Gene Inactivity Moderated by Metabolism and Expression (GIMME)

General concept

This method builds context-specific models that predict which pathways are expressed on possibly used in a cell. This approach sets a lower bound on the objective function and then finding the network topology that is able to attain the desired objective value, while minimizing a penalty score for adding reactions associated with non-expressed genes (i.e., reactions with gene expression lower than a user-specified threshold). The penalty score is the sum of the flux-adjusted difference between the absolute gene expression level and the threshold value.

Items to consider when implementing

Software packages with this method

Applications of interest

Description of study and link to study:

What was learned with this method:

Relevant references

Becker and Palsson

Related methods