Table 2.

Summary of the results for human liver expression data

	TM-1	TM-2	TM-3,4,5
TREMOR	• 17 TM-1s detected—HNF-1, HNF-3alpha, STAT5A, GFI1B, IRF1, MEIS1A, AIRE, NF-AT, Pbx1b, HNF-4alpha1, POU3F2, NF-Y, MEF-2, AFP1, SRF, C/EBP, TCF-4.	• 31 TM-2s detected (however, not significant after multiple testing correction)	• 217, 224 and 266 TM-3s, TM-4s and TM-5s
	• Well-known liver TFs HNF1-3,4 and C/EBP are included among these.	• 1 involved HNF-3 and 25 involved HNF-1.	• 185, 222 and 266 involved HNF.
	• 8 of the remaining 11 TFs have evidence of involvement in transcription in liver—STAT5 (44), GFI1b (45), IRF (46), Pbx1 (47), NF-Y (48), AFP1 (49), SRF (50) and Tcf-4 (51).	• Rank-1 TM-2 was (HNF-1 TATA). These TFs are known to interact (52).
		• TM-2s at rank 2, (HNF-1 HNF-4), and at rank 4, (HNF-1 NF-Y) are supported (53).
OPOSSUM2	TM-2	TM-3
	• 3 TM-2s detected	• 31 TM-3s detected TMs, but none of them include FORKHEAD TFs, while 188 of 234 TREMOR TM-3s include FORKHEAD factors.
	• These combine zinc finger TF X2H2 with FoxA2, FoxD3 and FoxI1.
	• TREMOR detects many more TMs but 81 of the 226 include FORKHEAD factors.
CREME	Even at the least stringent settings, namely, using the lowest matrix score threshold = 0.8 and the largest module length = 500 bp, as well as requiring only two TFs in the TM, CREME did not yield any TMs.

For oPOSSUM2 and CREME, the results are compared to TREMOR. Unless otherwise specified, for TREMOR we only mention the TMs whose P-values were lower than the lowest P-value for the corresponding randomly permuted set (see text).