Results of Amadeus with the binned enrichment score on the
compendium of metazoan TF and miRNA target sets

• Same as in the metazoan compendium benchmark.
• Listed here are the results of Amadeus using the binned enrichment score instead of the hypergeometric enrichment score. The binned score takes into account biases in the length and/or C+G content of the target-set sequences (w.r.t. the background sequences). We used the default setting of 3 length and 3 GC-content divisions (i.e., a total of 9 length x GC-content bins).

Benchmark	Organism	Target-set size	Promoter length	Correct motif	Program	Success	Time	Top 4 motifs (2 for length 8 and 2 for length 10)
CREB_Zhang	Human	2338	1201	M00039, M00113, M00177, M00178, M00916, M00917 (Transfac)	Amadeus	Yes	723		CREB[M00178] 0.1694 CREB[M00916] 0.1742 CREB[M00177] 0.1749 CREB[M00917] 0.1927 CREB[M00039] 0.2005 CREB[M00113] 0.2097		CREB[M00039] 0.0875 CREB[M00917] 0.1057 CREB[M00178] 0.1255 CREB[M00916] 0.1296 CREB[M00113] 0.1461 CREB[M00177] 0.1606
E2F4_Cam	Human	201	1201	M00050, M00516, M00919, M00920, M00938, M00940, M01114 (Transfac)	Amadeus	Yes	654	E2F[M01114] 0.1114 E2F-1[M00940] 0.1423 E2F[M00516] 0.1824 E2F[M00050] 0.1833 E2F-1[M00938] 0.1902 E2F[M00919] 0.1916 E2F[M00920] 0.1952	E2F[M00050] 0.2262	E2F[M00920] 0.1841 E2F-1[M00938] 0.191 E2F-1[M00940] 0.2119 E2F[M00516] 0.2194 E2F[M00050] 0.2213
E2F_Ren	Human	79	1201	M00050, M00516, M00919, M00920, M00938, M00940, M01114 (Transfac)	Amadeus	Yes	618	E2F[M00050] 0.1104 E2F[M00516] 0.1147 E2F-1[M00940] 0.118 E2F[M00919] 0.1386 E2F[M00920] 0.141 E2F[M01114] 0.1682 E2F-1[M00938] 0.1764		E2F[M00050] 0.084 E2F[M00516] 0.1215 E2F-1[M00940] 0.1245 E2F[M00920] 0.1314 E2F[M00919] 0.1401 E2F-1[M00938] 0.1593 E2F[M01114] 0.1806
ERa_Kwon	Human	496	1201	M00191, M00511, M00959 (Transfac)	Amadeus	No	552
ETS1_Hollenhorst	Human	1192	1201	M00032, M00074, M00339, M00743, M00771, M00971, M01078 (Transfac)	Amadeus	Yes	608	c-Ets-1[M01078] 0.1228 c-Ets-1(p54)[M00032] 0.151 ETS[M00771] 0.158 Ets[M00971] 0.1715 c-Ets-1[M00743] 0.1796 c-Ets-1(p54)[M00074] 0.195 c-Ets-1[M00339] 0.1961		c-Ets-1[M01078] 0.164 c-Ets-1(p54)[M00032] 0.1719 c-Ets-1[M00743] 0.197 ETS[M00771] 0.2105 c-Ets-1(p54)[M00074] 0.2155 c-Ets-1[M00339] 0.2201 Ets[M00971] 0.225
Foxp3_Marson	Mouse	1060	1201	M00992 (Transfac)	Amadeus	No	807
GATA_Pauli	Elegans	1342	1201	M00075, M00076, M00077, M00126, M00127, M00128, M00203, M00346, M00347, M00348, M00349, M00350, M00351, M00462, M00632, M00789 (Transfac)	Amadeus	Yes	573	GATA-2[M00348] 0.156 GATA-1[M00346] 0.1729 GATA-1[M00347] 0.1857 GATA-X[M00203] 0.1977 GATA-1[M00128] 0.2104 [M00789] 0.2131 GATA-3[M00350] 0.2136		GATA-X[M00203] 0.1718 GATA-2[M00348] 0.1794 [M00789] 0.1868 GATA-1[M00347] 0.193 GATA-1[M00346] 0.2158 GATA-3[M00350] 0.2396
