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Table 4 Non-conserved pTRR density is higher in intergenic proximal regions than intergenic distal regions.

From: Asymmetrical distribution of non-conserved regulatory sequences at PHOX2B is reflected at the ENCODE loci and illuminates a possible genome-wide trend

  

pTRR Density

Gene Type

ENCODE Sub-region

Conserved pTRRs/Conserved bp

Non-conserved pTRRs/Non-conserved bp

Conserved pTRRS/Conserved Non-repeat bp

Non-conserved pTRRs/Non-conserved Non-repeat bp

All

5' UTR

1/457

1/1,456

1/410

1/931

All

3' UTR

1/5,625

1/24,829

1/5,460

1/18,610

All

Intergenic Proximal

1/1,185

1/14,460

1/1,094

1/7,005

All

Intergenic Distal

1/7,528

1/62,541

1/7,073

1/29,635

All

Intronic Proximal

1/1,463

1/18,930

1/1,356

1/10,801

All

Intronic Distal

1/4,259

1/51,055

1/4,026

1/28,231

Developmental

Intergenic Proximal

1/1,591

1/16,403

1/1,508

1/8,796

Developmental

Intergenic Distal

1/11,370

1/78,961

1/10,714

1/47,792

Non-developmental

Intergenic Proximal

1/867

1/8,287

1/821

1/3,619

Non-developmental

Intergenic Distal

1/6,160

1/44,074

1/5,776

1/18,446

Non-gene Desert

Intergenic Proximal

1/1,078

1/14,303

1/991

1/6,877

Gene Desert

Intergenic Proximal

N/A

1/22,824

N/A

1/13,830

Non-gene Desert

Intergenic Distal

1/5,307

1/43,650

1/4,954

1/19,047

Gene Desert

Intergenic Distal

1/17,151

1/312,847

1/16,254

1/151,566

  1. Density of putative transcriptional regulatory regions (pTRRS) identified by King et al. [26]. The ENCODE interval was partitioned into sub-regions. Gene type of all represents analysis of whole ENCODE region. Developmental genes represent regions flanking genes labeled with Gene Ontology term GO:0032502, while non-developmental genes were those that were not labeled with GO:0032502. Gene deserts were ENCODE intervals overlapping ≥500 kb regions without a Reference Sequence gene. Non-gene deserts were all sub-regions that did not overlap gene deserts. Density of pTRRs was calculated by dividing the total number of conserved or non-conserved base pairs in the ENCODE defined region by number of conserved or non-conserved pTRRs in the ENCODE defined region. N/A= not applicable due to lack of conserved pTRRs in gene desert intergenic proximal regions
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BMC Genomics

ISSN: 1471-2164

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