Synergistic interactions - CLB2
i	id1	id2	consensus m1	consensus m2	ml1	ml2	map1	map2	map3	map4	r_oc_sp1	r_tr_sp1	n_cooc_all	n_cooc_tr_all	n_cooc_cl	n_cooc_tr_cl	p_binom
1	50	126	ryaaacahw	cynnwhndkknaanwnnndam	9	21	nan	7.66	n	n	38.27	38.9	62	61	12	12	1.00E-17
2	50	140	ryaaacahw	ynndhdnkknrandnrkmaaha	9	22	nan	25.00	n	n	24.71	26.23	104	98	13	13	1.00E-17
3	70	140	aawdnkkmaaca	ynndhdnkknrandnrkmaaha	12	22	3.58	25.00	n	n	22.99	21.97	129	126	15	14	1.00E-17
4	11	98	hndccywwwnnrkwmw	kknmaaandbmanhm	16	15	16.00	10.04	n	n	59.91	57.4	33	31	10	9	8.90E-16
5	70	126	aawdnkkmaaca	cynnwhndkknaanwnnndam	12	21	3.58	7.66	n	n	30.63	30.63	71	71	11	11	3.10E-15
6	50	98	ryaaacahw	kknmaaandbmanhm	9	15	nan	10.04	n	n	26.66	26.85	89	81	12	11	3.00E-14
7	11	140	hndccywwwnnrkwmw	ynndhdnkknrandnrkmaaha	16	22	16.00	25.00	n	n	42.98	39.54	46	45	10	9	1.50E-13
8	11	70	hndccywwwnnrkwmw	aawdnkkmaaca	16	12	16.00	3.58	n	n	43.25	47.73	32	29	7	7	1.90E-11
9	11	50	hndccywwwnnrkwmw	ryaaacahw	16	9	16.00	nan	n	n	28.25	29.29	56	54	8	8	7.00E-11
10	50	138	ryaaacahw	ttdscnnwwnkkk	9	13	nan	0.15	n	n	59.32	59.32	20	20	6	6	1.00E-10
11	50	58	ryaaacahw	vaarrrrnaaa	9	11	nan	62.09	n	n	7.2	6.48	577	488	21	16	1.70E-10
12	95	131	sanshnsrnnkntkncs	knhwhsknvanchwnknnd	17	19	0.42	1.05	n	n	123.57	123.57	8	8	5	5	6.30E-10
13	11	58	hndccywwwnnrkwmw	vaarrrrnaaa	16	11	16.00	62.09	n	n	20.06	20.06	69	69	7	7	2.40E-08
14	72	140	mccramrdkknm	ynndhdnkknrandnrkmaaha	12	22	2.08	25.00	n	n	131.81	131.81	6	6	4	4	2.80E-08
15	50	72	ryaaacahw	mccramrdkknm	9	12	nan	2.08	n	n	42.98	42.98	23	23	5	5	3.50E-08
16	72	138	mccramrdkknm	ttdscnnwwnkkk	12	13	2.08	0.15	n	n	47.73	41.19	29	24	7	5	4.60E-08
17	11	138	hndccywwwnnrkwmw	ttdscnnwwnkkk	16	13	16.00	0.15	n	n	8.86	7.66	357	284	16	11	5.30E-08
18	11	126	hndccywwwnnrkwmw	cynnwhndkknaanwnnndam	16	21	16.00	7.66	n	n	15.45	12.97	128	122	10	8	7.90E-08
19	58	70	vaarrrrnaaa	aawdnkkmaaca	11	12	62.09	3.58	n	n	8.85	8.31	268	238	12	10	1.10E-07
20	62	114	krwrkykaws	wnkrhnnwnwnnhnvncdwtkkdkr	10	25	8.65	1.44	n	n	52.72	60.84	15	13	4	4	1.40E-07
21	11	104	hndccywwwnnrkwmw	kaavaanrnnnhnwvna	16	17	16.00	1.02	n	n	31.89	32.95	31	30	5	5	1.80E-07
22	11	135	hndccywwwnnrkwmw	tthycnnramsk	16	12	16.00	1.60	n	n	56.49	56.49	14	14	4	4	2.20E-07
23	70	138	aawdnkkmaaca	ttdscnnwwnkkk	12	13	3.58	0.15	n	n	36.42	29.96	38	33	7	5	3.10E-07
24	3	138	vkaan	ttdscnnwwnkkk	5	13	5.00	0.15	n	n	18.54	19.13	64	62	6	6	3.60E-07
25	70	143	aawdnkkmaaca	yncydyhsraaanvk	12	15	3.58	2.80	n	n	49.43	49.43	16	16	4	4	4.50E-07
26	74	106	tkcwnndbmaky	knnknnnnnknwknnrmnrnws	12	22	0.79	6.32	n	n	52.03	49.43	19	16	5	4	4.50E-07
27	74	142	tkcwnndbmaky	kvnknwnnnkvtknnknnnv	12	20	0.79	3.21	n	n	43.94	46.52	18	17	4	4	6.10E-07
28	138	140	ttdscnnwwnkkk	ynndhdnkknrandnrkmaaha	13	22	0.15	25.00	n	n	26.96	25.35	44	39	6	5	8.00E-07
29	79	92	snvannkkcnssnnmb	krtsccnnndksnr	16	14	0.27	3.17	n	n	39.54	39.54	20	20	4	4	1.40E-06
