Table 6.

Top hypo-methylated (5 of 43) and hyper-methylated (5 of 41) individual cytosines associated with gene bodies (exons/introns)

Gene ID	Control %	Patient %	Difference	P value	Q value
MEGF6	55	17	− 38	1.12 × 10–11	4.63 × 10–9
CD6	41	3	− 38	1.90 × 10–16	1.02 × 10–13
KIF1A	50	14	− 36	1.83 × 10–10	7.16 × 10–8
MEGF11	84	52	− 32	6.09 × 10–12	2.54 × 10–9
TMCO3	94	61	− 33	3.28 × 10–9	1.20 × 10–6
LINC00664	53	95	+ 42	2.95 × 10–15	1.50 × 10–12
LOC642423	43	84	+ 41	2.60 × 10–14	1.24 × 10–11
KCNK10	54	93	+ 39	2.92 × 10–17	1.60 × 10–14
IDUA	59	95	+ 36	1.21 × 10–13	5.58 × 10–11
FAM182B	0	34	+ 34	8.99 × 10–16	4.71 × 10–13

Gene-associated cytosine significance values were calculated using a Fisher’s test. For each cytosine, there is also corresponding genomic location, the average methylation percentages for the control subjects and ME/CFS patients, with differences (− hypo-methylated, + is hyper-methylated). Corresponding P and Q values are indicated. The full dataset is available in Additional file 1: Excel file ‘MethylKit_Gene_Full’