Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers

BMC Genomics

Table 1 Frequency of KR motifs, compared to shuffled versions, in different test sets

Motif	CONDOR CNEs (from[57])	Human:Shark CNEs (from 13]	VISTA EB (all)[43]	VISTA EB set HB/BA/CN+ve (from[43])	VISTA EB set HB +ve (from[43])	Zebrafish CBset all[21]	Zebrafish CB set HB +ve (from[21])
TGATNNATKR	562	666	609	161	131	17	7
TGTANNATKR	171	188	388	65	52	12	3
GTATNNATKR	150	168	279	54	39	9	2
GTTANNATKR	150	178	325	79	65	8	2
TTGANNATKR	200	245	447	80	64	9	1
TTAGNNATKR	167	238	398	74	55	7	0
ATGTNNATKR	259	297	452	86	72	20	1
ATTGNNATKR	233	297	436	74	61	20	2
AGTTNNATKR	215	254	431	85	68	9	0
TAGTNNATKR	147	154	297	54	42	10	4
TATGNNATKR	176	198	365	74	60	10	3
GATTNNATKR	274	315	419	97	74	11	0
TGATNNTAKR	106	143	314	65	50	6	1
TGTANNTAKR	142	151	421	82	60	14	1
GTATNNTAKR	59	73	195	41	34	1	0
GTTANNTAKR	105	108	253	50	33	5	0
TTGANNTAKR	162	205	385	72	62	10	0
TTAGNNTAKR	73	97	235	41	31	0	0
ATGTNNTAKR	103	124	376	64	55	3	0
ATTGNNTAKR	136	158	305	57	42	6	1
AGTTNNTAKR	85	121	320	64	50	5	1
TAGTNNTAKR	66	69	198	37	27	1	0
TATGNNTAKR	84	94	345	80	62	5	1
GATTNNTAKR	144	177	292	58	42	2	0
mean	165.38	196.58	353.54	70.58	55.46	8.33	1.25
S.D	102.75	122.06	93.73	24.74	20.92	5.52	1.67
z-score for pbxhox	3.86	3.84	2.72	3.65	3.61	1.57	3.43
p-value	5.68E-05	6.16E-05	3.30E-03	1.00E-04	2.00E-04	N/S	3.00E-04

Enrichment analysis for Pbx-Hox KR motifs, relative to shuffled versions (retaining G+C content for each binding site), within different sets of CNEs. CNEs from the VISTA enhancer browser (EB) and zebrafish cneBrowser (CB) sets have also been grouped according to annotated expression in the hindbrain (HB), branchial arches (BA) or cranial nerves (CN). All sequences are human except the Zebrafish cneBrowser set. N/S = not significant

ISSN: 1471-2164