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Table 6 GO classes overrepresented in genes differentially expressed between control subjects and (subgroups of) MS patients

From: Transcriptome analysis of normal-appearing white matter reveals cortisol- and disease-associated gene expression profiles in multiple sclerosis

Patients – Controls

 

GO class

Genes present

Up

Positive regulation of apoptosis (GO:0043065)

SIVA1, HTATIP2, ZAK, PML, TNFSF14, RPS27L, TLR4, ITSN1, CTNNBL1, RPS3, CASP3, HTRA2, CD44, CDKN2C, RPS3A, SOS1, MTCH1, TGM2, AATF, RUNX3, RPS27A, DEDD2, CEBPG, FADD, BAD, SOD1, TXNDC12, EI24, RNF7, NAIF1, HSPD1

Activation of caspase activity (GO:0006919)

SIVA1, MTCH1, PML, HSPE1, HSPD1, RPS3

Regulation of T cell activation (GO:0050863)

CD47, CASP3, IL6ST, NCK1, TGFBR2, TNFSF14, BAD, HSPD1, SOD1

Cytokine binding (GO:0019955)

TNFRSF1A, ACVRL1, IL10RB, IL6ST, LEPR, TGFBR2, ENG, IFNAR1, ACVR1

Down

Neuron differentiation (GO:003082)

EGR2, GNAO1, ATL1, TBCE, NTNG2, DSCAML1, APP, RASGRF1, GHRL, MAPK8IP3, SEMA3B, NTM, C17ORF28

Cell projection (GO:0042995)

RTN4, MYO5A, BBS5, KIAA1598, SSH1, ATL1, NEDD9, GIPC1, DNAH2, CPEB1, APP, CTTN, DNAI1, ARHGEF4, DBNL, ARHGEF7, FSCN1, LDB3, DNAI2, PCM1, CAMK2N1, RASGRF1, IFT172, MAPK8IP3, GHRL, SPEF1

Regulation of lipid metabolic process (GO:0019216)

TNF, DHCR7, SF1, ACACB, PPARGC1A

MS High Cortisol – Low Cortisol

 

GO class

Genes present

Up

Immune response (GO:0006955)

LAIR1, CEBPB, IL1RL1, IFITM2, TLR2, TNFSF14, CALCOCO2, SLC11A1, C1QB, UNC13D, APOL1, XBP1, LILRB3, IL4R, BCL3, HSPD1, VSIG4

Regulation of cytokine production (GO:0001817)

INHBA, SLC11A1, CEBPB, TLR2, BCL3, NFKB1, BCL6, HSPD1, VSIG4, SRGN

Myeloid cell differentiation (GO:0030099)

INHBA, RPS19, JMJD6, RPS14, BCL6, ZBTB16, RUNX1, CBFB, TIMP1

Negative regulation of myeloid cell differentiation (GO:0045638)

INHBA, NFKBIA, ZBTB16, RUNX1

Down

Apoptosis (GO:0006915)

RTN4, CKAP2, POLR2G, DNM1L, TM2D1, EGLN3, RRAGA, PIGT, BAG1, NGFRAP1, EIF2AK2, MAGEH1, NDUFS1, PUF60, ZIM2

Negative regulation of neurogenesis (GO:0050768)

RTN4, NOG, NF1, OMG

MS Mild Disease – Severe Disease

 

GO class

Genes present

Up

Neuron projection development (GO:0031175)

APP, GNAO1, EGR2, ATL1, RASGRF1, TBCE, MAPK8IP3, NTNG2, DSCAML1, GHRL, SEMA3B

Neuron differentiation (GO:0030182)

EGR2, GNAO1, ATL1, TBCE, NTNG2, DSCAML1, APP, RASGRF1, GHRL, MAPK8IP3, SEMA3B, NTM, C17ORF28

Inflammatory response (GO:0006954)

HDAC5, YWHAZ, TNF, NDST1, TOLLIP, CCL3L3, ITIH4, CCL4L1, CCL4

Down

Lysosome (GO:0005764)

HGSNAT, SGSH, NAGLU, MFSD8, LIPA, GM2A, PPT1, CD63, ASAH1

Steroid metabolic process (GO:0008202)

HSD17B11, MBTPS2, LIPA, CYB5R2, INSIG2, PRKAA1, CLN6