Summary of results for different parameters
program_name=summary_results
last_modified=07_05_2005
p=0.05, rm=1
species	threshold	mind	maxd	rm	cons	p	bonferroni	n 4way	n 2wstrand	n 2worder	n expression	ov 4w 2ws	ov 4w 2wo	ov 4w exp	ov 2ws exp	ov w2o exp
hs	low FN	-1	25	1	no	0.05	6.00E-06	809	806	74	0	725	70	0	0	0
hs	low FN	-1	50	1	no	0.05	5.90E-06	673	756	31	0	635	31	0	0	0
hs	low FN	-1	200	1	no	0.05	5.60E-06	338	443	8	0	329	7	0	0	0
hs	low FN	500	1000	1	no	0.05	5.50E-06	16	19	0	0	16	0	0	0	0
hs	low FP	-1	25	1	no	0.05	5.40E-06	107	124	7	77	92	7	1	2	0
hs	low FP	-1	50	1	no	0.05	5.40E-06	99	127	4	78	89	4	2	2	0
hs	low FP	-1	200	1	no	0.05	5.40E-06	74	105	2	82	69	2	1	1	0
hs	low FP	500	1000	1	no	0.05	5.40E-06	2	4	0	11	2	0	0	0	0
hs	very low FP	-1	25	1	no	0.05	0.00022	7	10	4	23	4	1	2	5	1
hs	very low FP	-1	50	1	no	0.05	0.00013	8	11	4	30	6	0	1	0	1
hs	very low FP	-1	200	1	no	0.05	2.70E-05	4	6	24	15	3	0	0	0	0
hs	very low FP	500	1000	1	no	0.05	1.30E-05	0	1	19	27	0	0	0	0	0
mm	low FN	-1	50	1	no	0.05	5.90E-06	764	788	68	27	686	65	0	1	0
mm	low FN	-1	200	1	no	0.05	5.60E-06	402	448	17	0	365	17	0	0	0
mm	low FN	500	1000	1	no	0.05	5.50E-06	17	19	1	0	16	1	0	0	0
mm	low FP	-1	25	1	no	0.05	5.40E-06	121	136	11	89	106	9	2	3	0
mm	low FP	-1	50	1	no	0.05	5.40E-06	103	124	6	99	96	6	1	1	0
mm	low FP	-1	200	1	no	0.05	5.40E-06	91	110	2	102	84	2	1	1	0
mm	low FP	500	1000	1	no	0.05	5.40E-06	1	3	0	34	1	0	0	0	0
mm	very low FP	-1	25	1	no	0.05	0.00023	6	13	3	17	4	0	0	0	0
mm	very low FP	-1	50	1	no	0.05	0.00013	3	8	1	2	2	0	0	0	0
mm	very low FP	-1	200	1	no	0.05	2.20E-05	4	6	22	18	4	0	0	0	1
mm	very low FP	500	1000	1	no	0.05	9.80E-06	1	1	25	31	0	1	0	0	0
hs	low FN	-1	25	1	yes	0.05	6.90E-06	567	610	54	41	509	50	2	3	0
hs	low FN	-1	50	1	yes	0.05	6.60E-06	488	540	26	37	458	26	2	3	0
hs	low FN	-1	200	1	yes	0.05	6.30E-06	219	283	4	58	213	4	0	1	0
hs	low FN	500	1000	1	yes	0.05	6.20E-06	14	15	0	77	14	0	0	0	0
hs	low FP	-1	25	1	yes	0.05	8.90E-06	33	39	9	73	30	1	1	0	0
hs	low FP	-1	50	1	yes	0.05	6.10E-06	31	34	3	92	25	0	0	0	0
hs	low FP	-1	200	1	yes	0.05	5.40E-06	17	22	0	105	15	0	0	0	0
hs	low FP	500	1000	1	yes	0.05	5.40E-06	0	0	0	38	0	0	0	0	0
hs	very low FP	-1	25	1	yes	0.05	0.005	0	1	0	0	0	0	0	0	0
hs	very low FP	-1	50	1	yes	0.05	0.0019	0	2	3	0	0	0	0	0	0
hs	very low FP	-1	200	1	yes	0.05	0.00046	0	3	1	4	0	0	0	0	0
hs	very low FP	500	1000	1	yes	0.05	0.0004	0	0	0	2	0	0	0	0	0
mm	low FN	-1	25	1	yes	0.05	6.80E-06	636	630	67	4	557	64	0	0	0
mm	low FN	-1	50	1	yes	0.05	6.60E-06	529	578	43	12	482	40	1	1	0
mm	low FN	-1	200	1	yes	0.05	6.30E-06	247	286	6	32	233	6	1	2	0
mm	low FN	500	1000	1	yes	0.05	6.10E-06	13	15	0	74	13	0	0	0	0
mm	low FP	-1	25	1	yes	0.05	9.40E-06	38	36	9	73	30	4	1	1	0
mm	low FP	-1	50	1	yes	0.05	6.20E-06	32	31	0	87	28	0	1	1	0
mm	low FP	-1	200	1	yes	0.05	5.40E-06	20	23	1	104	14	1	0	1	0
mm	low FP	500	1000	1	yes	0.05	5.40E-06	0	1	0	2	0	0	0	0	0
mm	very low FP	-1	25	1	yes	0.05	0.005	0	0	0	0	0	0	0	0	0
mm	very low FP	-1	50	1	yes	0.05	0.002	0	1	1	0	0	0	0	0	0
mm	very low FP	-1	200	1	yes	0.05	0.00045	0	0	1	0	0	0	0	0	0
mm	very low FP	500	1000	1	yes	0.05	0.00038	0	0	0	0	0	0	0	0	0
species	threshold	mind	maxd	rm	cons	p	bonferroni	n 4way
species = upstream sequences from this species were used (hs = Homo sapiens, mm = Mus Musculus)
threshold = threshold used for sequence scanning (low FN = low false negative regime, low FP = low false positive regime (p<10-4), very low FP = very low false positive regime (p<10-5)
maxd = maximum distance between motifs (for maxd=1000 bp, the minimum distance was 500 bp)
cons = whether sequences not conserved between hs and mm were masked (cons=yes) or not (cons=no)
bonferroni = bonferroni threshold p value
n 4way = number of PWM pairs that showed a significant deviation from a uniform distribution of order/orientation patterns