30	62	127	krwrkykaws	kanrvnranrmnnrnk	10	16	8.65	6.75	n	n	19.38	21.49	51	46	5	5	2.00E-06
31	113	128	yarnkkcrwnwnc	knnrntkymdndkynnnnnhsnm	13	23	3.30	6.55	n	n	32.95	35.95	24	22	4	4	2.20E-06
32	3	80	vkaan	wanhkknannnnsndaka	5	18	5.00	8.17	n	n	31.64	34.39	25	23	4	4	2.70E-06
33	50	103	ryaaacahw	csndhndkkaaaym	9	14	nan	1.44	n	n	41.19	34.39	24	23	5	4	2.70E-06
34	103	138	csndhndkkaaaym	ttdscnnwwnkkk	14	13	1.44	0.15	n	n	17.45	12.76	102	93	9	6	4.50E-06
35	75	78	cnnsarvkknrkm	tnynkytknakra	13	13	0.68	0.34	n	n	29.29	29.29	27	27	4	4	5.80E-06
36	3	114	vkaan	wnkrhnnwnwnnhnvncdwtkkdkr	5	25	5.00	1.44	n	n	27.27	27.27	29	29	4	4	8.00E-06
37	58	143	vaarrrrnaaa	yncydyhsraaanvk	11	15	62.09	2.80	n	n	29.96	26.36	33	30	5	4	9.30E-06
38	99	100	rmnkadksnkwwk	knndndnnkrnnknnkndbnak	13	22	3.19	3.16	n	n	19.29	19.77	41	40	4	4	3.30E-05
39	24	67	yyaccck	cdkktadcsm	7	10	7.00	6.73	n	n	12.89	11.5	92	86	6	5	5.20E-05
40	58	138	vaarrrrnaaa	ttdscnnwwnkkk	11	13	62.09	0.15	n	n	25.63	16.14	54	49	7	4	7.80E-05
i	id1	id2	consensus m1	consensus m2	ml1	ml2	map1	map2	map3	map4	r_oc_sp1	r_tr_sp1	n_cooc_all	n_cooc_tr_all	n_cooc_cl	n_cooc_tr_cl	p_binom
PARAMETERS
motifs_filename=/data/kreiman/databh/spellman98etal/analysis/cooc/check/clb2.25.4.2.0.38.1000.0.0.check-sgd.out.txt
consensus_filename=/data/kreiman/databh/spellman98etal/analysis/clb2.sc.70.consensus.txt
transcripts_filename=/data/kreiman/databh/spellman98etal/clb2.list.txt
number of transcripts = 32 [n_transcripts_cl]
number of motifs = 147 [n_motifs_cl]
maximum distance (bp) = 25 [max_distance]
minimum distance factor = 0.50 [min_dist_factor]
interactions of 2 motifs [max_n_motifs]
scan threshold column = 38 [thresh_column]
seqlengths_filename = /data/kreiman/databh/spellman98etal/upstream_sequences/clb2.sc.sgd.lengths.txt and none
motifpos_filename = /data/kreiman/databh/spellman98etal/analysis/cooc/check/clb2.25.4.2.0.38.1000.0.0.check-sgd.pos-cl.txt and none
seqs_filename = /data/kreiman/databh/spellman98etal/upstream_sequences/clb2.sc.sgd.fasta and none
robustness_filename = /data/kreiman/databh/spellman98etal/analysis/cooc/check/compare_cooc_outputs.mul.2.txt
wm_filename = /data/kreiman/databh/spellman98etal/analysis/clb2.sc.70.matlab.txt
species = sc
max_n_motifs = 2
order constraint = false
number of modules = 40 [n_cooc]
number of modules after filter = 40 [n_cooc_actual]
Click on the motif ID numbers to get further information about the motifs.
Click on n_cooc_tr_cl (the number of transcripts with non-overlapping co-occurrences within the distance and order constraints) to see a list of the transcripts and positions
Click on p_binom_sp1 to see a plot of the occurrences of the motif cluster in each transcript (Figure legend)
Questions? --> kreiman@mit.edu
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