) Islet Core
5) Cardiovascular Core
6) Humanized Mouse Core
7) Microbiome Core
1) Animal Care and Germ-Free
Mouse Core
2) Metabolism, Bariatric
Surgery and Behavior Core
3) Microvascular
Complications Core
4) Microbiome Core
Patrick Tso, Ph.D. Jason Kim, Ph.D. Malcolm Low, Ph.D.

8. MMPC Center Cores (cont.)
1) Animal Care, Surgery and
Pathology Core
2) Endocrinology and
Metabolism Core
3) Energy Balance, Exercise
and Behavior Core
4) Microbiome and Host
Response Core
1) Metabolic Regulation Core
2) Cardiovascular Pathophysiology
3) Analytical Resources Core
4) Body Weight Regulation Core
K.C. Kent Lloyd, DVM, Ph.D David Wasserman, Ph.D.

9. MMPC Services
Diabetes
Hormone Measurements
Insulin/Insulin Function
Pancreas/Islet/Beta Cells
Vascular Function
Cardiac Function
Blood Count / Chemistry
Circulation
Microvascular Comp.
Body Composition
Food/Water Intake
Energetics
Carbohydrate Metabolism
Obesity
Amino Acid Metabolism
Lipid Metabolism
Carbohydrate Metabolism
Energy Expenditure
Exercise
Metabolite Concentration
Bariatric Surgery
Microbiota/Microbiome
Fat Absorption
Lymphatic System
Chylomicron Metabolism
Immunohistochemistry
Histopathology
Amino Acid Metabolism
Lipid Metabolism
Carbohydrate Metabolism

10. MMPC
Web Portal Overview

11. MMPC Home
Client/Center
Login
Public
Communications
MMPC
Organization
Steering
Committee
Standing
Committee
External
Advisors
MMPC
Public Data
Repository
MMPC
Centers
Data
Analysis
Data
Query
Query by
Strain
Query by
Animals
Query by
Organ Site
Query by
Gene Product
Measurement
Query by
Experiment
Query by
Investigator
Next
Page
Site Map
Phenotype
Exploration
Strain
Info
Measurements
Histology
Charts/ Plots
MMPC
Meetings
MMPC
Announcements
MMPC
Brochures
MMPC
Catalog of
Services
Principal
Investigators
Projects
Institutions
Involved
Publications
Application
For
Services
Catalog Items

12. MMPC Home
Client/Center
Login
MMPC
Public Data
Repository
MMPC
Organization
Public
Communications
MMPC
Investigators
Site
Administration
Data
Submission
Member
Resources
Member
Administration
Policy
Enforcement
Security
Roles
Catalog
Information
Mouse
Strains
Mouse
Experiment
Database
Mouse
Histology
Database
Strain
Submission
Forms
Submitter
Strain Designation
Mutation Type
Gene Info
Transgene Info
etc.
Data
Submission
Forms
Submitter
Strain
Assay
Measurements
etc.
Histology
Submission
Forms
Submitter
Strain
Image Info
Anatomy Info
etc.
Catalog
Information
Forms
Center Cores
Catalog Items
Catalog groups
Assays
Keywords
Data Query
(Private Data)
Same
Capabilities
as public
Data Analysis
(Private Data)
Same
Capabilities
as public
Meetings/
Workshops
Registration
Information
Site Map, cont.

13. www.mmpc.org

14. The site adjusts the look and options based on users privileges

15. MMPC Catalog Search
Center
Center Core
Test Group
Research Area
Keywords
Anatomy
Metabolism
Endocrine
Cardiovascular
Energy Balance
Gastrointestinal
Analytical Resources
Histology
Decision Tree:
Answer questions
about phenotype to
suggest tests.
The current COS contains 564 catalog items and averages 112 tests per center.
On average, each Center accepts ~60 orders per year.

17. Basic workflow for an order request and data upload process.
Client Request
Order
Created
Rejected Order
Status
Updated
MMPC
AFS
Review
Process
Accepted
Create
Experiment
For Order
Order
Status
Updated
Add Data
To
Experiment
Catalog
Center Updates Order Status to:
‘Complete’

21. MMPC Data

22. Protocols
1. Continue to work on adding Center protocols into the system.
2. All five centers have submitted protocols to be uploaded into the
National MMPC website.
a. University of California Davis – 86 protocols
b. University of Massachusetts – 60 protocols
c. Vanderbilt University - 20 protocols
d. University of Michigan - 18 protocols
e. University of Cincinnati - 8 protocols

24. Strain Data
• Strain Name (using standard rules)
• Basic breeding information, parentage
• Creation method and protocol
• Genotype
– Genes involved, allele types, inheritance mode
• Phenotype
– From experimental data
https://www2.jax.org/nomenclature-tutorial/

25. Phenotype Assays
• Quantitative measures
– hormone, cell counts, severity scores
• “Qualitative” measures
– E.g. lymphocytic infiltration present/absent
– Categorical data
• Standardized Across Centers
• Assay names and groupings
• Min-max range
• Unit of measure
• Assays can be associated with Catalog Items
– Not required, can be independent of catalog

26. Experiments
• Associated with orders
• All data uploaded to system is associated with an
experiment.
• Identified by title and description unique to the client
• Optionally assigned “experimental conditions”
• Specification of animals used
– Strain, Sex, Age, Unique ID
• Specification of samples
– Unique Animal ID (client specific)
– Animal age when sample was obtained
– Associated experimental conditions

27. 1. MMPC Policy: Data uploaded to the system is released to the public if
either:
1. The data is published
2. The data has been in the system for two years.
2. An experiment can have one or more documents attached. This can be
used for delivery of results to the client.
Experiments

