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

From: Ancient Pbx-Hox signatures define hundreds of vertebrate developmental enhancers

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
  1. 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