TABLE IV.

The Six Most Important Categories for Each Task Ranked Using the RF Gini Variable Importance Criterion

Order	Co-complex	Importance	Direct interaction	Importance	Co-pathway	Importance
1	Gene expression	0.4217	Gene expression	0.1906	Gene expression	0.4766
2	GO process	0.2009	GO process	0.1709	GO process	0.1729
3	GO component	0.1365	GO component	0.1107	GO function	0.1297
4	GO function	0.1198	TAP MS	0.1035	GO component	0.0958
5	TAP MS	0.0731	GO function	0.0852	Mutant phenotype	0.0488
6	Protein class	0.0109	Mutant phenotype	0.0668	Gene fusion/gene cooccurrence	0.0207

Each ranked list contains the normalized Gini importance scores for the top six categories of the three prediction tasks (using the “Detailed” encoding type). The score for each feature category is the sum over the scores from all the members of the given feature group.