Synergistic interactions - dm_patterns
motifs_filename=/data/kreiman/databh/dm_patterns/analysis/cooc/check/dm_patterns2.50.4.2.0.38.5000.5000.5000.check-ensembl.out.txt
consensus_filename=/data/kreiman/databh/dm_patterns/analysis/dm_patterns2.dm.80.consensus.txt
transcripts_filename=/data/kreiman/databh/dm_patterns/dm_patterns2.txt
number of transcripts = 13 [n_transcripts_cl]
number of motifs = 271 [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/dm_patterns/upstream_sequences/dm_patterns2.dm.ensembl.lengths.txt and none
motifpos_filename = /data/kreiman/databh/dm_patterns/analysis/cooc/check/dm_patterns2.50.4.2.0.38.5000.5000.5000.check-ensembl.pos-cl.txt and none
seqs_filename = /data/kreiman/databh/dm_patterns/upstream_sequences/dm_patterns2.dm.ensembl.fasta and none
robustness_filename = /data/kreiman/databh/dm_patterns/analysis/cooc/check/compare_cooc_outputs.dm_patterns2.mul.2.txt
wm_filename = /data/kreiman/databh/dm_patterns/analysis/dm_patterns2.dm.80.matlab.txt
species = dm
max_n_motifs = 2
order constraint = false
number of modules = 44 [n_cooc]
number of modules after filter = 44 [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)
Summary of results
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	100	268	kckmrnnnaandyk	nnnyaaad	14	8	2.20732	8	75.84	66.4	83	79	6	5	5.80E-09
2	64	215	raaannrnvarar	ynncyckvkrnnannnk	13	17	8.72593	2.25513	163.93	144.71	32	29	5	4	8.00E-09
3	87	267	kbmmaaankkc	hdaakcbb	11	8	8.52225	8	119.9	119.9	35	35	4	4	1.90E-08
4	64	173	raaannrnvarar	knsnnmnnnskcrkvnr	13	17	8.72593	9.89915	13.33	12.93	787	649	10	8	2.50E-08
5	95	135	shynhtkkccka	rntykkccavnnks	12	14	6.2064	3.37689	27.48	18.22	420	403	11	7	2.60E-08
6	102	243	tnttknnndnwnaawaa	kkkrttty	17	8	35.9758	95.1165	43.35	48.13	121	109	5	5	3.20E-08
7	144	201	rvdhkmtkckaw	vnnbnnnvkcakckr	12	15	2.70818	14.5729	52.46	44.08	120	119	6	5	5.00E-08
8	72	205	rmaaanvkcnkmnm	ynkcdknkmbynkc	14	14	10.4987	8.69747	85.65	87.43	49	48	4	4	7.60E-08
9	35	177	dkccawaaam	tdnnmhhnammaaaa	10	15	44.4408	1.84039	22.48	23.23	280	271	6	6	8.20E-08
10	189	220	kkrnnnkbkknnnknkk	rmknncrvdarnck	17	14	2.08843	2.19853	112.41	80.7	56	52	6	4	1.10E-07
11	178	182	ssnnnnnknnknnsnnknkskc	kdkckrnnndnannnnnnknbnk	22	23	19.3435	3.26998	33.41	37.47	157	140	5	5	1.10E-07
12	35	212	dkccawaaam	vaaaahnnnnnnnnnnnnvnnnnaaa	10	26	44.4408	96.7282	9.77	10.57	966	794	9	8	1.20E-07
13	88	192	kckytkkvmr	ksckbykyhkbnknbnnnk	10	19	5.34337	8.39723	103.2	74.94	61	56	6	4	1.50E-07
14	264	264	aayccktt	aayccktt	8	8	114.762	114.762	45.06	32.79	326	160	14	5	2.30E-07
15	68	194	ttnnnnwnnnnwwwnaaaw	dnkcnkscnrncra	19	14	77.8171	3.83721	55.22	63.59	76	66	4	4	3.00E-07
