MGI Redesigns Alleles & Phenotypes pages
JAX® NOTES Issue 512, Winter 2008
The Mouse Genome Informatics (MGI) phenotype pages now contain powerful new options for exploring the relationships between genotypes and phenotypes. View the quick tour of these changes or read the example below.
The Phenotype section of each allele detail page now includes two distinct presentations of phenotype data. As an example, go to the allele detail page for the Adcy1tm1Drs targeted mutation, (Figure 1).
Figure 1. The Allele Detail Page for targeted allele Adcy1tm1Drs. Phenotype data are presented differently in each of the bottom two panels:
1) "Phenotype summary" and
2) "Phenotypic data by genotype". In the first panel, you can explore how various genotypic combinations affect phenotype: you expand the general "Affected System" phenotype term to view more specific phenotypes in the context of different genotypes. In the second panel, you expand a specific genotype of interest to view the detailed phenotype annotations or to link to the reference describing that phenotype.
In the "Phenotype summary" panel, users can compare effects of different allelic combinations (such as homozygous, heterozygous, conditional, and complex) in different genetic backgrounds. The vertical axis lists relatively general phenotypes, such as "behavior/neurological"; the horizontal axis lists genotypes (note the color key in the header section). By clicking on the arrow to its right, you can expand a general phenotype to more specific phenotypes. For example, clicking on the arrow to the right of "behavior/neurological" expands the view to more specific phenotypes, such as "increased chemical nociceptive threshold", "hyporesponsive to tactile stimuli", and "abnormal spatial learning" (Figure 2).
The "Phenotypic data by genotype" panel allows you to see detailed phenotype annotations for each genotype. For example, by clicking on the arrow to the right of "hm2", you can see the detailed phenotype for a mouse with a mixed 129S7/SvEvBrd and C57BL/6 genetic background homozygous for the Adcy1tm1Drs targeted mutation (Figure 3). You can also select "show" or "hide" all options at the top left of the panel.
MGI staff are excited about these improvements and are eager to help you if you have any questions. For questions and more information, contact User Support at mgi-help@informatics.jax.org. Also, check out the Quick Tour of Allele & Phenotype changes at www.informatics.jax.org/faq/Allele_tour and the Understanding Phenotype Allele Detail Pages at
www.informatics.jax.org/userdocs/allele_detail_report.
Figure 2. Expanded view of the general phenotype "behavior/neurological" (a red bar on the left of your computer screen denotes expansion). Specific phenotypes for the genotype combinations selected are visible and can easily be visually compared. You may expand or contract each general phenotype independently. You may also select "show" or "hide" all options at the top left of the panel. Clicking on the genotype abbreviation (e.g., hm1 — for homozygous 1) opens a new window, where you can view the detailed phenotypic annotations for this genotype (Figure 3). Each phenotype term is linked to the Mammalian Phenotype Ontology where terms are defined and links are available to all (genome-wide) mutations with this phenotype. There are also links to references describing each phenotype.
Figure 3. Expanded view for the hm2 Adcy1tm1Drs genotype on a mixed genetic 129S7/SvEvBrd and C57BL/6 background (a red bar at the left of your computer screen denotes expansion). Phenotypic terms and details are visible. You can expand or contract each genotype independently. You can also select "show" or "hide" all options at the top left of the panel.
