Use this page as a starting point if you're considering ways of looking at the data in MPD.
Much of the information in MPD is "strain survey" data, meaning that a set of investigator-selected inbred strains
is tested in a cohesive project where baseline phenotype, intervention- or aging-related phenotype effects,
expression, or genotype are measured.
Because the mice of each inbred strain are considered genetically uniform,
analyses are often based on strain/sex averages which can come from a variety of labs and experiments,
making this paradigm useful for finding reference values as well as
correlations and other more involved analyses, with the opportunity to
leverage available high-resolution strain-specific genotype data.
More recently MPD has expanded into other data paradigms such as heterogeneous populations.
For more discussion of data types and study designs see the About MPD page.
Look up data for one or two strains
• Find data for a specific strain
Find phenotype, SNP/variation, or expression data for a certain strain,
or list phenotypes and probesets where a certain strain is a high-end or low-end outlier.
• Compare two strains
For two strains of interest see how they compare in phenotypes, polymorphisms, and expression.
Work with a particular strain panel or set
MPD has data for a number of research strain panels and sets including
BXD, ILSXISS and other RI panels, HMDP, consomics, Diversity Outcross populations, and Collaborative Cross emerging lines,
and provides strain panel-specific navigation entry points.
Phenotype strain survey data [Home]
• Tools and views
Web-based tools for plotting, correlations, criteria-fit, finding outliers, downloading selected data, and looking at ratios and differences.
Normally you navigate to phenotype data of interest, or go to your cart, then click on Apply Tools.
MPD phenotype strain survey data have been mapped to MP, VT, and MA ontology terms.
Find phenotype data by ontology term, or navigate the ontologies and term-specific linkouts to other resources.
• Your collection
While browsing MPD collect phenotype measurements into your shopping cart.
Then go to your cart (at top of page) to work with them.
• By intervention or by
Drug, alcohol, diet, pathogen, challenge, toxicity intervention studies are available.
Data can be queried by phenotyping methodology, and each data set has associated protocol
documentation with methodology details (via the symbols).
• Aging studies
MPD has comprehensive characterization of aged mice.
• Create user vectors and find correlated objects.
To create a "user vector" you can
input strain averages from your own assays, or take the
ratio or difference of two existing MPD phenotype measurements.
Then with this vector you can list correlated phenotype measurements and expression data from across MPD.
• EMMA association study
Genome-wide association studies of selected MPD phenotypes were run by the ZarLab at UCLA using their EMMA
• Sex differences
List measured traits by average amount of sex difference. Or if you have a set of measurements, you can use Apply Tools
to list the strains that exhibit the most sex difference.
• Sampling variation over time
Several studies measured seasonal variation of C57BL/6J mice in various phenotypes.
Genotype variation strain survey data [Home]
• SNP / variation query
Retrieve SNPs, indels, or SVs from a number of data sets. View the result or download as CSV.
• Polymorphism matrix view After running a query as above,
a strain matrix of %polymorpic for the retrieval can be viewed.
• Haplotypes / strain groupings view After running a query as above,
a strain group summary can be viewed.
• Find genes where selected strains are polymorphic
Select from the 29 strains assayed in Sanger1 and list the
genes where selected strains are highly polymorphic, across the entire genome or a particular chromosome. Based on
tabulations made in advance on Sanger1 data.
Gene expression strain survey data [Home]
• Correlations and outliers.
Mathematical correlations between phenotypes and expression probesets, and finding probesets where
certain strains are outliers.
• Differential expression analysis
Studies are available comparing treatments vs. controls, females vs. males, or cell types.
Treatments include high-fat diet, LPS, TCE, OxPAPC.
QTL studies [Home]
MPD has 70+
QTL studies in various research areas, each having phenotype and genotype data
for members of a population derived from a specific cross.
Each study has a web page listing the phenotypes studied, as well as downloadable data files.
Users download the data and run analyses locally using software such as R/qtl.
Finding data associated with particular gene(s)
If you have a specific gene or genomic region in mind, begin at
MPD's gene search page and
click through to the desired gene or region page for links to available data.
MPD has SNP/variation strain survey data,
expression strain survey data, and certain phenotype strain survey and QTL data that can be queried by gene or region.
Capture gene sets
Help Desk is happy to assist you in your work. Let us know how we can help.
Our video demo / tutorial series is also available.