Table 5.

Filtration criteria for identification of differentially methylated CpG sites in the two RA patient cohorts compared to the healthy controls.

Cell type	Cohort vs. controls	Number of sites	Mean coverage	Significant sites	Significant genes	Gene names
						Increased methylation in RA patients	Decreased methylation in RA patients
CD4+ naïve T cells	Newly diagnosed DMARD naïve RA patients	1 538 979	1 389 561	3	2	SPTA1, MCC	-
CD4+ naïve T cells	MTX treated RA patients	1 657 054	1 447 202	16	11	SNX11, PLA1A, ZNF732, EPS15L1, STON1-GTF2A1L, STON1,	CACTIN, LOC100134317, RGPD3, PLEKHM1P1, SMYD3
CD4+ memory T cells	Newly diagnosed DMARD naïve RA patients	984 219	933 808	51	37	YPEL1, NELFA, CTNNA2, PARD3B, ZFP14, PHTF2, IL4I1, PGBD4, EMC7, PCSK7, RNF214, PLEKHD1, POLE2, KLHDC1, NEMF, RNF180, MIR129-2, SAMD10, PRPF6, REST, SUDS3, TRANK1, AP4E1, TEAD4, ZFP3, POM121C	FAM63B, MAPK8IP3, STAT5A, ZNF668, ZNF646, TMED10, CES2, GRID2IP, PLEKHA2, IQGAP3, GGCX,
CD4+ memory T cells	MTX treated RA patients	1 067 343	1 035 857	853	542	C7orf77, DENND5B, YWHAEP7, TMC5, SLCO2B1, SOX9	TTC37, MOXD1, TMEM129, TACC3, HIST2H3C, ISPD, LINC00862, DPP6, RORA, RNFT2, CAMKK1, TBXAS1, HIPK2, GNA15, DIAPH3, KCNJ6, LHFPL3, TRAF2, COL4A4, GALNT9, CYBA, MAP6, TBC1D3, ITPK1, PALM, TTC39B, EVI5L, MN1, S100A1, S100A13, PTPRO, FNDC3B, DLG2, UBIAD1

The number, names and methylation status of top 40 significant genes are also included.

RA, Rheumatoid arthritis; DMARD, Disease modifying antirheumatic drugs; MTX, Methotrexate; p.adj.fdr. p-value adjusted for false discovery rate.