Synergistic interactions - CLB2
motifs_filename=/data/kreiman/databh/spellman98etal/analysis/cooc/check/clb2.50.4.2.0.38.1000.0.0.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) = 50 [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/clb2.50.4.2.0.38.1000.0.0.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 = 74 [n_cooc]
number of modules after filter = 74 [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)
i	id1	id2	consensus m1	consensus m2	ml1	ml2	map1	map2	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	22.16	24.71	116	104	13	13	1.00E-17
2	70	140	aawdnkkmaaca	ynndhdnkknrandnrkmaaha	12	22	3.58	25.00	23.51	20.66	143	134	17	14	1.00E-17
3	50	140	ryaaacahw	ynndhdnkknrandnrkmaaha	9	22	nan	25.00	21.52	22.99	147	129	16	15	1.00E-17
4	50	138	ryaaacahw	ttdscnnwwnkkk	9	13	nan	0.15	35.08	38.02	62	52	11	10	6.20E-15
5	70	126	aawdnkkmaaca	cynnwhndkknaanwnnndam	12	21	3.58	7.66	29.29	27.88	81	78	12	11	1.60E-14
6	11	98	hndccywwwnnrkwmw	kknmaaandbmanhm	16	15	16.00	10.04	47.08	46.83	42	38	10	9	2.20E-14
7	11	140	hndccywwwnnrkwmw	ynndhdnkknrandnrkmaaha	16	22	16.00	25.00	40.8	31.78	63	56	13	9	1.70E-12
8	50	98	ryaaacahw	kknmaaandbmanhm	9	15	nan	10.04	17.85	17.13	144	127	13	11	7.10E-12
9	11	135	hndccywwwnnrkwmw	tthycnnramsk	16	12	16.00	1.60	62.91	65.91	22	18	7	6	4.00E-11
10	138	140	ttdscnnwwnkkk	ynndhdnkknrandnrkmaaha	13	22	0.15	25.00	38.02	32.19	52	43	10	7	5.70E-10
11	95	131	sanshnsrnnkntkncs	knhwhsknvanchwnknnd	17	19	0.42	1.05	131.81	123.57	9	8	6	5	6.30E-10
12	135	140	tthycnnramsk	ynndhdnkknrandnrkmaaha	12	22	1.60	25.00	123.57	123.57	8	8	5	5	6.30E-10
13	11	50	hndccywwwnnrkwmw	ryaaacahw	16	9	16.00	nan	15.57	16.33	127	109	10	9	1.20E-09
14	11	70	hndccywwwnnrkwmw	aawdnkkmaaca	16	12	16.00	3.58	27.27	27.14	58	51	8	7	2.30E-09
15	115	127	tkcndnkrcnnyhknnhm	kanrvnranrmnnrnk	18	16	0.24	6.75	61.79	61.79	16	16	5	5	3.10E-09
16	50	58	ryaaacahw	vaarrrrnaaa	9	11	nan	62.09	5.42	4.43	1095	803	30	18	4.00E-09
17	11	138	hndccywwwnnrkwmw	ttdscnnwwnkkk	16	13	16.00	0.15	10.49	8.24	396	288	21	12	4.70E-09
18	62	114	krwrkykaws	wnkrhnnwnwnnhnvncdwtkkdkr	10	25	8.65	1.44	49.43	58.15	20	17	5	5	4.70E-09
19	108	129	kkvnnnwnnrnnkwnkknnnnk	bnnnnndsnwknchmntkk	22	19	5.27	6.29	197.72	197.72	4	4	4	4	5.70E-09
20	74	142	tkcwnndbmaky	kvnknwnnnkvtknnknnnv	12	20	0.79	3.21	49.43	52.03	24	19	6	5	1.00E-08
21	63	106	rahhcnkarkrsa	knnknnnnnknwknnrmnrnws	13	22	8.01	6.32	158.18	158.18	5	5	4	4	1.40E-08
