Table 2 Differentially expressed immune genes, their annotated proteins, and their annotated biological processes based on gene ontologies in CFS patients as compared to healthy controls, adjusted for age and gender differences across groups and sorted according to foldchange

Downregulated gene expression in CFS patients as compared to healthy controls

CD79A

ENSG00000105369

CD79a molecule

B cell differentiation

GO:0030183

B cell proliferation

GO:0042100

B cell activation

GO:0042113

B cell receptor signaling pathway

GO:0050853

TNFRSF13C

ENSG00000159958

Tumor necrosis factor receptor superfamily member 13C

B cell homeostasis

GO:0001782

FLT3

ENSG00000122025

Fms related tyrosine kinase 3

Myeloid progenitor cell differentiation

GO:0002318

Pro-B cell differentiation

GO:0002328

Transmembrane receptor protein tyrosine kinase signaling pathway

GO:0007169

Positive regulation of cell proliferation

GO:0008284

Cytokine-mediated signaling pathway

GO:0019221

B cell differentiation

GO:0030183

Lymphocyte proliferation

GO:0046651

Cellular response to cytokine stimulus

GO:0071345

Cellular response to glucocorticoid stimulus

GO:0071385

EBF1

ENSG00000164330

Early B cell factor 1

Multicellular organism development

GO:0032501

CXCR5

ENSG00000160683

C-X-C motif chemokine receptor 5

Positive regulation of cytokinesis

GO:0032467

B cell activation

GO:0042113

Lymph node development

GO:0048535

Chemokine-mediated signaling pathway

GO:0070098

IRF4

ENSG00000137265

Interferon regulatory factor 4

Negative regulation of toll-like receptor signaling pathway

GO:0034122

HIPK2

ENSG00000064393

Homeodomain interacting protein kinase 2

Positive regulation of cell proliferation

GO:0008284

Positive regulation of cytokine production

GO:0001819

Activation of innate immune response

GO:0002218

Inflammatory response

GO:0006954

Myeloid cell differentiation

GO:0030099

Monocyte differentiation

GO:0030224

Positive regulation of type I interferon production

GO:0032481

Positive regulation of interleukin-1 beta production

GO:0032731

Negative regulation of viral genome replication

GO:0045071

Innate immune response

GO:0045087

SLC25A6

ENSG00000169100

Solute carrier family 25 member 6

Active induction of host immune response by virus

GO:0046732

EEF2

ENSG00000167658

Eukaryotic translation elongation factor 2

Hematopoietic progenitor cell differentiation

GO:0002244

ST6GAL1

ENSG00000073849

ST6 beta-galactoside alpha-2,6-sialyltransferase 1

Humoral immune response

GO:0006959

Upregulated gene expression in CFS patients as compared to healthy controls

OGT

ENSG00000147162

O-linked N-acetylglucosamine (GlcNAc) transferase

Positive regulation of granulocyte differentiation

GO:0030854

ATG7

ENSG00000197548

Autophagy related 7

Positive regulation of macroautophagy

GO:0016239

LCP2

ENSG00000043462

Lymphocyte cytosolic protein 2

Immune response

GO:0006955

PTPRE

ENSG00000132334

Protein tyrosine phosphatase, receptor type E

Transmembrane receptor protein tyrosine phosphatase signaling pathway

GO:0007185

PRKCD

ENSG00000163932

Protein kinase C delta

Activation of phospholipase C activity

GO:0007202

TNFRSF25

ENSG00000215788

Tumor necrosis factor receptor superfamily member 25

Inflammatory response

GO:0006954

TLR8

ENSG00000101916

Toll like receptor 8

Toll-like receptor signaling pathway

GO:0002224

BTN3A3

ENSG00000111801

Butyrophilin subfamily 3 member A3

T cell mediated immunity

GO:0002456

S100A8

ENSG00000143546

S100 calcium binding protein A8

Cytokine production

GO:0001816

NBEAL2

ENSG00000160796

Neurobeachin like 2

Hematopoietic progenitor cell differentiation

GO.0002244

IFI16

ENSG00000163565

Interferon gamma inducible protein 16

Negative regulation of innate immune response

GO:0045824

Adaptive immune response

GO:0002250

Positive regulation of germinal center formation

GO:0002636

Positive regulation of B cell proliferation

GO:0030890

T cell costimulation

GO:0031295

B cell costimulation

GO:0031296

Positive regulation of T cell proliferation

GO:0042102

Positive regulation of interferon-gamma biosynthetic process

GO:0045078

BST1

ENSG00000109743

Bone marrow stromal cell antigen 1

Humoral immune response

GO:0006959

JAML

ENSG00000160593

Junction adhesion molecule like

Neutrophil chemotaxis

GO:0030593

TRIM25

ENSG00000121060

Tripartite motif containing 25

Viral process

GO:0016032

FAM111A

ENSG00000166801

Family with sequence similarity 111 member A

Negative regulation of viral genome replication

GO:0045071

Defense response to virus

GO:0051607

CASP1

ENSG00000137752

Caspase 1

Regulation of inflammatory response

GO:0050727

RIPK3

ENSG00000129465

Receptor interacting serine/threonine kinase 3

Regulation of T cell mediated cytotoxicity

GO:0001914

CLEC2B

ENSG00000110852

C-type lectin domain family 2 member B

Regulation of immune response

GO:0050776

IL1RN

ENSG00000136689

Interleukin 1 receptor antagonist

Negative regulation of cytokine-mediated signaling pathway

GO:0001960

IRF9

ENSG00000213928

Interferon regulatory factor 9

Cell surface receptor signaling pathway

GO:0007166

ADCY4

ENSG00000129467

Adenylate cyclase 4

cAMP-mediated signaling

GO:0019933

PLSCR1

ENSG00000188313

Phospholipid scramblase 1

Platelet activation

GO:0030168

PDE1B

ENSG00000123360

Phosphodiesterase 1B

Monocyte differentiation

GO:0030224

APOBEC3A

ENSG00000128383

Apolipoprotein B mRNA editing enzyme catalytic subunit 3A

Defense response to virus

GO:0051607