Cell-composition effects in the analysis of DNA methylation array data: a mathematical perspective

BMC Bioinformatics

Table 2 Gene sets analyzed

Abbrev	Description or KEGG pathway		Total # of CpGs
Abbrev	Description or KEGG pathway		27K (all)	27K (auto)	450K (pass)
	Total CpGs included in analyses		27578	26,486	319,264
DMR	500 previously published leukocyte DMRs [27K] [18] or overlap with 600 previously published leukocyte DMRs [450K] [46]		500	500	417
PcG	Polycomb targets compiled from four sources [48-51]		3614	3523	41,942
Apoptosis	04210	Apoptosis	157	149	1126
Bcell	04662	B cell receptor signaling pathway	138	136	1168
CardiacM	04260	Cardiac muscle contraction	121	116	967
CellCycle	04110	Cell cycle	250	245	2028
CyCy	04060	Cytokine-cytokine receptor interaction	437	426	2088
DorsoV	04320	Dorso-ventral axis formation	38	38	565
ErbB	04012	ErbB signaling pathway	154	148	1470
Hemato	04640	Hematopoietic cell lineage	153	152	779
HepC	05160	Hepatitis C	209	205	1536
Hhog	04340	Hedgehog signaling pathway	92	90	1090
JakStat	04630	Jak-STAT signaling pathway	254	250	1579
MAPK	04010	MAPK signaling pathway	469	457	4535
mTOR	04150	mTOR signaling pathway	92	88	1117
NK	04650	Natural killer cell mediated cytotoxicity	219	215	1530
Notch	04330	Notch signaling pathway	67	67	1097
p53	04115	p53 signaling pathway	144	142	1034
Tcell	04660	T cell receptor signaling pathway	191	187	1568
TGF	04350	TGF-beta signaling pathway	154	154	1314
VascSm	04270	Vascular smooth muscle contraction	193	189	1903
VEGF	04370	VEGF signaling pathway	131	131	1104

ISSN: 1471-2105