22	65	138	aaarknknmaww	ttdscnnwwnkkk	12	13	7.69	0.15	60.18	49.43	23	20	7	5	1.40E-08
23	58	70	vaarrrrnaaa	aawdnkkmaaca	11	12	62.09	3.58	6.58	6.56	481	392	16	13	1.50E-08
24	34	123	vskvmhnnbkkm	wnsnnnmvtkkdbkka	12	16	nan	0.54	131.81	131.81	6	6	4	4	2.80E-08
25	69	72	mtkcarnrkmnnm	mccramrdkknm	13	12	5.06	2.08	131.81	131.81	6	6	4	4	2.80E-08
26	69	99	mtkcarnrkmnnm	rmnkadksnkwwk	13	13	5.06	3.19	79.09	79.09	10	10	4	4	2.80E-08
27	50	72	ryaaacahw	mccramrdkknm	9	12	nan	2.08	29.45	27.59	47	43	7	6	3.20E-08
28	2	140	nndnrtcrybnhdnackdnnnh	ynndhdnkknrandnrkmaaha	22	22	22.00	25.00	42.98	42.98	23	23	5	5	3.50E-08
29	11	104	hndccywwwnnrkwmw	kaavaanrnnnhnwvna	16	17	16.00	1.02	16.28	18.45	85	75	7	7	4.40E-08
30	11	132	hndccywwwnnrkwmw	wdnnndnadnnnnaawnaaarnr	16	23	16.00	31.99	18.61	18.21	85	76	8	7	4.90E-08
31	70	138	aawdnkkmaaca	ttdscnnwwnkkk	12	13	3.58	0.15	35.31	25.79	56	46	10	6	5.00E-08
32	72	140	mccramrdkknm	ynndhdnkknrandnrkmaaha	12	22	2.08	25.00	123.57	112.98	8	7	5	4	5.30E-08
33	11	131	hndccywwwnnrkwmw	knhwhsknvanchwnknnd	16	19	16.00	1.05	112.98	112.98	7	7	4	4	5.30E-08
34	50	129	ryaaacahw	bnnnnndsnwknchmntkk	9	19	nan	6.29	79.09	71.9	15	11	6	4	5.30E-08
35	72	138	mccramrdkknm	ttdscnnwwnkkk	12	13	2.08	0.15	50.84	39.54	35	25	9	5	5.90E-08
36	3	114	vkaan	wnkrhnnwnwnnhnvncdwtkkdkr	5	25	5.00	1.44	21.97	23.73	54	50	6	6	8.80E-08
37	3	144	vkaan	kkbnntknbvdtnwtk	5	16	5.00	2.46	65.91	65.91	12	12	4	4	8.90E-08
38	83	121	kknykmhknnsahknt	tkntksyddkky	16	12	3.16	1.09	98.86	98.86	8	8	4	4	8.90E-08
39	11	58	hndccywwwnnrkwmw	vaarrrrnaaa	16	11	16.00	62.09	10.02	10.23	217	174	11	9	9.10E-08
40	3	112	vkaan	twnnnwnmsrnahknk	5	16	5.00	0.30	35.31	36.61	28	27	5	5	9.50E-08
41	3	138	vkaan	ttdscnnwwnkkk	5	13	5.00	0.15	13.54	12.65	146	125	10	8	9.70E-08
42	69	94	mtkcarnrkmnnm	krwkmybcmnhnk	13	13	5.06	0.45	60.84	60.84	13	13	4	4	1.40E-07
43	121	141	tkntksyddkky	bkakransnnnwnkr	12	15	1.09	4.19	60.84	60.84	13	13	4	4	1.40E-07
44	11	126	hndccywwwnnrkwmw	cynnwhndkknaanwnnndam	16	21	16.00	7.66	17.37	11.89	148	133	13	8	1.60E-07
45	98	104	kknmaaandbmanhm	kaavaanrnnnhnwvna	15	17	10.04	1.02	15.36	15.21	103	91	8	7	1.80E-07
46	75	99	cnnsarvkknrkm	rmnkadksnkwwk	13	13	0.68	3.19	52.72	56.49	15	14	4	4	2.20E-07
47	50	103	ryaaacahw	csndhndkkaaaym	9	14	nan	1.44	30.42	30.89	39	32	6	5	2.60E-07
48	103	138	csndhndkkaaaym	ttdscnnwwnkkk	14	13	1.44	0.15	19.59	14.27	111	97	11	7	2.90E-07
49	3	68	vkaan	kaakkdknyndw	5	12	5.00	5.67	26.72	29.96	37	33	5	5	3.10E-07
