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Table 4 Intronic regions harboring putative novel promoters found deleted in NDD patients

From: Novel promoters and coding first exons in DLG2 linked to developmental disorders and intellectual disability

Entry Chr Start End Width Gene name Strand Number of cases Number of control CEGA score Splicing site Type
a Chr2 236577649 236583540 5892 AGAP1 + 2 1 31 236579701-2 P
b Chr3 114167766 114174803 7038 ZBTB20 - 2 0 832 114173425-6 P
c Chr5 14440397 14444098 3702 TRIO + 1 1 192 14441469-70 P
d Chr5 58722748 58727155 4408 PDE4D - 1 4 300 58726119-20 N
e Chr7 75266093 75269827 3735 HIP1 - 3 2 144 75268368-9 N
f Chr11 84147024 84149361 2338 DLG2* - 11 5 557 84148430-1 Pa
g Chr11 84429842 84432885 3044 DLG2* - 13 2 97 84431338-9 Nb
h Chr11 84843131 84844944 1814 DLG2 - 3 0 862 84843811-2 P
i Chr17 61227923 61231987 4065 TANC2 + 2 6 194 61228741-2 E
j Chr22 28832791 28840308 7518 TTC28 - 2 1 553 28838873-4 P
k Chr22 36355185 36358538 3354 RBFOX2 - 1 0 NA 36357610-1 P
  1. Each row details an intronic H3K4me3 peak region overlapping any smallest region of overlap (SRO) meeting the following criteria: deleted in at least one case individual and demonstrating the presence of both transcription factor binding sites and CAGE peaks, of a H3K4me3/H3K4me1 peak ratio greater than 1, and of at least one abrupt RNA-Seq delta coverage of 20. We provide the name of the gene the intron belongs to, the number of case and control patients (sum of DGV and GDD/ID) found in the cohorts, and the exact location of the splicing site. The asterisk next to the gene name represents a significant statistical enrichment after Bonferroni correction of NDD patients in such region with p < 0.05 (see “Results”; Additional file 2). “CEGA score” documents the conservation score across vertebrates as reported in the Conserved Elements from Genomics Alignments database [63]. The “Type” column reports whether such a region is predicted as promoter (P) or exon (E) by Ensembl (archive 75, Feb 2014) or as novel (N). Coordinates are in hg19
  2. aThis region corresponds to HPin8
  3. bThis region corresponds to HPin7