Table 2 Transcription factor flexible models (TFFMs) in promoters of genes harboring UHP and DHP exons

From: Alternative splicing is coupled to gene expression in a subset of variably expressed genes

motif

model

Type 0

UHP

DHP

Type 0 vs. UHP

Type 0 vs. DHP

UHP vs. DHP

PRDM14

TFFM0987.1

41.5%

44.5%

44.2%

p < 1.0 × 10–6 *

p < 1.0 ×10–6 *

n.s.

SP1

TFFM0097.2

39.2%

37.9%

36.8%

n.s.

p < 1.0 ×10–6 *

n.s.

KLF4

TFFM0056.3

36.7%

38.0%

35.8%,

n.s.

n.s.

6.80 ×10–5 *

KLF4

TFFM0056.2

35.1%

35.3%

33.3%

n.s.

2.20 ×10–5 *

0.000394

ZNF75D

TFFM0647.1

34.4%

34.2%

32.3%

n.s.

p < 1.0 ×10–6 *

0.000751

KLF15

TFFM0515.1

34.1%

33.8%

32.0%

n.s.

p < 1.0 ×10–6 *

0.001070

ZBTB6

TFFM0624.1

32.7%

30.6%

30.2%

p < 1.0 × 10–6 *

p < 1.0 ×10–6 *

n.s.

FLI1

TFFM0031.1

31.6%

29.7%

31.9%

p < 1.0 × 10–6 *

n.s.

5.90 ×10–5 *

CTCF

TFFM0014.1

29.7%

31.6%

30.6%

p < 1.0 × 10–6 *

n.s.

n.s.

NEUROD1

TFFM0143.1

30.6%

28.4%

29.2%

p < 1.0 × 10–6 *

n.s.

n.s.

  1. TBFSs were assessed for overrepresentation in genes harboring UHP or DHP exons compared to genes only harboring one or more type 0 exon. 291 models showed a significant difference in permutation testing in which labels of exons (UHP, DHP, type 0) were randomly permuted and the p-value was calculated empirically as the proportion of permutations in which the observed difference between UHP (DHP) and type 0 exons was at least as extreme as the observed difference. The top ten are shown in this table and all results are presented in Supplementary Table 3. Of the significant models, the mean difference was 1.7% (UHP vs. type 0) and 1.1% (DHP vs. type 0). No significant differences were observed between UHP and DHP (not shown). *: significant at a Bonferroni-corrected threshold of 9.11 × 10–5.
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