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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.
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Genome Biology

ISSN: 1474-760X

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