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. Author manuscript; available in PMC: 2014 Nov 1.
Published in final edited form as: Nat Neurosci. 2013 Nov 24;17(1):121–130. doi: 10.1038/nn.3588

Table 2.

Overlap between differentially expressed genes with associated DMRs and previous microarray studies of multiple sclerosis and control NAWM samples

Upregulated RNA-seq (979) Downregulated RNA-seq (1,201)
Hypomethylated DMRs (495) 50
P = 1.0 × 10−18 		ARHGAP22, C10orf54, C17orf62, C1QA, C1QB, C1QC, CD37, CD4, CD48, CD84, CEPT1, CFD, CHI3L2, CNPPD1, CTSD, CTSZ, DAPP1, DOK3, FAM46A, FERMT3, GPR84, GSDMD, HLA-DOA, IRF9, LGMN, LSP1, MFNG, MGAT1, MRPL23, MRPS22, MSX1, NAPSB, NOL12, OSCAR, PATL2, PCK2, RBM14-RBM4, RBM4, RIN3, SECTM1, SGCE, SLC17A9, SP110, STIP1, STXBP2, TBL2, TRIM10, TSSC4, UBE2Z, VPS26A 20
P = 0.049		 AIFM2, ANO2, CLYBL, CPAMD8, DNAJB14, FLRT1, HLA-F, HOXC8, IRF6, KIFC1, KYNU, OSBPL5, PFKFB2, PITRM1, PPP1R13L, PTPN14, SYT8, TTC22, VWF, ZNF365
Hypermethylated DMRs (439) 18
P = 0.008		 AFMID, ATP6V0E1, BIRC5, C9orf142, CD37, FGD2, INO80E, MSLN, MYO1F, OTX2, PPP4C, RNF185, SDF2L1, SGCE, SLC47A2, SPI1, SYNGR2, UBE2L3 24
P = 9.8 × 10−5 		ATP1A1, ATP1A1OS, ATP1A2, ATP1A4, BCL2L2, CRY2, DAB2IP, FLRT1, MED24, NOTCH4, OBSCN, OSBPL5, PPT2, PRDM16, RBP2, SEC14L1, SH2D4B, SIPA1L1, TPM3, UBAP2L, WDR37, WHSC1, WNK2, ZSCAN18
Graumann et al.49 (349) 14
P = 0.039		 ADORA3, BCL2L1, CCR1, CSF1, CSK, CTSD, DDIT3, IRF9, MSX1, NGFR, PLAUR, SERPINA1, TGB2, UBE2A 37
P = 1.5 × 10−11 		ATP1A1, BCL2L2, CAMK4, CDH3, CNTN1, DDR2, EGFR, ELAVL4, ERBB4, ERG, FLT1, FLT3, GABRB1, GRM5, HIVEP2, ICAM1, ITSN1, KCNA2, MAPK10, MAPK9, MCAM, NF1, NF2, NTRK2, PAK1, PDGFRB, PKD1, PPP2R2B, PRKAR1A, PRKCB, PTPN11, PTPRG, RAB6A, RASA1, SMARCA2, SMARCA4, TFRC
Lindberg et al.50 (47) 13
P = 3.6 × 10−11 		ARPC1B, CASP1, DOK1, FCER1G, FOLR2, GDPD5, HCK, IRF5, LY86, MAX, MMP2, NCF4, TGB2 3
P = 0.150		 ASB1, DDR2, ZNF365

Numerals indicate the number of genes in the category.