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Table 4 GO classes overrepresented in modules identified by WGCNA

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

Lightgreen module

 GO class

Genes present

  Immune response (GO:0006955)

EXO1, IL18RAP, PRG2, PGLYRP1, CFP, BPI, CST7, SP2, S1PR4, LILRA5, FCN1, CEACAM8, CTSG

  Defense response (GO:0006952)

IL18RAP, RNASE3, S100A8, CEBPE, PRG2, S100A9, PGLYRP1, S100A12, AZU1, CFP, BPI, DEFA4, MPO, CTSG

  Regulation of cytokine production (GO:0001817)

AZU1, BPI, ELANE, NLRP12, GHRL

  Regulation of IL-1b production (GO:0032652)

AZU1, NLRP12, GHRL

  Negative regulation of cytokine biosynthetic process (GO:0042036)

ELANE, NLRP12, GHRL

  Immune system development (GO:0002520)

EXO1, CCNB2, CEBPE, FLT3, MMP9

  Phagocytosis (GO:0006909)

CEBPE, FCN1, ELANE

Pink module

 GO class

Genes present

  Regulation of caspase activity (GO:0043281)

FOXL2, ADORA2A, SMAD6, HSPE1, HSPD1, PMAIP1, DNAJB6

  Response to unfolded protein (GO:0006986)

HSP90AB1, HSP90AA2, HSP90AA1, HSPA1A, HSPA1B, SERPINH1, HSPA1L, HSPH1, HSPA4L, DNAJA1, HSPA6, HSPB1, HSPA4, HSPE1, DNAJB1, HSPD1, DNAJB4, HSPA8, DNAJB6

  Heat shock protein binding (GO:0031072)

FKBP4, PPID, DNAJA1, DNAJB1, DNAJB4, DNAJA4, DNAJB6

  Antigen processing and presentation (KEGG pathway hsa04612)

HSPA1L, HSP90AA2, HSP90AB1, HSP90AA1, HSPA6, HSPA4, HSPA1A, HSPA1B, HSPA8

  Regulation of lymphocyte activation (GO:0051249)

TRAF2, ADORA2A, TNFSF14, HSPD1, SOD1, IL7R, SART1

  Regulation of T cell mediated immunity (GO:0002709)

TRAF2, HSPD1, IL7R

  Cellular response to oxidative stress (GO:0034599)

PYCR1, EPAS1, SIRT7, SOD1

  Oxidation reduction (GO:0055114)

CTBP2, HTATIP2, HSD17B1, UGDH, SIRT7, CRYZ, SOD1, PYCR1, CYP39A1, PLOD1, KDM2A, P4HA2, NXN, P4HA1, JMJD6, PLOD3, SPR, BCO2

Tan module

 GO class

Genes present

  Generation of precursor metabolites and energy (GO:0006091)

ALDOA, NDUFA5, UQCRC1, AIFM3, NDUFB10, ACO2, FDX1, TMX4, CRAT, UQCRFS1, ATP5G3, COX6C, SDHA, ATP6V0C, ATP5C1, SLC25A3, ATPIF1, NDUFS1, MDH1, PYGB

  Mitochondrion (GO:0005739)

RNASEL, UQCRC1, FDX1, NIT2, TMX4, HINT2, GCAT, WARS2, BPHL, UQCRFS1, ATP5G3, SFXN5, GOT2, DDX28, NT5M, GPX4, SLC25A3, TIMM23B, ACAD9, NDUFS1, HSD17B8, PDK1, PDK2, NDUFA5, NDUFB10, AIFM3, ACO2, SLC25A5, AMACR, CRAT, SARS2, COX6C, SDHA, NFU1, MRPS18A, ATP5C1, ATPIF1, PRODH

Yellow module

 GO class

Genes present

  Lipid biosynthetic process (GO:0008610)

TM7SF2, CYP51A1, ACSS2, PEX7, ELOVL1, FAR1, ELOVL5, DHCR7, SERINC1, PRKAA1, HSD17B3, PCYT1B, SCD5, PCYT2, AGPAT4, GAL3ST1, PLD1, PLP1, LPGAT1, FADS1, FA2H, PIGT, PIGS, CFTR, CERCAM, PIGP, PTGDS, C5ORF4, SMPD1, MVK, IDI1, DEGS1

  Steroid metabolic process (GO:0008202)

TM7SF2, SREBF1, OSBPL5, MBTPS2, CYP51A1, CFTR, ABCA2, DHCR7, INSIG1, PRKAA1, MVK, HSD17B3, IDI1, LIPE, VLDLR, CLN6

  1. GO gene ontology; KEGG Kyoto Encyclopedia of Genes and Genomes