Journal of Immunology Research

Research Article

Immune Response to Rotavirus and Gluten Sensitivity

Table 3

Biological processes and pathways enriched in the 15 modules.
Biological processes valuePathways value
M0
Exocytosis<0.001None 
Secretion by cell<0.001  
Secretion<0.001  
Vesicle-mediated transport0.0018  
Single-organism transport0.0220  
Single-organism localization0.0308  
M1
T cell receptor signaling pathway<0.001T cell activation<0.001
Transmembrane receptor protein tyrosine kinase signaling pathway<0.001B cell activation0.0012
T cell costimulation<0.001Cadherin signaling pathway0.0056
Viral process<0.001Integrin signaling pathway0.0081
Fc-gamma receptor signaling pathway involved in phagocytosis<0.001  
Peptidyl-tyrosine modification0.0016  
Adaptive immune response0.0017  
Positive regulation of antigen receptor-mediated signaling pathway0.0029  
Positive regulation of alpha-beta T cell proliferation0.0038  
Phosphatidylinositol phosphorylation0.0060  
Phosphatidylinositol-mediated signaling0.0162  
Positive regulation of calcium-mediated signaling0.0192  
T cell selection0.0244  
Leukocyte migration0.0303  
Interleukin-2-mediated signaling pathway0.0324  
MAPK cascade0.0371  
Positive regulation of immune effector process0.0466  
Positive regulation of defense response0.0485  
M2
mRNA export from nucleus<0.001None 
Spliceosomal complex assembly<0.001  
Termination of RNA polymerase II transcription<0.001  
Regulation of mRNA splicing, via spliceosome<0.001  
Positive regulation of RNA splicing<0.001  
mRNA 3′-end processing<0.001  
Regulation of gene silencing by miRNA<0.001  
tRNA export from nucleus0.0010  
Viral gene expression0.0054  
Intracellular transport of virus0.0078  
Protein sumoylation0.0294  
Regulation of cellular response to heat0.0310  
Fibroblast growth factor receptor signaling pathway0.0414  
M3
Positive regulation of T cell activation0.0035T cell activation<0.001
Interleukin-2-mediated signaling pathway0.0065Interleukin signaling pathway<0.001
Interleukin-4-mediated signaling pathway0.0065PDGF signaling pathway0.0010
Protein phosphorylation0.0349Integrin signaling pathway0.0017
  JAK/STAT signaling pathway0.0057
  Hypoxia response via HIF activation0.0110
  Insulin/IGF pathway-protein kinase B signaling cascade0.0136
  p53 pathway feedback loops 20.0176
  PI3 kinase pathway0.0182
  VEGF signaling pathway0.0238
  Endothelin signaling pathway0.0284
  p53 pathway0.0290
M4
Pospholipase C-activating G-protein-coupled receptor signaling pathway<0.001Heterotrimeric G-protein signal. pathway-Gq α and Go α med. pathway<0.001
G-protein coupled acetylcholine receptor signaling pathway<0.001  
Activation of phospholipase C activity<0.001PI3 kinase pathway<0.001
Positive regulation of cytosolic calcium ion concentration<0.001Endothelin signaling pathway0.0013
Adenylate cyclase-modulating G-protein-coupled receptor signaling pathway0.0048Wnt signaling pathway0.0015
M5
Translational initiation<0.001None 
Nuclear-transcribed mRNA catabolic process, nonsense mediated decay<0.001  
SRP-dependent cotranslational protein targeting to membrane<0.001  
rRNA processing<0.001  
Ribosomal small subunit assembly0.0083  
M6
Regulation of small GTPase-mediated signal transduction<0.001None 
Positive regulation of GTPase activity<0.001  
Small GTPase-mediated signal transduction<0.001  
Actin cytoskeleton organization0.0108  
M7
T cell costimulation<0.001T cell activation<0.001
Phosphatidylinositol-mediated signaling<0.001Integrin signaling pathway0.0041
T cell receptor signaling pathway<0.001  
Phosphatidylinositol phosphorylation<0.001  
Transmembrane receptor protein tyrosine kinase signaling pathway0.0016  
Peptidyl-tyrosine autophosphorylation0.0033  
Viral process0.0035  
Fc receptor signaling pathway0.0050  
Regulation of apoptotic process0.0055  
Leukocyte differentiation0.0122  
Leukocyte migration0.0232  
Lymphocyte activation0.0237  
B cell receptor signaling pathway0.0256  
Positive regulation of defense response0.0340  
M8
Response to unfolded protein<0.001None 
Response to topologically incorrect protein<0.001  
Chaperone-mediated protein complex assembly<0.001  
Protein folding<0.001  
Protein transmembrane transport<0.001  
Response to stress<0.001  
M9
Activation of innate immune response<0.001Toll-like receptor signaling pathway<0.001
Positive regulation of innate immune response<0.001Ras pathway<0.001
Toll-like receptor signaling pathway<0.001Apoptosis signaling pathway<0.001
Fc-epsilon receptor signaling pathway0.0020T cell activation<0.001
MAPK cascade0.0026p38 MAPK pathway<0.001
Positive regulation of type I interferon production0.0029Oxidative stress response<0.001
Positive regulation of cytokine production0.0035Angiogenesis<0.001
TRIF-dependent toll-like receptor signaling pathway0.0136B cell activation<0.001
Positive regulation of interferon-beta production0.0202FGF signaling pathway<0.001
Response to lipopolysaccharide0.0268EGF receptor signaling pathway<0.001
Type I interferon biosynthetic process0.0419Integrin signaling pathway0.0024
  Inflammation mediated by chemokine and cytokine signaling pathway0.0079
   