HCC-G1S_Whitfield	Human	266	1201	M00050, M00516, M00919, M00920, M00938, M00940, M01114 (Transfac)	Amadeus	Yes	688	E2F[M01114] 0.1063 E2F[M00050] 0.1235 E2F[M00516] 0.177 E2F-1[M00940] 0.1816 E2F[M00919] 0.1969 E2F[M00920] 0.2114 E2F-1[M00938] 0.2302		E2F[M00050] 0.078 E2F[M00516] 0.1215 E2F[M00919] 0.1428 E2F[M00920] 0.1498 E2F-1[M00940] 0.1774 E2F-1[M00938] 0.1809 E2F[M01114] 0.2094	E2F[M00919] 0.2315
HCC-G2M_Whitfield	Human	344	1201	M00185, M00287, M00775 (Transfac)	Amadeus	Yes	675				NF-Y[M00775] 0.1118 NF-Y[M00287] 0.1262 NF-Y[M00185] 0.1839
HNF1a_Odom	Human	206	1201	M00132, M00206, M00790, M01011 (Transfac)	Amadeus	Yes	619			HNF-1[M00132] 0.1101 HNF1[M01011] 0.1511 HNF-1[M00790] 0.159 HNF-1[M00206] 0.1997
HNF4a_Odom	Human	1475	1201	M00134, M00411, M00638, M00764, M01031 (Transfac)	Amadeus	No	710
HNF6_Odom	Human	212	1201	M00639 (Transfac)	Amadeus	Yes	579				HNF-6[M00639] 0.1474
HSF1_Page	Human	328	1201	M00146, M01023 (Transfac)	Amadeus	Yes	627	HSF1[M01023] 0.202 HSF1[M00146] 0.2104
HSF_Machin	Fly	183	1201	M00163, M00164, M00165, M00166 (Transfac)	Amadeus	Yes	480				HSF[M00166] 0.1893 HSF[M00165] 0.1893
ImmuneResponse_GO_Hs	Human	586	1201	M00062, M00063, M00258, M00453, M00747, M00772, M00972, M00052, M00053, M00194, M00774 (Transfac)	Amadeus	Yes	739	NF-kappaB[M00052] 0.1964 c-Rel[M00053] 0.2328		IRF1[M00747] 0.2021 NF-kappaB[M00052] 0.2318
ImmuneResponse_GO_Mm	Mouse	329	1201	M00062, M00063, M00258, M00453, M00747, M00772, M00972, M00052, M00053, M00194, M00774 (Transfac)	Amadeus	Yes	701			IRF1[M00747] 0.123 IRF[M00972] 0.1391 IRF[M00772] 0.1433 IRF-2[M00063] 0.163 IRF-1[M00062] 0.1657 ISRE[M00258] 0.1804 NF-kappaB[M00052] 0.2359	NF-kappaB[M00052] 0.1432 c-Rel[M00053] 0.1538 NF-kappaB[M00774] 0.2242 NF-kappaB[M00194] 0.2247
MEF2_Blais	Mouse	25	1201	M00006, M00231, M00232, M00233, M00405, M00406, M00941 (Transfac)	Amadeus	Yes	602	MEF-2[M00941] 0.2294	MEF-2[M00232] 0.1646 MEF-2[M00231] 0.1754 MEF-2[M00233] 0.1978		MEF-2[M00941] 0.2332
MEF2_Sandmann	Fly	208	1201	M00006, M00231, M00232, M00233, M00405, M00406, M00941 (Transfac)	Amadeus	No	526
MSL1_Legube	Fly	116	1201	M00488 (Transfac)	Amadeus	Yes	476			DREF[M00488] 0.2367
Myc_Oryan	Fly	714	1201	M00118, M00119, M00123, M00322, M00615, M00799, M01034 (Transfac)	Amadeus	Yes	576		Myc[M00799] 0.2148 c-Myc:Max[M00123] 0.2261		Myc[M00799] 0.1414
MyoD_Blais	Mouse	102	1201	M00001, M00184, M00929 (Transfac)	Amadeus	Yes	641	MyoD[M00001] 0.1928 MyoD[M00184] 0.1998 MyoD[M00929] 0.2103		MyoD[M00184] 0.167 MyoD[M00001] 0.1901 MyoD[M00929] 0.1925
MyoD_Cao	Mouse	102	1201	M00001, M00184, M00929 (Transfac)	Amadeus	Yes	636	MyoD[M00929] 0.1882 MyoD[M00184] 0.1883 MyoD[M00001] 0.1964		MyoD[M00184] 0.1509 MyoD[M00929] 0.2237 MyoD[M00001] 0.2295