29. Data Curation Workflow
Experiment status set to “Complete” by Center
Database curation record inserted, curation status set
Email sent to Data Curator notifying that data has
been uploaded to an experiment.
Data Curator begins review of data uploaded to
system and uses workflow to keep track of status
and interact with Center personnel.
Experiment curation flags determined

30. Data Curation
Experiments that that have only ‘experiment’ or only ‘control’ animals.
Experiments where the strains are the same for the ‘experiment’ and
‘control’ animals.
Experiments where all the metadata fields for the ‘experiment’ and
‘control’ animals are the same.
Experiments where the number of animals in the order is different from
the number of animals in the experiment.
Experiments where no data was uploaded.
Experiments where the ‘Experimental Group’ condition has been
removed.
Automated Script

31. •Mice/samples metadata not consistent between experiment/control
1.This happens where the data shows a clear control with experimental
conditions different from those of the experiment subjects, but the labels
appear to be different between mice.
•Drug administration is not consistent with the order
1. the order states drug A but drug B was used
2. the title or description states that a drug was administered, but
there is no experimental condition for this in the data
•Mouse diet not consistent with the order
1. order requested HFD vs. regular chow, but only one diet
appears in the experimental conditions
•Description of experiment field is blank
•Experimental conditions should be added to delineate between control and
experiment
•Strain nomenclature is not consistent with the order
1. the title or description states that KO mice were used but the only
strain listed is C57BL/6
Manual Curation Flags

35. Experiment status set to “Complete” by Center
Model Outputs
Stored: e.g. effect size
Results reviewed by
biostatistician
Curation status set to ‘Curation Complete’
Curation Workflow
MMPC Semi-Automated
Interface
Mammalian Phenotype
(MP) Ontologies Stored
Status=‘Analysis Generated’
Status=‘Analysis Complete’ Status=‘Analysis Verified’

37. The MMPC Data is much more complicated and required us to modify the
PhenStat library to accommodate the differences by including more
covariates and interactions since they could be potential confounders (e.g.
mouse diet, drug dosage, surgical procedure, etc.).

38. Modified libraries “completed”, will be available via GitHub
Constantly testing PhenStatMMPC on current data sets.
Can successfully analyze ~95% of the data sets.
MMPC Data File
PhenStatMMPC
Schema file+
PhenStatMMPC
R Calling Code
PhenStatMMPC
Library

39. PhenStatMMPC
1. Handles more than one covariate
2. Handles time course data
3. Handles more than two mouse strains
4. Handles batch effects
5. Confirmed PhenStatMMPC results using SAS.

45. MP Term Assignment Based on PhenStatMMPC analysis.

50. https://dknet.org/about/hypothesis_center
dkNET partnered with the Signaling Pathways Project (SPP) knowledge base,
which has developed a powerful new meta-analysis platform, consensomes,
that surveys across millions of DK mission-relevant biocurated 'omics data
points to make high-confidence connections between genomic targets, their
upstream regulatory pathways, and the disease states in which their
expression is altered.

51. Transcriptomic
Expression array & RNA-Seq
Cistromic
ChIP-Seq
Receptors
Enzymes
Transcription
Factors
Co-nodes
Signaling Pathways Project (SPP): two universes of biocurated
transcriptional data points mapped to cell signaling pathway nodes
SPP node types
Hs
Mm
Rn
Hs Mm
Kindly provided by Neil McKenna, Ph.D.

52. Consensomes are list of genes ranked according to a meta-analysis of their
differential expression in publicly archived transcriptomic datasets involving
perturbations of a specific signaling pathway in a given biosample category.
Consensomes are intended as a guide to identifying those genes most
consistently impacted by a given pathway in a given tissue context.

53. Source Phenotype(s) Obs Exp Enrichment P-val
MMPC MP:0014143 - decreased body fat mass
MP:0014142 - increased body fat mass
IMPC MP:0014143 - decreased body fat mass
MP:0014142 - increased body fat mass
MGI
MP:0005666 - abnormal adipose tissue
physiology
60/146 14.9/146 4.03 1.36E-22
GO GO Term: fat cell differentiation 92/250 25.5/250 3.61 1.63E-29
Kulyte et al.
Insulin resistant v sensitivie human
adipocytes
118/413 42.1/413 2.8 5.64E-26
85/480 48.9/480 1.74 2.93E-07
n(%) genes in 90th %ile of SPP MATTC
11/22 2.24/22 4.91 2.92E-06
Can data from the MMPC provide experimental evidence to support
genes in the SPP consensomes?
Calculated p-value for enrichment based on the cumulative distribution function (CDF) of the
hypergeometric distribution
SPP Consensome for Mouse Adipose Tissue (26277 genes)

54. Kindly provided by Neil McKenna, Ph.D.
Fbxo31 - F-box protein 31
CPV = 3.1E-14
%ile = 95th

56. Final Thoughts
1. The MMPC Centers can provide fee service phenotyping of
live mice over a broad range of research areas.
2. The MMPC data is highly curated and available to the public.
3. Data can be search based on the gene, phenotype or catalog
item of interest to the user.
4. We are working on integrating these data with the SPP at
dkNET to increase the range of uses for the data.

57. MMPC Coordinating Unit
Web portal / Database: Michael Aufiero
Bioinformatics: Ashok Sharma, Ph.D.
Data Curation: Colby Williams, M.S.
Biostatistician: Nathan Xu, Ph.D.
Administration: Sarah Gross
NIDDK Program Officers (MMPC)
Maren Laughlin, Ph.D.
Kristin Abraham, Ph.D.
Collaborators
dkNET: Jeffrey Grethe, Ph.D.
SPP: Neil McKenna, Ph.D Funding Provided by:
Thank You!