Determining significance of pairwise co-occurrences of events in bursty sequences

BMC Bioinformatics

Table 5 Significant pairs in chromosome data

chr	TF 1	TF 2	# TF 1	# TF 2	C	num	FL	ref
1	MA0042, FOXI1	MA0045, HMG-IY	1656	3958	550	10	Y
1	MA0041, Foxd3	MA0045, HMG-IY	1643	3958	547	10	Y
9	MA0045, HMG-IY	MA0119, TLX1-NFIC	3771	985	458	7	Y
2	MA0073, RREB1	MA0079, SP1	1968	447	317	6	Y	[16]
1	MA0045, HMG-IY	MA0088, Staf	3958	583	180	4	Y
9	MA0045, HMG-IY	MA0137, STAT1	3771	642	173	3	Y
4	MA0045, HMG-IY	MA0079, SP1	2661	744	170	2	Y	[17]
9	MA0042, FOXI1	MA0119, TLX1-NFIC	1439	985	170	4	Y
6	MA0045, HMG-IY	MA0082, SQUA	4029	579	164	2	N
9	MA0003, TFAP2A	MA0073, RREB1	856	1756	131	4	Y	[18]
1	MA0029, Evi1	MA0045, HMG-IY	856	1756	131	4	Y
4	MA0045, HMG-IY	MA0112, ESR1	465	3958	129	2	Y	[19]
9	MA0041, Foxd3	MA0119, TLX1-NFIC	2661	605	121	1	N
9	MA0022, dl_1	MA0045, HMG-IY	1162	985	118	4	Y
1	MA0045, HMG-IY	MA0049, hb	365	3771	110	4	Y
9	MA0003, TFAP2A	MA0123, ABI4	3958	387	110	1	N
4	MA0073, RREB1	MA0123, ABI4	856	355	107	10	Y
4	MA0045, HMG-IY	MA0048, NHLH1	1971	303	103	4	Y
4	MA0079, SP1	MA0119, TLX1-NFIC	744	1013	102	1	Y
6	MA0073, RREB1	MA0138, REST	1868	615	100	1	Y

The significant pairs (p ≤ 0.001) in chromosome data with the highest C scores. The parameters used are w = 300 bp, minimum distance d = 20 bp, and significance is determined according to the FL(r) null model for the C score. There are in total 241 unique significant pairs in chromosomes 1–10 with these parameters. The chromosome where the C score is highest, and the total number of times that each TF occurs in the corresponding chromosome are given, as well as the C score. The following two columns state the number of chromosomes (1–10) in which the pair is significant, and if the pair is significant according to the FL null model. The last column gives a reference when one exists. Additional file 2 contains the full names of the factors.

ISSN: 1471-2105