Functional constraint and small insertions and deletions in the ENCODE regions of the human genome

Table 5 Comparison of ENCODE and Bhangale et al. (ten ENCODE regions) indel data

	ENCODE (44 ENCODE regions/Baylor)				Bhangale et al. (ten ENCODE regions/Baylor)
	Indels		Rate (per 100 kb)		Indels		Rate (per 100 kb)
	n	bp	n	bp	n	bp	n	bp
Manual	2,186	6,504	14.6	43.4	362	1,122	13.0	40.4
Random	2,300	6,506	15.3	43.4	502	1,350	14.3	38.6
Overall	4,486	13,010	15.0	43.4	864	2,472	13.8	39.4
RNA transcription
CDS	5	5	0.7	0.7	1	1	1.2	1.2
TSS	2	2	3.3	3.3	0	0	0.0	0.0
RACEfrags	9	28	2.1	6.6	0	0	0.0	0.0
TARs/transfrags	37	78	5.8	12.3	6	11	7.5	13.7
Pseudo-exons	9	26	6.6	19.1	2	10	9.7	48.7
3' UTR	48	103	11.0	23.6	11	29	18.7	49.2
5' UTR	7	32	6.0	27.4	4	8	37.3	74.6
TUF	53	160	12.2	36.9	4	18	8.1	36.4
Open chromatin
FAIRE sites	106	327	7.7	23.8	17	72	5.6	23.6
DHS (NHGRI)	19	61	6.1	19.7	1	1	2.8	2.8
DHS (Regulome)	43	135	8.6	27.0	15	40	8.5	22.6
DNA-protein intreraction/transcript Regulation
HisPolTAF	141	348	13.1	32.4	32	114	12.8	45.5
Seq_specific (all motifs)	131	420	11.2	35.8	28	122	33.4	145.3
SeqSp (sequence specific factors)	54	225	10.2	42.5	9	45	5.1	25.6
Ancestral repeats	532	1,592	7.9	26.5	110	280	8.7	22.1
Evolutionary constraint
MCS strict	19	31	2.5	4.1	5	9	3.3	5.9
MCS moderate	78	170	5.1	11.2	17	36	5.4	11.4
MCS loose	356	960	9.8	26.4	63	136	8.4	18.1
Cell cycle
EarlyRepSeg	1,124	2,989	16.4	43.5	161	495	16.4	50.4
MidRepSeg	1,190	3,352	15.4	43.2	270	797	16.4	48.3
LateRepSeg	1,110	3,345	13.9	41.9	300	819	11.3	31.0

Both datasets (Encyclopedia of DNA Elements [ENCODE] and that reported by Bhangale and coworkers [19]) are based on a subset of 8 African Americans (the Baylor samples). bp, base pairs; CDS, coding sequence; CI, confidence interval; DHS, DNAse hypersensitive sites; ENCODE, Encyclopedia of DNA Elements; FAIRE, formaldehyde assisted isolation of regulatory elements; kb, kilobases; MCS, multi-species conserved sequence; NHGRI, National Human Genome Research Institute; transfrag, transcribed fragment; RACEfrag, rapid amplification of cDNA ends fragment; SNP, single nucleotide polymorphism; TAR, transcriptionally active region; TSS, transcription start site; TUF, transcripts of unknown function; UTR, untranslated region.

ISSN: 1474-760X