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Table 2 Enrichment of functional elements in the patterns

From: ChARM: Discovery of combinatorial chromatin modification patterns in hepatitis B virus X-transformed mouse liver cancer using association rule mining

Functional elements Mouse genome (MG) BPa Ratio (MG)b Patterns (P:P0) BPc Ratio (P)d Odds (M)e Odds (P)f Odds ratio (P/MG)g
Mouse genomes 2,725,765,481   12,537,400     
Non-gene 1,687,863,859 0.619 5,268,326 0.420 1.626 0.725 0.446
Promoter 60,956,000 0.022 636,400 0.051 0.023 0.053 2.338
Genes 976,945,622 0.358 6,936,145 0.553 0.559 1.238 2.217
Introns 917,470,255 0.337 6,319,444 0.504 0.507 1.016 2.003
Exons 63,877,330 0.023 1,841,546 0.147 0.024 0.172 7.175
Coding Exons 34,016,873 0.012 1,424,442 0.114 0.013 0.128 10.143
5′-UTR 6,222,075 0.002 211,139 0.017 0.002 0.017 7.487
3′-UTR 24,574,772 0.009 389,841 0.031 0.009 0.032 3.527
  1. All of the 200 base pair intervals (62,687 intervals identified by a genome-wide scan) that met the conditions of the P155 pattern for promoters were mapped to the functional elements of the mouse genome
  2. a, bBase pairs of functional elements in the mouse genome and their ratio over the mouse genome
  3. c, dBase pairs of functional elements overlapping with the 200 base pair intervals in the pattern and their ratio over the pattern
  4. e, fOdds for each functional element in the mouse genome and Pattern 155, calculated by Eq. 1
  5. gOdds ratio for each functional element between the pattern and the mouse genome, representing functional element enrichment in the pattern in comparison to the mouse genome