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Table 5 Fold change in pTRR density of intergenic versus 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

  Fold change of pTRR density between Intergenic Proximal and Intergenic Distal Sub-regions
Gene Type 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 6.35 4.33 6.47 4.23
Developmental 7.15 4.81 7.10 5.43
Non-developmental 7.10 5.32 7.04 5.10
Gene Desert N/A 13.71 N/A 10.96
Non-gene Desert 4.92 3.05 5.00 2.77
  1. 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. Fold change in gene density was calculated for each gene type by dividing the intergenic proximal pTRR density by the intergenic distal pTRR density (Table 4). The pTRR densities were calculated for conserved pTRRs divided by conserved bp, non-conserved pTRRs divided by non-conserved bp, conserved pTRRs divided by conserved non-repeat bp and non-conserved pTRRs divided by non-conserved non-repeat bp (Table 3). N/A = not applicable due to lack of conserved pTRRs in gene desert intergenic proximal regions.