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Genomic study of F2 cohort

1. Genetic architecture

Illustrates the relationship between the genomic location of a gene vs. the locus to which that gene’s expression maps, or its eQTL. Cis-eQTL are shown along the diagonal and are back, whereas trans-eQTL are colored and form vertical bands where many trans-eQTL co-map to the same locus. Allows for genome-wide survey or for specific genomic locations. Data is easily downloaded.

2. QTL scans

Performs QTL scans for gene expression in each of 6 tissues, or >100 diabetes-related clinical traits. Generates graphical plots genome-wide or for specific chromosomes. Sex-specific scans and allele-dependence plots are available. For multiple traits, heat maps can be used for easy visualization.

3. Correlation search tool

Allows for gene-gene or gene-clinical trait correlation analysis among all F2 mice in each of 6 tissues (islet, liver, adipose, muscle, hypothalamus, kidney). Can also search for genes within a particular tissue that correlate with specific clinical traits. Correlated genes lists can be downloaded or easily transferred to DAVID for Gene Ontology enrichment analysis. 

4. SNP search tool

Searches for SNPs identified between B6 and BTBR genomes. Can enter either a genomic region or a specific gene. SNPs are classified according to functional consequence. Data is easily downloaded.

5. eQTL viewer

This software provides a view of the genetic architecture of gene expression in one of 6 tissues. You can also search for single genes, plot their genome-wide LOD profile and view a plot illustrating their allele dependence in male and female F2 mice.

UW-Madison Department of Biochemistry Department of Biochemistry
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