Table 4 Interactions of commonly mutated immune response genes Indicating biological process and biological pathways

Biological process

GO term

Strength

False discovery rate

 Complement activation, lectin pathway

GO:0001867

2.64

0.0055

 Positive regulation of heterotypic cell–cell adhesion

GO:0034116

2.43

0.0108

 Humoral immune response

GO:0002445

2.3

8.07e-06

 Innate immune response in mucosa

GO:0002227

2.22

0.0217

 Regulation of inflammatory response to antigenic stimulus

GO:0002861

2.21

0.0227

Molecular pathways (Gene Ontology)

 MHC class II receptor activity

GO:0032395

2.68

0.0334

Cellular component Gene Ontology

 MHC class II protein complex

GO:0042613

2.49

0.0382

 Integral component of lumenal side of endoplasmic reticulum

GO:0071556

2.22

0.0438

 Clathrin-coated endocytic vesicle membrane

GO:0030669

2.09

0.0438

 Side of membrane

GO:0098552

1.21

0.0438

 Extracellular space

GO:0005615

0.68

0.0438

Reactome pathways

Description

Pathway

Strength

False discovery rate

 Lectin pathway of complement activation

HSA-166662

2.79

0.0073

 Translocation of ZAP-70 to Immunological synapse

HSA-202430

2.46

0.0163

 Phosphorylation of CD3 and TCR zeta chains

HSA-202427

2.38

0.0163

 PD-1 signaling

HSA-389948

2.36

0.0163

 Generation of second messenger molecules

HSA-202433

2.18

0.0209

Wiki pathways

 LTF danger signal response pathway

WP4478

2.36

0.0089

 Cytokines and inflammatory response

WP530

2.22

0.0120

Protein domains (Pfam)

 Class II histocompatibility antigen, beta domain

Domain

PF00969

2.68

0.0355

Protein domains (SMART)

 Class II histocompatibility antigen, beta domain

Domain

SM00921

2.68

0.0075