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Table 2 Frequency of KR motifs in CNEs at different gene loci

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

GENE # KR motifs in test set Length of CNE seq for locus (kb) #hits per kb # hits in control set (mean) standard deviation z-score p-value
ZNF503 36 27.781 1.30 3.18 1.76 18.62 0.00E+00
TSHZ3 30 23.323 1.29 3.09 1.77 15.23 0.00E+00
IRX5 27 37.059 0.73 5.39 2.33 9.29 0.00E+00
IRX2 21 23.981 0.88 3.10 1.80 9.95 0.00E+00
TSHZ1 16 10.351 1.55 1.63 1.32 10.93 0.00E+00
PBX3 16 17.886 0.89 1.89 1.35 10.44 0.00E+00
HOXD9 16 17.77 0.90 2.19 1.44 9.59 0.00E+00
NR2F2 16 18.99 0.84 2.52 1.59 8.49 0.00E+00
NR2F1 16 25.655 0.62 3.72 1.84 6.67 2.53E-11
MEIS2 16 24.553 0.65 3.42 1.91 6.59 4.49E-11
ZFHX1B 13 23.275 0.56 3.13 1.72 5.73 9.86E-09
SALL3 12 11.405 1.05 1.43 1.21 8.76 0.00E+00
FOXP1 12 15.857 0.76 1.73 1.24 8.25 2.22E-16
MAF 11 7.334 1.50 1.15 1.10 8.95 0.00E+00
NKX6-1 10 6.853 1.46 0.82 0.92 9.94 0.00E+00
  1. Details are shown for the 15 gene loci from the CONDOR CNE set with the highest number of Pbx-Hox KR motifs in their CNEs, showing enrichment relative to shuffled CNE sets (Methods and Additional File 6). For each gene locus, the number of Pbx-Hox KR motifs in the associated CNEs is given. The number of Pbx-Hox KR motifs per kb of CNE sequence for each locus (column 4) is calculated by dividing the number of Pbx-Hox KR motifs in the CNEs of that locus (column 2) by the total combined length of the CNEs in that locus (column 2). Control sets were generated by zero order Markov shuffling of CNEs at each locus in 1000 randomisations (Methods). Some gene loci also contain other genes besides the one after which they are named, for instance the IRX5 locus contains Irx3, Irx5 and Irx6.