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Table 3 Binding affinities of RELA-containing dimers for canonical and non-canonical sequences

From: Extensive characterization of NF-κB binding uncovers non-canonical motifs and advances the interpretation of genetic functional traits

   RELARELA RELAp50 RELAp52
   Binding affinity (z-score) Binding affinity (Kd) Binding affinity (z-score) Binding affinity (Kd) Binding affinity (z-score) Binding affinity (Kd)
11-mer sequence MATCH_score Microarray EMSA-Seq UV-laser footprint Microarray EMSA-Seq UV-laser footprint Microarray EMSA-Seq UV-laser footprint
AGGAAATTCCG 0.86 3.70 40.90 3.25 1.20 20.42 4.60 0.55 13.00 1.70
AGGGGGATCTG 0.49 Non-binding Non-binding Non-binding 2.39 23.10 10.50 1.76 18.35 2.00
AGGGGAAGTTA 0.43 NA 3.78 Non-binding NA 35.41 26.00 NA 27.50 20.00
CTGGGGATTTA 0.29 NA 10.84 Non-binding NA 24.17 16.00 NA 19.54 13.80
  1. Binding affinities were measured using microarrays, EMSA-Seq and UV laser footprinting. Canonical sequences have MATCH scores ≥ 0.75 whilst non-canonical sequences have MATCH scores < 0.75. Where a sequence was not present on the microarrays this has been indicated with 'NA'. Decreasing binding affinities correspond to decreasing z-scores for both microarrays and EMSA-Seq, but increasing Kd values in the case of measurements done with UV laser footprinting. All values were derived from three and two independent experiments for microarrays and UV laser footprinting, respectively. Values for EMSA-Seq were derived from datasets obtained from the pooling of three independent experiments per dimer.