MyoG_Cao	Mouse	78	1201	M00712 (Transfac)	Amadeus	Yes	616	myogenin[M00712] 0.1538		myogenin[M00712] 0.1056
Myogenin_Blais	Mouse	106	1201	M00712 (Transfac)	Amadeus	Yes	627	myogenin[M00712] 0.1375		myogenin[M00712] 0.1179
NFkB_Schreiber	Human	270	1201	M00052, M00053, M00194, M00774 (Transfac)	Amadeus	Yes	623	NF-kappaB[M00052] 0.1013 c-Rel[M00053] 0.1644 NF-kappaB[M00774] 0.1696 NF-kappaB[M00194] 0.2206		c-Rel[M00053] 0.096 NF-kappaB[M00052] 0.1099 NF-kappaB[M00774] 0.1833 NF-kappaB[M00194] 0.2057
Nanog_Boyer	Human	714	1201	M01123 (Transfac)	Amadeus	No	685
Nrf1_Cam	Human	674	1201	M00652 (Transfac)	Amadeus	Yes	567	Nrf-1[M00652] 0.0833		Nrf-1[M00652] 0.0918
Oct4_Boyer	Human	241	1201	M00795, M01124, M01125 (Transfac)	Amadeus	No	655
SRF_Myers	Human	172	1201	M00152, M00186, M00810, M00922, M01007 (Transfac)	Amadeus	Yes	616	SRF[M01007] 0.2018 SRF[M00810] 0.2163 SRF[M00152] 0.2193 SRF[M00922] 0.2273		SRF[M01007] 0.1238 SRF[M00810] 0.1254 SRF[M00186] 0.142 SRF[M00152] 0.1444 SRF[M00922] 0.1458
Sox2_Boyer	Human	575	1201	M01014, M01125 (Transfac)	Amadeus	No	693
YY1_Ren	Human	713	1201	M00059, M00069, M00793, M01035, jMA0095 (Transfac)	Amadeus	Yes	558	YY1[jMA0095] 0.1122 YY1[M00069] 0.1466 YY1[M01035] 0.1888		YY1[M00793] 0.1028 YY1[jMA0095] 0.1425 YY1[M01035] 0.1596 YY1[M00069] 0.1638
let7_Brueckner	Human	177	10001	MIMAT0000062 (miRBase)	Amadeus	No	676
let7_Johnson	Human	182	10001	MIMAT0000062 (miRBase)	Amadeus	Yes	697	hsa-let-7a[MIMAT0000062] 0.0582		hsa-let-7a[MIMAT0000062] 0.1227
miR106b_Linsley	Human	88	10001	MIMAT0000680 (miRBase)	Amadeus	Yes	649	hsa-miR-106b[MIMAT0000680] 0.1166		hsa-miR-106b[MIMAT0000680] 0.0361
miR124_Lim	Human	116	10001	MIMAT0000422 (miRBase)	Amadeus	Yes	646	hsa-miR-124a[MIMAT0000422] 0.0333		hsa-miR-124a[MIMAT0000422] 0.1484
miR155_Rodriguez	Mouse	95	10001	MIMAT0000165 (miRBase)	Amadeus	Yes	551	mmu-miR-155[MIMAT0000165] 0.0748		mmu-miR-155[MIMAT0000165] 0.1015
miR16_Linsley	Human	90	10001	MIMAT0000069 (miRBase)	Amadeus	Yes	627	hsa-miR-16[MIMAT0000069] 0.0983		hsa-miR-16[MIMAT0000069] 0.1289
miR1_Lim	Human	65	10001	MIMAT0000416 (miRBase)	Amadeus	Yes	619	hsa-miR-1[MIMAT0000416] 0.1293		hsa-miR-1[MIMAT0000416] 0.1173
miR34_Chang	Human	89	10001	MIMAT0000255, MIMAT0000685, MIMAT0000686 (miRBase)	Amadeus	No	609
miR34_Lin	Human	367	10001	MIMAT0000255, MIMAT0000685, MIMAT0000686 (miRBase)	Amadeus	Yes	662	hsa-miR-34a[MIMAT0000255] 0.1244 hsa-miR-34c[MIMAT0000686] 0.1355 hsa-miR-34b[MIMAT0000685] 0.202	hsa-miR-34c[MIMAT0000686] 0.2058 hsa-miR-34a[MIMAT0000255] 0.2058	hsa-miR-34c[MIMAT0000686] 0.1334 hsa-miR-34b[MIMAT0000685] 0.1348 hsa-miR-34a[MIMAT0000255] 0.1435
miR373_Lim	Human	43	10001	MIMAT0000726 (miRBase)	Amadeus	Yes	634	hsa-miR-373[MIMAT0000726] 0.0		hsa-miR-373[MIMAT0000726] 0.0166
p53_Kannan	Human	38	1201	M00034, M00272, M00761 (Transfac)	Amadeus	No	587