50	135	138	tthycnnramsk	ttdscnnwwnkkk	12	13	1.60	0.15	59.32	52.72	20	15	6	4	3.20E-07
51	98	132	kknmaaandbmanhm	wdnnndnadnnnnaawnaaarnr	15	23	10.04	31.99	16.21	13.98	122	99	10	7	3.40E-07
52	126	132	cynnwhndkknaanwnnndam	wdnnndnadnnnnaawnaaarnr	21	23	7.66	31.99	14.38	13.84	110	100	8	7	3.60E-07
53	2	70	nndnrtcrybnhdnackdnnnh	aawdnkkmaaca	22	12	22.00	3.58	19.49	17.45	71	68	7	6	6.40E-07
54	3	62	vkaan	krwrkykaws	5	10	5.00	8.65	13.29	12.36	119	112	8	7	8.10E-07
55	70	143	aawdnkkmaaca	yncydyhsraaanvk	12	15	3.58	2.80	43.94	43.94	18	18	4	4	8.20E-07
56	126	138	cynnwhndkknaanwnnndam	ttdscnnwwnkkk	21	13	7.66	0.15	49.43	43.94	20	18	5	4	8.20E-07
57	3	128	vkaan	knnrntkymdndkynnnnnhsnm	5	23	5.00	6.55	12.07	11.73	131	118	8	7	1.20E-06
58	2	126	nndnrtcrybnhdnackdnnnh	cynnwhndkknaanwnnndam	22	21	22.00	7.66	22.47	23.54	44	42	5	5	1.20E-06
59	58	143	vaarrrrnaaa	yncydyhsraaanvk	11	15	62.09	2.80	25.63	21.97	54	45	7	5	1.80E-06
60	3	140	vkaan	ynndhdnkknrandnrkmaaha	5	22	5.00	25.00	12.36	10.98	144	126	9	7	1.90E-06
61	79	92	snvannkkcnssnnmb	krtsccnnndksnr	16	14	0.27	3.17	35.95	35.95	22	22	4	4	2.20E-06
62	50	71	ryaaacahw	ytttkwndvakm	9	12	nan	3.21	34.39	35.95	23	22	4	4	2.20E-06
63	59	74	rnkkvtknhknwk	tkcwnndbmaky	13	12	11.13	0.79	30.42	35.95	26	22	4	4	2.20E-06
64	74	106	tkcwnndbmaky	knnknnnnnknwknnrmnrnws	12	22	0.79	6.32	38.27	34.39	31	23	6	4	2.70E-06
65	3	73	vkaan	abtkkcmrhnknns	5	14	5.00	1.09	20.45	19.38	58	51	6	5	3.50E-06
66	62	127	krwrkykaws	kanrvnranrmnnrnk	10	16	8.65	6.75	14.12	16.48	70	60	5	5	8.20E-06
67	75	78	cnnsarvkknrkm	tnynkytknakra	13	13	0.68	0.34	26.36	26.36	30	30	4	4	9.30E-06
68	58	65	vaarrrrnaaa	aaarknknmaww	11	12	62.09	7.69	6.18	7	288	226	9	8	9.90E-06
69	3	80	vkaan	wanhkknannnnsndaka	5	18	5.00	8.17	28.93	24.71	41	32	6	4	1.20E-05
70	3	131	vkaan	knhwhsknvanchwnknnd	5	19	5.00	1.05	35.49	24.71	39	32	7	4	1.20E-05
71	11	65	hndccywwwnnrkwmw	aaarknknmaww	16	12	16.00	7.69	32.95	24.71	36	32	6	4	1.20E-05
72	132	140	wdnnndnadnnnnaawnaaarnr	ynndhdnkknrandnrkmaaha	23	22	31.99	25.00	12.2	14.76	81	67	5	5	1.50E-05
73	99	100	rmnkadksnkwwk	knndndnnkrnnknnkndbnak	13	22	3.19	3.16	16.14	17.57	49	45	4	4	5.50E-05
74	24	67	yyaccck	cdkktadcsm	7	10	7.00	6.73	11.75	11.23	101	88	6	5	5.80E-05
i	id1	id2	consensus m1	consensus m2	ml1	ml2	map1	map2	r_oc_sp1	r_tr_sp1	n_cooc_all	n_cooc_tr_all	n_cooc_cl	n_cooc_tr_cl	p_binom
Questions? --> kreiman@mit.edu
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