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Table 4 Differences in functional enrichments between EPA and promoters using Pathway Commons

From: Characteristics of functional enrichment and gene expression level of human putative transcriptional target genes

Cell type Term of functional annotation No. of TF EPA (Association rule 4) No. of TF Promoter P-value Experimental support
Monocytes IFN-gamma pathway 51 10 6.89 × 10−4 [12]
  IL3-mediated signaling events 46 11 4.69 × 10−3 [13]
  GMCSF-mediated signaling events 43 10 5.25 × 10−3 [14]
  PDGF receptor signaling network 43 8 1.34 × 10−2 [15]
  VEGF and VEGFR signaling network 44 9 2.10 × 10−3 [16]
CD4+ T cell Integrin family cell surface interactions 112 13 2.59 × 10−12 [17]
  IFN-gamma pathway 107 12 5.26 × 10−12 [18]
  LKB1 signaling events 107 11 1.96 × 10−12 [19]
  TCR signaling in naive CD4+ T cells 103 21 3.98 × 10−8 [20]
  IL3-mediated signaling events 100 8 9.54 × 10−13 [21]
CD20+ B cell Integrin family cell surface interactions 69 2 5.17 × 10−11 [22]
  IL5-mediated signaling events 64 0 2.21 × 10−11 [23]
  Insulin Pathway 63 0 3.15 × 10−11 [24]
  mTOR signaling pathway 63 0 3.15 × 10−11 [25]
  Sphingosine 1-phosphate (S1P) pathway 63 0 3.15 × 10−11 [26]
  1. Immune cell-related functional annotations were enriched more in ‘promoter and extended regions for enhancer-promoter association (EPA)’ than promoters. Five annotations are shown in each cell type. These functions are confirmed to be related to the cellular functions by reference journal papers. Chi-square tests were conducted using the total number of putative transcriptional target genes (Additional file 1: Figure S14)
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BMC Genomics

ISSN: 1471-2164

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