Table 1.

Overview of the parameters for 3N and 4N

	External for 3N	External for 4N	Affects totalnumber ofproteins incomplexes	Description
L	Yes		Yes	Length of topList
T	Yes		Yes	Co-occurrence thresholdinfluencing param.
C	Yes	Yes	Yes	Cosinus-distance threshold
S	Yes	No	Yes	Jaccard coefficient threshold for building CCs
U		No	Yes	Jacc. coeff. threshold forbuilding NNNs
P		Yes	No	Jaccard coefficient threshold for joining CCs

External parameters are those that need to be adjusted by the user. The non-external parameters of 4N are set automatically by the algorithm.