From: Beyond differential expression: the quest for causal mutations and effector molecules
Measure | Algebra formulae | Description | Example in skeletal muscle context |
---|---|---|---|
Phenotype Impact Factor |
| Average (normalized) expression of the i-th gene across the two conditions multiplied by its differential expression. In other words, PIF weights the differential expression of a given gene by its overall abundance. | MYL2 very strongly. |
Regulatory Impact Factor, Option 1 |
| For the i-th regulator and across all the j differentially expressed genes (j = 1, …, n dE ) RIF1 looks at the average PIF of the i-th regulator weighted by the squared differential co-expression between the i-th regulator and the j-th differentially expressed gene. It addresses the question: Which regulator is consistently highly differentially co-expressed with the abundant differentially expressed gene? | MSTN very strongly. |
Regulatory Impact Factor, Option 2 |
| For the i-th regulator and across all the j differentially expressed genes (j = 1, …, n dE ) RIF1 looks at the average change in predictive ability of the i-th regulator to predict the abundance of the j-th differentially expressed gene. It addresses the question: Which regulator has the most altered ability to predict the abundance of differentially expressed genes. | MSTN very strongly. |