Synergistic interactions - dm_patterns
motifs_filename=/data/kreiman/databh/dm_patterns/analysis/cooc/check/dm_patterns2.25.4.4.0.38.5000.5000.5000.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) = 25 [max_distance]
minimum distance factor = 0.50 [min_dist_factor]
interactions of 4 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_patterns2.25.4.4.0.38.5000.5000.5000.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.4.txt
wm_filename = /data/kreiman/databh/dm_patterns/analysis/dm_patterns2.dm.80.matlab.txt
species = dm
max_n_motifs = 4
order constraint = false
number of modules = 12 [n_cooc]
number of modules after filter = 12 [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	id3	id4	consensus m1	consensus m2	consensus m3	consensus m4	ml1	ml2	ml3	ml4	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	144	201	n	n	rvdhkmtkckaw	vnnbnnnvkcakckr	none	none	12	15	0	0	2.70818	14.5729	n	n	61.12	51.43	103	102	6	5	2.20E-08
2	95	135	n	n	shynhtkkccka	rntykkccavnnks	none	none	12	14	0	0	6.2064	3.37689	n	n	27.74	18.41	416	399	11	7	2.40E-08
3	233	264	n	n	yakktakv	aayccktt	none	none	8	8	0	0	124.29	114.762	n	n	97.6	97.6	43	43	4	4	4.70E-08
4	9	233	n	n	bvvhwaaran	yakktakv	none	none	10	8	0	0	I_HB_01	124.29	n	n	77.72	77.72	54	54	4	4	1.30E-07
5	41	241	n	n	vakhrarhkrk	ccmtttcs	none	none	11	8	0	0	22.0843	116.042	n	n	74.94	76.3	56	55	4	4	1.40E-07
6	80	212	n	n	rnnhnkcnaaaama	vaaaahnnnnnnnnnnnnvnnnnaaa	none	none	14	26	0	0	20.0061	96.7282	n	n	8.93	9.15	1057	917	9	8	3.70E-07
7	156	201	n	n	kntcrywkcka	vnnbnnnvkcakckr	none	none	11	15	0	0	2.46783	14.5729	n	n	58.29	58.29	72	72	4	4	4.30E-07
8	101	222	n	n	aawdwnhnnnnaawaaw	wrnkcnkvnaaar	none	none	17	13	0	0	37.1278	14.4391	n	n	23.42	25.1	224	209	5	5	8.70E-07
9	117	183	n	n	rncrdcrscaknns	kssrknkssrnnk	none	none	14	13	0	0	21.0061	1.68525	n	n	28.55	29.76	147	141	4	4	6.80E-06
10	187	201	n	n	ckctkbkwdns	vnnbnnnvkcakckr	none	none	11	15	0	0	4.07677	14.5729	n	n	18.35	15.8	343	332	6	5	8.70E-06
11	81	227	n	n	kynkscakcsm	kksnknbdnnnndnnnkckks	none	none	11	21	0	0	5.18876	16.9015	n	n	21.86	23.19	192	181	4	4	1.80E-05
12	110	201	n	n	yckckkckaw	vnnbnnnvkcakckr	none	none	10	15	0	0	2.62415	14.5729	n	n	23.31	19.08	225	220	5	4	4.00E-05
i	id1	id2	id3	id4	consensus m1	consensus m2	consensus m3	consensus m4	ml1	ml2	ml3	ml4	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
Questions? --> kreiman@mit.edu
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