Table 3 The list of KEGG pathways significantly expressed over three healing states of hemostasis, inflammation and proliferation for different wounds of skin and tongue, and their corresponding p-values calculated by LLCT method
From: Longitudinal linear combination test for gene set analysis
|  | Geneset size | Hemostasis (< 12 h) | Inflammation (12–72 h) | Proliferation (3–7 days) | Differentially expressed at unwounded status? | Prioritization Score | |||
|---|---|---|---|---|---|---|---|---|---|
p-value | q-value* | p-value | q-value* | p-value | q-value* | Â | Â | ||
Metabolism | |||||||||
 Nucleotide metabolism | |||||||||
  Purine metabolism | 789 | < 0.01 | < 0.01 | 0.01 | 0.03 | < 0.01 | < 0.01 | Yes | 9.0% |
 Glycan biosynthesis and metabolism | |||||||||
  Mucin type O-glycan biosynthesis | 156 | 0.01 | 0.03 | <0.01 | <0.01 | 0.01 | 0.01 | Yes | 10.7% |
  Glycosaminoglycan degradation | 108 | 0.03 | 0.09 | 0.01 | 0.02 | <0.01 | < 0.01 | No | 9.6% |
Genetic Information Processing | |||||||||
 Transcription | |||||||||
  Spliceosome | 984 | <0.01 | < 0.01 | < 0.01 | < 0.01 | < 0.01 | < 0.01 | Yes | 0.4% |
 Replication and repair | |||||||||
  DNA replication | 237 | <0.01 | < 0.01 | < 0.01 | < 0.01 | < 0.01 | < 0.01 | Yes | 0.4% |
  Mismatch repair | 135 | <0.01 | 0.01 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 5.7% |
Folding, sorting and degradation | |||||||||
  Protein processing in endoplasmic reticulum | 1164 | <0.01 | <0.01 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 0.4% |
Environmental Information Processing | |||||||||
 Signal transduction | |||||||||
  MAPK signaling pathway | 2127 | 0.02 | 0.08 | 0.02 | 0.04 | <0.01 | <0.01 | No | 9.4% |
  Ras signaling pathway | 1566 | 0.02 | 0.07 | 0.01 | 0.02 | <0.01 | <0.01 | No | 8.5% |
  Calcium signaling pathway | 1206 | 0.01 | 0.03 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 3.1% |
  NF-kappa B signaling pathway | 702 | <0.01 | < 0.01 | < 0.01 | < 0.01 | < 0.01 | < 0.01 | Yes | 0.4% |
  HIF-1 signaling pathway | 804 | <0.01 | <0.01 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 0.4% |
  Hedgehog signaling pathway | 378 | <0.01 | < 0.01 | 0.01 | 0.02 | 0.01 | 0.01 | Yes | 8.9% |
  JAK-STAT signaling pathway | 972 | <0.01 | <0.01 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 0.4% |
 Signaling molecules and interaction | |||||||||
  Cytokine-cytokine receptor interaction | 1308 | <0.01 | <0.01 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 0.4% |
  Neuroactive ligand-receptor interaction | 1557 | <0.01 | 0.01 | <0.01 | <0.01 | <0.01 | <0.01 | No | 2.2% |
Cellular Processes | |||||||||
 Transport and catabolism | |||||||||
  Autophagy - animal | 996 | <0.01 | 0.01 | 0.02 | 0.04 | <0.01 | <0.01 | No | 10.8% |
  Lysosome | 771 | <0.01 | <0.01 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 0.4% |
 Cell growth and death | |||||||||
  Apoptosis | 951 | 0.03 | 0.09 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 5.1% |
  Necroptosis | 849 | 0.01 | 0.03 | <0.01 | <0.01 | <0.01 | <0.01 | No | 3.5% |
 Cellular community - eukaryotes | |||||||||
 Adherens junction | 609 | 0.02 | 0.06 | 0.01 | 0.01 | 0.01 | 0.01 | Yes | 12.6% |
Organismal Systems | |||||||||
 Immune system | |||||||||
  Toll-like receptor signaling pathway | 615 | 0.01 | 0.02 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 3.0% |
  RIG-I-like receptor signaling pathway | 426 | 0.02 | 0.06 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 3.8% |
  Cytosolic DNA-sensing pathway | 345 | 0.00 | 0.00 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 4.3% |
  Hematopoietic cell lineage | 492 | 0.01 | 0.04 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 3.6% |
  Natural killer cell mediated cytotoxicity | 720 | 0.02 | 0.06 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 6.7% |
  IL-17 signaling pathway | 552 | <0.01 | 0.01 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 2.2% |
  B cell receptor signaling pathway | 540 | 0.03 | 0.09 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 5.0% |
 Fc epsilon RI signaling pathway | 444 | 0.02 | 0.07 | 0.01 | 0.03 | <0.01 | <0.01 | No | 8.9% |
  Fc gamma R-mediated phagocytosis | 696 | 0.04 | 0.11 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 5.4% |
  Leukocyte transendothelial migration | 753 | 0.03 | 0.08 | <0.01 | 0.01 | <0.01 | <0.01 | Yes | 8.4% |
 Circulatory system | |||||||||
  Adrenergic signaling in cardiomyocytes | 1092 | <0.01 | 0.01 | 0.01 | 0.01 | <0.01 | <0.01 | Yes | 10.5% |
 Development | |||||||||
  Axon guidance | 1389 | <0.01 | <0.01 | <0.01 | <0.01 | 0.02 | 0.03 | Yes | 5.4% |
 Nervous system | |||||||||
  Glutamatergic synapse | 777 | 0.02 | 0.07 | <0.01 | <0.01 | 0.01 | 0.01 | Yes | 8.6% |
  Cholinergic synapse | 831 | 0.03 | 0.08 | <0.01 | <0.01 | <0.01 | <0.01 | No | 7.8% |
  Dopaminergic synapse | 1041 | <0.01 | <0.01 | <0.01 | 0.01 | 0.01 | 0.02 | Yes | 0.4% |
Endocrine system | |||||||||
  Oxytocin signaling pathway | 1125 | <0.01 | 0.01 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 5.1% |
  AGE-RAGE signaling pathway in diabetic complications | 717 | 0.01 | 0.03 | <0.01 | <0.01 | <0.01 | <0.01 | Yes | 3.1% |