Biodiversity · Database
Mouse Phenome Database
A database of strain-level phenotype and genotype measurements across diverse laboratory mouse populations.
What Mouse Phenome Database is
The Mouse Phenome Database (MPD) is an integrated scientific resource providing strain characterisation records for the laboratory mouse. Begun in 2000 and headquartered at The Jackson Laboratory, it aims to support translational research into human health and disease by facilitating the exploration of physiology and behaviour via genetics and genomics.
The platform brings together phenotype, genotype, and quantitative trait locus (QTL) datasets alongside associated protocols and study details. Phenotypic measurements frequently consist of strain surveys assessing between 10 and 40 commonly used mouse strains across physiological areas such as haematology, bone mineral density, cholesterol levels, endocrine function, and aging processes.
Genotypic data within the database are primarily represented by single-nucleotide polymorphisms (SNPs). Researchers can interrogate, select, and analyse data online or contribute their own datasets to the repository.
How it is organised
The database integrates data contributed by participating scientists as well as records sourced from public repositories. Datasets are organised into phenotypes, genotypes, strain panels, QTL studies, and experimental protocols. Strains represented include standard inbred strains as well as diversity panels such as Diversity Outbred (DO) mice, Collaborative Cross (CC) lines, and the Hybrid Mouse Diversity Panel (HMDP).
Users can search and select datasets, access specific analytical tools through the web interface, organise custom data views via MyMPD, or download data files directly for external evaluation.
Key facts
- Host institution
- The Jackson Laboratory
- Year established
- 2000
- Primary data types
- Phenotypes, genotypes, QTLs, and protocols
- Genotypic coverage
- Single-nucleotide polymorphisms (SNPs)
- Study subjects
- Laboratory mouse inbred strains and diversity panels
What you can use it for
- Mouse strain phenotypic comparison
- Comparing physiological parameters such as cholesterol levels, bone mineral density, endocrine function, and haematology across 10 to 40 commonly used inbred mouse strains.
- Quantitative trait locus (QTL) mapping
- Investigating the genetic basis of behavioural and physiological traits, such as locomotor responses to substances in crossbred populations.
- SNP and genomic variation analysis
- Accessing large-scale single-nucleotide polymorphism data, including tens of millions of SNP locations across diverse inbred strains.
- Dietary and behavioural phenotype assessment
- Examining data from studies on dietary interventions, such as high-fat high-sucrose diets in Diversity Outbred mice, or oral self-administration assays in HMDP strains.
Query it here
The research agent queries Mouse Phenome Database directly — no account, no API key — and every answer links back to the record it came from. Ask in plain language and it writes the query.
Strengths and limits
Good at
- Integrates both phenotypic measurements and SNP genotypic data for laboratory mouse strains within a single resource.
- Provides documented experimental protocols alongside characterisation data to support study reproducibility.
- Includes built-in web tools and a personalised portal (MyMPD) to find, select, and analyse data online.
Watch out for
- Genotypic data are primarily limited to single-nucleotide polymorphisms rather than other structural genomic variants.
- Phenotype strain surveys are predominantly restricted to comparisons among sets of 10 to 40 commonly used strains.
Questions
Can I search Mouse Phenome Database without writing code?
Yes. The research agent queries Mouse Phenome Database directly, with no account or API key, and cites the record behind every answer. Ask in plain language — for a gene, a protein, a compound or a study — and it builds the query for you.
Can I reuse data from Mouse Phenome Database?
Contributors waive copyright; free reuse for any purpose, citation requested. Terms: https://phenome.jax.org/about
What types of mouse populations are covered in the database?
The database includes classic inbred mouse strains as well as diversity panels, including Diversity Outbred (DO) mice, Collaborative Cross (CC) lines, and the Hybrid Mouse Diversity Panel (HMDP).
What phenotypic domains are included?
Documented phenotypic areas include haematology, bone mineral density, cholesterol levels, endocrine function, aging processes, and behavioural responses.
Where does the data come from?
Records are contributed by participating scientific researchers or imported from public data resources.
Can external researchers submit their own data?
Yes, the repository provides tools and procedures for researchers to submit phenotype and study data.
Written from Mouse Phenome Database's own website and reference material. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.