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Gene expression strain surveys
A collection of gene expression microarray data sets (strain surveys) as well as functionality such as correlations with phenotypes and strain outlier analyses. See also MGI's GXD database which has expression data and images from many other types of study designs. MPD requirements for gene expression data: strain survey of 15 or more strains; sexes segregated; 3+ biological replicates preferred. Treatment-control and other multi-cohort studies are accessioned as multiple data sets and can be analysed using the differential analysis tool below.
• Interpretation of these data, and usage caveats
• Data sets       • Strain coverage       • Annotation notes



Starting with a particular gene or genomic region....
Click here to enter your gene symbol or location, then on the next page see the gene expression section. From there you can list probesets in the vicinity or:
    • List phenotype measurements mathematically correlated to probesets in vicinity
    • List strain outliers for probesets in vicinity


Starting with one or two strains of interest.... click here
List locations where one or two selected strains are expression outliers relative to other strains tested. Entire genome or a specific region. One, several, or all data sets.


Starting with two strains (or strain sets)... click here
List the genes / probesets where there's the most expression difference found between two selected strain sets, in one expression data set.


Differential expression analysis... click here.   Studies are available comparing treatments vs. controls (high-fat diet, LPS, TCE, OxPAPC) as well as females vs. males.


Starting with MPD phenotype measurements
Navigate to phenotype data of interest. Begin by clicking on the Apply Tools link. When you get to the toolbox page click on the green gene expression icon. This will list genes and locations that have probesets mathematically correlated to the phenotypes. A more advanced approach is to gather the desired phenotype measurements into your shopping cart, then go to your cart, click Apply Tools, and go from there.


Other approaches
    • Correlate to your own strain means   Type in your unpublished strain means and find expression data (probesets and genes) that are mathematically correlated.

    • Download file of all computed correlations: All computed correlations between probesets and MPD phenotype measurements with correlation p value ≥ 0.005   This file is available by request (phenome@jax.org)

    • Downloading expression data sets: Most expression data in MPD are available via public resources such as GEO. However, if a particular type of download file is needed let us know, we may be able to help.



• Video tutorial sessions 7 and 14 include demonstrations of MPD's gene expression functionality.


 




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