  Interleukin signaling pathway0.0104
M10
T cell receptor signaling pathway<0.001T cell activation<0.001
T cell costimulation<0.001EGF receptor signaling pathway<0.001
Fc-epsilon receptor signaling pathway<0.001Integrin signaling pathway<0.001
phosphatidylinositol phosphorylation<0.001p53 pathway feedback loops 2<0.001
Peptidyl-tyrosine autophosphorylation<0.001VEGF signaling pathway<0.001
Fc-gamma receptor signaling pathway involved in phagocytosis<0.001B cell activation<0.001
Leukocyte migration<0.001Ras pathway<0.001
Growth hormone receptor signaling pathway<0.001Angiogenesis<0.001
Regulation of defense response to virus<0.001Insulin/IGF pathway-protein kinase B signaling cascade<0.001
Innate immune response<0.001 
Positive regulation of MAP kinase activity<0.001Inflammation mediated by chemokine and cytokine signaling pathway<0.001
T cell differentiation<0.001 
Regulation of apoptotic process<0.001PI3 kinase pathway<0.001
JAK–STAT cascade0.0011p53 pathway<0.001
Positive regulation of immune effector process0.0031Interferon-gamma signaling pathway<0.001
MAPK cascade0.0056FGF signaling pathway<0.001
Adaptive immune response0.0088Endothelin signaling pathway0.0101
B cell receptor signaling pathway0.0121JAK/STAT signaling pathway0.0176
Phosphatidylinositol 3-kinase signaling0.0214  
Stimulatory C-type lectin receptor signaling pathway0.0363  
Innate immune response activ. cell surface receptor signal. pathway0.0387  
M11
Cellular response to cytokine stimulus<0.001JAK/STAT signaling pathway<0.001
JAK–STAT cascade involved in growth hormone signaling pathway<0.001Interleukin signaling pathway<0.001
Positive regulation of cytokine production<0.001PDGF signaling pathway<0.001
Response to interleukin-2<0.001Interferon-gamma signaling pathway<0.001
Positive regulation of T cell differentiation<0.001EGF receptor signaling pathway<0.001
Positive regulation of tyrosine phosphorylation of STAT protein<0.001Integrin signaling pathway<0.001
Regulation of interferon-gamma-mediated signaling pathway<0.001Inflammation mediated by chemokine and cytokine signaling pathway<0.001
MAPK cascade<0.001  
Adaptive immune response<0.001p53 pathway feedback loops 20.0025
Innate immune response0.0014PI3 kinase pathway0.0027
Positive regulation of T cell proliferation0.0022VEGF signaling pathway0.0045
Positive regulation of inflammatory response0.0025B cell activation0.0045
Antigen receptor-mediated signaling pathway0.0072Ras pathway0.0050
T cell differentiation0.0085T cell activation0.0078
Inflammatory response0.0194Cadherin signaling pathway0.0201
Positive regulation of antigen receptor-mediated signaling pathway0.0227  
Transcription factor import into nucleus0.0313  
T cell costimulation0.0396  
M12 Inflammation mediated by chemokine and cytokine signaling pathway<0.001
G-protein-coupled receptor signaling pathway<0.001 
Chemokine-mediated signaling pathway<0.001Heterotrimeric G-protein signaling pathway-Gi alpha and Gs alpha-mediated pathway0.0473
Positive regulation of cytosolic calcium ion concentration<0.001 
Inflammatory response<0.001  
Cell chemotaxis<0.001  
Positive regulation of neutrophil chemotaxis0.0136  
Response to lipopolysaccharide0.0268  
M13
Adherens junction assembly<0.001Integrin signaling pathway<0.001
Phosphatidylinositol phosphorylation0.0015Cadherin signaling pathway<0.001
Vesicle-mediated transport0.0026  
Positive regulation of protein localization to nucleus0.0043  
Actin cytoskeleton organization0.0105  
Cell differentiation0.0308  
M14
Positive regulation of T cell activation0.0035T cell activation<0.001
Interleukin-2-mediated signaling pathway0.0065Integrin signaling pathway<0.001
Interleukin-4-mediated signaling pathway0.0065Angiogenesis0.0032
Regulation of immune response0.0430Toll like receptor signaling pathway0.0269
  VEGF signaling pathway0.0387
  B cell activation0.0387
  Ras pathway0.0431