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

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

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	P^a
g	Chr11	84429842	84432885	3044	DLG2*	-	13	2	97	84431338-9	N^b
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

ISSN: 1756-994X