16	180	258	vnaaannnnnnmamamd	rtaaaaar	17	8	98.7525	102.496	8.41	6.96	1747	1356	14	9	4.40E-07
17	113	268	aaarnndkraaa	nnnyaaad	12	8	0.542878	8	13.82	11.94	683	615	9	7	4.70E-07
18	156	201	kntcrywkcka	vnnbnnnvkcakckr	11	15	2.46783	14.5729	56.71	56.71	74	74	4	4	4.80E-07
19	146	233	cmaamaarmr	yakktakv	10	8	0.120609	124.29	26.9	27.9	195	188	5	5	5.10E-07
20	45	98	kkbkrkcvkc	skksnnkkkknrd	10	13	7.71919	1.48853	49.96	53.8	84	78	4	4	6.00E-07
21	199	208	srkcrrsnnnkvy	kskrknrrknkvk	13	13	6.37941	4.55535	31.93	24.4	230	215	7	5	1.00E-06
22	258	269	rtaaaaar	ntttttrnbnb	8	11	102.496	11	7.1	7.86	1182	1068	8	8	1.20E-06
23	233	264	yakktakv	aayccktt	8	8	124.29	114.762	90.79	42.82	104	98	9	4	1.50E-06
24	80	212	rnnhnkcnaaaama	vaaaahnnnnnnnnnnnnvnnnnaaa	14	26	20.0061	96.7282	10.78	7.56	1460	1110	15	8	1.60E-06
25	9	233	bvvhwaaran	yakktakv	10	8	I_HB_01	124.29	49.49	41.14	106	102	5	4	1.80E-06
26	95	122	shynhtkkccka	cdkscakbnks	12	11	6.2064	7.16415	20.25	21.24	259	247	5	5	2.00E-06
27	233	263	yakktakv	kmctrmct	8	8	124.29	85.2079	13.91	12.93	528	487	7	6	2.70E-06
28	10	87	mkaad	kbmmaaankkc	5	11	I_HSF_01	8.52225	13.58	12.82	618	491	8	6	2.80E-06
29	183	199	kssrknkssrnnk	srkcrrsnnnkvy	13	13	1.68525	6.37941	13.99	12.67	600	497	8	6	3.00E-06
30	170	188	wnnsakmkannnhk	aawthkcykb	14	10	6.50325	3.55742	34.68	35.56	121	118	4	4	3.30E-06
31	270	270	vamnkrrtbd	vamnkrrtbd	10	10	10	10	24.08	18.8	610	279	14	5	3.70E-06
32	247	261	yctstmkc	kcactcav	8	8	114.515	105.574	22.6	18.47	325	284	7	5	4.00E-06
33	113	231	aaarnndkraaa	tttttatk	12	8	0.542878	113.063	16.76	18.47	313	284	5	5	4.00E-06
34	44	88	crncrkcrrnrs	kckytkkvmr	12	10	9.94679	5.34337	44.02	33.31	143	126	6	4	4.30E-06
35	165	194	vnnkknknnnknknndnnksndnks	dnkcnkscnrncra	25	14	1.07912	3.83721	40.35	32.79	130	128	5	4	4.60E-06
36	233	270	yakktakv	vamnkrrtbd	8	10	124.29	10	54.15	28.74	155	146	8	4	7.80E-06
37	187	201	ckctkbkwdns	vnnbnnnvkcakckr	11	15	4.07677	14.5729	17.15	14.86	367	353	6	5	1.20E-05
38	212	241	vaaaahnnnnnnnnnnnnvnnnnaaa	ccmtttcs	26	8	96.7282	116.042	11.07	9.49	758	663	8	6	1.60E-05
39	50	181	wwnnnaannawwttnnnw	rnnkcnkmmrmnrc	18	14	74.5083	6.7106	14.4	13.73	437	382	6	5	1.70E-05
40	67	223	aaaawnwnnnnnwnwtnd	knsrnbrknrknkknndnnr	18	20	81.3547	15.6694	28.74	21.3	219	197	6	4	2.60E-05
41	110	201	yckckkckaw	vnnbnnnvkcakckr	10	15	2.62415	14.5729	22.42	18.73	234	224	5	4	4.30E-05
42	81	227	kynkscakcsm	kksnknbdnnnndnnnkckks	11	21	5.18876	16.9015	17.49	16.99	300	247	5	4	6.30E-05
43	121	173	atbkccksbk	knsnnmnnnskcrkvnr	10	17	7.23416	9.89915	13.94	15.6	301	269	4	4	8.90E-05
44	21	21	srkattad	srkattad	8	8	I_BCD_01	I_BCD_01	12.31	13.03	682	322	8	4	0.00018
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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