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KOMP 2 Phenotyping Effort

About 3D Data Representations

3-dimensional representations of heat maps are available as zip compressed X3D formatted files. A helper application is required to view these files. FreeWRL is a free and open source application available for Linux, Apple, and Windows platforms.

The 3D representation provides a quick comparison between knockout populations that can display more information than a 2D heat map. Through the use of the helper application, the 3D images can be freely rotated and zoomed for rapid identification of knockout models of interest.

At all levels, the 3D representations include knockouts with observations displayed in an X, Y grid. When more than one phenotype group or phenotype observation is included, the Z-axis represents accumulated exceptions as defined as the selected gender and genotype population mean beyond a two-tailed 85, 90, or 95 percentile of the entire wild type population. The exception level is penalized on a specific phenotype observation when the wildtype cohort from which the knockout mice where derived display the same exception, thereby controlling for background effects. Resulting positive values are colored green, neutral values blue, and negative values red.

When a single phenotype observation (e.g. Blood Chemistry/Sodium) and genotype (e.g. homozygous) are selected, the Z-axis of each knockout represents the mean measurement of the specific phenotype observation. Mean values above the specified two-tailed percentile cut-off are colored green, those below are colored red.

The KOMP Phenotyping Project is funded by an ARRA grant to UC Davis and CHORI.

Questions? Comments? Please contact us: 1-888-KOMP-MICE or service@komp.org