Table 7.

Combination rules for differentially expressed genes

Combinations
RNA	PROT or PH	Output
Significant/Insignificant	Significant	PROT or PH
Significant/Insignificant	Insignificant	Not taken
Significant	Not Detected	RNA
Insignificant	Not Detected	Not taken
Not Detected	Not Detected	Not taken

The genes at the downstream level are combined as follows: If the protein is significantly changed at the proteome or phosphoproteome levels, it is taken into account in the set of differentially expressed genes/proteins given as input in NetICS. If the protein is detected but not significantly changed at the proteome or phosphoproteome levels, it is not taken into account. If the protein or its phosphosites are not detected at all, then the change at the RNA level is taken into account.