Table 2. Number of remained ceRNA pairs after each ceRNA interaction filtering step in Crinet.

Step	# of Pairs	# of Genes
ALL	212,994,480	20,640
Step1	16,082,000	20,640
Step2	247,885	11,910
Step3	209,220	11,726
Step4	52,858	7,263
Step5	17,443	4,494

ALL: All candidate pairs after keeping proper genes with effective regulation; Step1: pairs with a significant overlap for common miRNAs; Step2: pairs after filtered based on partial correlation between gene expressions excluding copy number aberration effect; Step3: pairs after filtered based on collective regulation; Step4: pairs after applying random sampling for Step2 and Step3; Step5: pairs after applying the network deconvolution method to exclude the spurious ceRNA pairs.