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Table 3 Most significant GO and KEGG pathways enriched in lung clusters

From: Analysis of gene expression profiles and protein-protein interaction networks in multiple tissues of systemic sclerosis

Go Biological ProcessP-valueKEGG PathwayP-value
cluster L.1 (Inflammation & immunity) – size/DEGs = 56/54
 - cytokine-mediated signaling pathway1.65E-17- Cytokine-cytokine receptor interaction5.61E-22
 - inflammatory response3.73E-11- Hematopoietic cell lineage1.05E-10
 - cellular response to cytokine stimulus1.25E-12- Chemokine signaling pathway2.66E-09
 - chemokine-mediated signaling pathway2.78E-10- JAK-STAT signaling pathway1.06E-08
 - positive regulation of leukocyte migration6.87E-08- TNF signaling pathway3.78E-07
cluster L.2 (Inflammation & immunity) – size/DEGs = 48/47
 - regulation of transcription from RNA polymerase II promoter1.92E-12- MAPK signaling pathway1.48E-09
 - positive regulation of transcription from RNA polymerase II promoter1.04E-10- TNF signaling pathway1.04E-05
 - positive regulation of transcription, DNA-templated6.58E-10- Osteoclast differentiation2.04E-05
 - regulation of cell cycle1.13E-08- Inflammatory bowel disease (IBD)0.000298
 - regulation of transcription, DNA-templated7.42E-06- Amphetamine addiction0.000298
cluster L.3 (Cell proliferation & cell death) - size/DEGs = 20/19
 - positive regulation of cyclin-dependent protein serine/threonine kinase activity0.000225- p53 signaling pathway1.44E-07
 - positive regulation of cell cycle0.000225- Cell cycle1.4E-06
 - mitotic cell cycle phase transition0.000225- FoxO signaling pathway6.39E-05
 - G1/S transition of mitotic cell cycle0.000225- Progesterone-mediated oocyte maturation0.000704
 - cell cycle G2/M phase transition0.000284- Oocyte meiosis0.001103
cluster L.4 (GPCR signaling) - size/DEGs = 9/9
 - adenylate cyclase-activating G-protein coupled receptor signaling pathway5.98E-17- Neuroactive ligand-receptor interaction7.6E-09
 - adenylate cyclase-modulating G-protein coupled receptor signaling pathway2.53E-15- Regulation of lipolysis in adipocytes0.001669
 - cAMP-mediated signaling1.11E-11- Renin secretion0.001669
 - G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger4.58E-08- Salivary secretion0.002418
 - positive regulation of cAMP metabolic process5.94E-06- Vascular smooth muscle contraction0.003501
cluster L.5 (GPCR signaling) - size/DEGs = 19/19
 - regulation of small GTPase mediated signal transduction1E-10- Axon guidance0.006298
 - regulation of intracellular signal transduction3.27E-07 
 - regulation of actin filament-based process2.44E-05
 - regulation of cell migration2.44E-05
 - regulation of actin cytoskeleton organization3.37E-05
cluster L.6 (ECM organization) - size/DEGs = 13/11
 - extracellular matrix organization3.55E-11- Protein digestion and absorption1.08E-15
 - collagen fibril organization1.56E-07- AGE-RAGE signaling pathway in diabetic complications6.03E-05
 - protein complex subunit organization6.15E-07- Amoebiasis6.03E-05
 - skeletal system development6.58E-07- ECM-receptor interaction6.03E-05
 - skin development6.58E-07- Platelet activation8.48E-05
cluster L.7 (Metabolic process) - size/DEGs = 8/7
 - secondary alcohol biosynthetic process1.83E-08- Terpenoid backbone biosynthesis5.16E-07
 - cholesterol biosynthetic process1.83E-08- Synthesis and degradation of ketone bodies2.52E-05
 - sterol biosynthetic process1.87E-08- Steroid biosynthesis7.07E-05
 - cholesterol metabolic process1.19E-07- Metabolic pathways8.42E-05
 - acetyl-CoA metabolic process2.02E-07- Butanoate metabolism8.42E-05
cluster L.8 (Regulation of BMPs) - size/DEGs = 20/20
 - regulation of BMP signaling pathway5.24E-11- Signaling pathways regulating pluripotency of stem cells1.69E-09
 - BMP signaling pathway4.87E-08- Hedgehog signaling pathway1.8E-08
 - cellular response to BMP stimulus5E-08- Basal cell carcinoma1.96E-08
 - regulation of ossification5.47E-08- Hippo signaling pathway4.83E-08
 - positive regulation of cartilage development2.94E-07- TGF-beta signaling pathway8E-06
cluster L.9 (Metabolic process) - size/DEGs = 11/11
 - keratan sulfate catabolic process0.00139- Phospholipase D signaling pathway0.001041
 - keratan sulfate metabolic process0.002787- Rap1 signaling pathway0.001615
 - sulfur compound catabolic process0.002787- cAMP signaling pathway0.029672
 - keratan sulfate biosynthetic process0.002787- Ras signaling pathway0.029672
 - glycosaminoglycan catabolic process0.005613 
cluster L.10 (GPCR signaling) - size/DEGs = 22/21
 - axon guidance0.00022- Axon guidance1.8E-07
 - transmembrane receptor protein tyrosine kinase signaling pathway0.000396- Focal adhesion0.0014420.011273
 - axonogenesis0.000396- Primary immunodeficiency0.032572
 - cell migration involved in sprouting angiogenesis0.007527- B cell receptor signaling pathway 
 - ephrin receptor signaling pathway0.007527 
cluster L.11 (ECM degradation) - size/DEGs = 23/23
 - proteolysis0.000176None
 - extracellular matrix disassembly0.00022
 - regulation of endopeptidase activity0.005145
 - extracellular matrix organization0.007401
 - regulation of membrane protein ectodomain proteolysis0.014697
cluster L.12 (Inflammation and immunity) - size/DEGs = 12/11
 - neutrophil degranulation0.004647- Insulin secretion0.010314
 - neutrophil mediated immunity0.004647- Osteoclast differentiation0.012295
 - neutrophil activation involved in immune response0.004647 
 - potassium ion transport0.014375
 - metal ion transport0.027277
  1. Abbreviation: GPCR: G-protein coupled receptor; BPMs: Bone morphogenetic proteins