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

Table 2 Enrichment of functional elements in the patterns

Functional elements	Mouse genome (MG) BP^a	Ratio (MG)^b	Patterns (P:P0) BP^c	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

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
^{a, b}Base pairs of functional elements in the mouse genome and their ratio over the mouse genome
^{c, d}Base pairs of functional elements overlapping with the 200 base pair intervals in the pattern and their ratio over the pattern
^{e, f}Odds for each functional element in the mouse genome and Pattern 155, calculated by Eq. 1
^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

ISSN: 1471-2105