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 |
- 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
-
aThis region corresponds to HPin8
-
bThis region corresponds to HPin7