I see more significant parameters in the All Measurements chart, than significant phenotypes in the Significant Phenotype table; why does this happen?

This situation is encountered when more than one parameter is annotated to the same phenotype.

For example, for gene Tmem63b. When you filter by significant systems and take note of the nervous system hits in the Graphical Analysis chart, 6 significant parameters are displayed.

Interestingly, if you click on the Significant Phenotypes table, then sort by system, you will see only 2 nervous system significant genotype-phenotype associations. This is due to 5 of these parameters having been collapsed to measure the same phenotype, “hyperactivity” (MP:0001399), and the remaining one that measures other phenotype, “limb grasping” (MP:0001513).

If you click on the relevant phenotypes on the Significant Phenotype table to see the underlying data, you find the results for five parameters measuring hyperactivity, and for one parameter measuring limb grasping.