Table 1 Biological process and molecular function enrichment for media proteins significantly affected by Dex/injury treatment. Proteins with a significant effect (either increased or decreased, p < 0.05) of Dex versus control (D/N), mechanical injury and cytokine treatment versus control (IC/N), or injury, cytokines, and Dex versus injury and cytokines (ICD/IC) were analyzed with STRING protein association network analysis, and the five biological processes and molecular functions with the strongest enrichment (log₁₀(number of observed proteins/number of expected proteins)) were selected

 Increased

Cellular response to vitamin k

0.0282

Fibronectin binding

0.00012

Negative regulation of smooth muscle cell-matrix adhesion

0.0282

Proteoglycan binding

2.03E−06

UDP-glucuronate biosynthetic process

0.0418

Collagen binding

1.08E−06

Positive regulation of substrate-dependent cell migration, cell attachment to substrate

0.0418

Laminin binding

0.04

Negative regulation of plasminogen activation

0.005

Lipoprotein particle binding

0.04

 Decreased

Positive regulation of cell proliferation by vegf-activated pdgf receptor signaling pathway

0.0029

Procollagen-lysine 5-dioxygenase activity

0.0066

Esophagus smooth muscle contraction

0.0383

Phosphodiesterase i activity

0.0213

Hydroxylysine biosynthetic process

0.0383

Platelet-derived growth factor binding

0.00028

Glomerular capillary formation

0.0093

Extracellular matrix structural constituent conferring tensile strength

2.89E−10

Peptidyl-lysine hydroxylation

0.0153

Low-density lipoprotein particle binding

0.0159

 Increased

Actin filament fragmentation

0.0023

Peroxiredoxin activity

0.00033

Helper t cell extravasation

0.0151

Thioredoxin peroxidase activity

0.0108

Cellular hyperosmotic salinity response

0.0151

Copper chaperone activity

0.0108

Positive regulation of establishment of protein localization to telomere

2.99E−06

Extracellular matrix constituent conferring elasticity

0.0027

CRD-mediated mRNA stabilization

0.0037

Threonine-type endopeptidase activity

1.35E−06

 Decreased

Collagen fibril organization

4.85E−05

Extracellular matrix structural constituent conferring tensile strength

1.31E−07

Chondroitin sulfate proteoglycan biosynthetic process

0.0053

Heparan sulfate proteoglycan binding

0.0126

Chondroitin sulfate biosynthetic process

0.0275

Insulin-like growth factor binding

0.00021

Protein hydroxylation

0.0301

Extracellular matrix structural constituent

3.48E−09

Chondroitin sulfate proteoglycan metabolic process

0.0025

Proteoglycan binding

0.0131

 Increased

Actin filament fragmentation

0.0031

Peroxiredoxin activity

0.00041

Fumarate metabolic process

0.0188

Threonine-type endopeptidase activity

5.16E−12

Helper t cell extravasation

0.0188

Thioredoxin peroxidase activity

0.0143

Protein unfolding

0.0188

Copper chaperone activity

0.0143

Cellular hyperosmotic salinity response

0.0188

Extracellular matrix constituent conferring elasticity

0.004

 Decreased

Hydroxylysine biosynthetic process

0.0346

Procollagen-lysine 5-dioxygenase activity

0.0021

Peptidyl-lysine hydroxylation

0.0112

Insulin-like growth factor ii binding

0.0145

pdgf receptor-beta signaling pathway

0.0112

Extracellular matrix structural constituent conferring tensile strength

3.20E−08

Type b pancreatic cell proliferation

0.0137

Insulin-like growth factor i binding

0.0242

Basement membrane assembly

0.0137

Platelet-derived growth factor binding

0.0291

 Increased

Negative regulation of plasminogen activation

0.0011

Threonine-type endopeptidase activity

1.11E−07

Viral translational termination-reinitiation

0.0126

Peptide disulfide oxidoreductase activity

0.0031

Proteasomal ubiquitin-independent protein catabolic process

4.16E−08

S100 protein binding

0.0041

Modulation of age-related behavioral decline

0.0033

Fibroblast growth factor binding

0.0136

Negative regulation of dendritic cell apoptotic process

0.0224

Low-density lipoprotein particle receptor binding

0.0153

 Decreased

Hydroxylysine biosynthetic process

0.0235

Heparan sulfate proteoglycan binding

0.0021

Gonadotrophin-releasing hormone neuronal migration to the hypothalamus

0.0345

CXCR chemokine receptor binding

0.0478

Positive regulation of cell proliferation by vegf-activated platelet-derived growth factor receptor signaling pathway

0.0345

Fibronectin binding

0.0088

Formaldehyde catabolic process

0.0345

Extracellular matrix structural constituent conferring tensile strength

0.0096

Facioacoustic ganglion development

0.0345

Laminin binding

0.0105