Fibroblasts: gene co-expression modules

Mesenchymal stromal cells producing collagen and matrix; they define tissue architecture, supply niche factors to epithelium and immune cells, and drive fibrosis when chronically activated.

SCUBA's reference network for Fibroblasts holds 129 gene modules covering 1,785 genes. Each module is a group of genes that rise and fall together across these cells, annotated with the biological process it most likely represents.

View the Fibroblasts network in SCUBA

Cytoskeletal (8)

• Actin Cytoskeletal Organization · 17 genes
• Actin Cytoskeleton · 15 genes
• Caveolae Mechanosensing · 19 genes
• Myofibroblast Contractile · 16 genes
• Rho GTPase Cytoskeletal · 11 genes
• Rho-ROCK Contractility · 10 genes
• Smooth Muscle Identity · 21 genes
• WAVE-RAC1 Actin · 10 genes

Developmental (26)

• Adventitial Fibroblast State · 18 genes
• BMP Developmental Identity · 12 genes
• BMP-antagonizing Fibroblast · 10 genes
• BMP-Wnt Fibroblast Program · 9 genes
• BMP-Wnt Niche Signaling · 17 genes
• Chromatin Transcriptional Regulation · 13 genes
• Fibroblast Niche Identity · 19 genes
• Intestinal Fibroblast Identity · 16 genes
• Neural-crest Fibroblast · 17 genes
• Notch Fibroblast Activation · 11 genes
• OSR1+ Deep Fibroblast · 14 genes
• Quiescent Anti-inflammatory Fibroblast · 12 genes
• Quiescent Stromal Identity · 10 genes
• Retinoid Stromal Quiescence · 14 genes
• Smooth Muscle Differentiation · 9 genes
• Stromal Niche Identity · 8 genes
• Stromal Niche Signaling · 16 genes
• Subepithelial Fibroblast · 17 genes
• Subepithelial Fibroblast Identity · 21 genes
• Submucosal Fibroblast · 18 genes
• Telocyte Identity Program · 19 genes
• Wnt-BMP Fibroblast · 14 genes
• WNT-modulating Fibroblast · 18 genes
• Wnt-Niche Fibroblast · 19 genes
• Wnt-niche Fibroblast · 14 genes
• WNT4+ Stromal Fibroblast · 16 genes

ECM production (16)

• ASPN+ Submucosal Fibroblast · 14 genes
• Basement Membrane ECM · 11 genes
• CCL11 Secretory Fibroblast · 14 genes
• CD34+ Quiescent Fibroblast · 17 genes
• COL13A1+ Deep Fibroblast · 15 genes
• Collagen ECM Production · 21 genes
• Elastic Fiber ECM · 9 genes
• Elastin-Fibronectin ECM · 9 genes
• Homeostatic Fibroblast Identity · 15 genes
• Homeostatic Stromal Identity · 13 genes
• Lamina Propria ECM · 23 genes
• Microfibril ECM Fibroblast · 11 genes
• PI16+ Fibroblast Identity · 19 genes
• TGF-beta ECM Regulation · 9 genes
• TGF-beta Fibroblast Niche · 17 genes
• TGF-beta Fibrosis · 8 genes

ECM remodeling (10)

• BMP-ECM Fibroblast · 8 genes
• ECM Glycan Remodeling · 12 genes
• ECM Homeostasis · 9 genes
• Heparan Sulfate Remodeling · 20 genes
• Inflammation-activated ECM · 11 genes
• Inflammatory ECM Remodeling · 14 genes
• MMP-driven Fibroblast Remodeling · 13 genes
• Proteolytic Fibroblast State · 12 genes
• Stromal Fibroblast Activation · 8 genes
• TGF-beta Response · 16 genes

Gut motility (4)

• ICC contractility · 16 genes
• ICC electrophysiological machinery · 14 genes
• ICC neuromuscular junction · 15 genes
• ICC niche interactaion · 19 genes

Housekeeping (14)

• Co-transcriptional RNA Processing · 8 genes
• Cullin-RING Ubiquitin Ligase · 12 genes
• CYGB+ Quiescent Fibroblast · 14 genes
• ER Protein Folding · 19 genes
• ER Secretory Processing · 11 genes
• Fibroblast Quiescence · 14 genes
• General Housekeeping · 13 genes
• Homeostatic Fibroblast State · 14 genes
• Metabolic Homeostasis · 13 genes
• Proteasome & OxPhos · 18 genes
• Proteasome Assembly · 13 genes
• Proteasome Biogenesis · 10 genes
• Ribosome Biogenesis · 10 genes
• Translation Initiation · 12 genes

Immune interaction (2)

• Complement-secreting Fibroblast · 18 genes
• FRC function · 12 genes

Inflammatory (24)

• AP-1 Inflammatory Stress · 10 genes
• Chemokine-secreting Fibroblasts · 19 genes
• Complement-producing Fibroblast · 17 genes
• Cytokine Chemokine Secretion · 10 genes
• Cytokine Inflammatory Response · 13 genes
• IFN-γ MHC-II Response · 12 genes
• IL-1 Receptor Signaling · 9 genes
• Immunoproteasome MHC-I · 16 genes
• Inflammatory Fibroblast Activation · 13 genes
• Inflammatory Fibroblast Activation · 13 genes
• Inflammatory Fibroblast Activation · 8 genes
• Inflammatory Fibroblast Activation · 14 genes
• Inflammatory Fibroblast Activation · 20 genes
• Inflammatory TF Response · 11 genes
• Interferon Response · 14 genes
• NF-κB Epigenetic Reprogramming · 12 genes
• NF-κB Immediate Early · 13 genes
• NF-κB Inflammatory Activation · 14 genes
• NF-κB Stress Response · 12 genes
• NFAT-cAMP Signaling · 12 genes
• OSM Cytokine Response · 8 genes
• Thrombin Receptor Signaling · 19 genes
• Type I Interferon · 15 genes
• Type I Interferon · 11 genes

Migration & adhesion (4)

• Actin-Integrin Adhesion · 14 genes
• Caveolae Mechanosensing · 15 genes
• Focal Adhesion ECM · 15 genes
• Pericyte-like Fibroblast · 16 genes

Mitochondrial & OxPhos (3)

• Mitochondrial Energy Metabolism · 9 genes
• Mitochondrial OXPHOS · 10 genes
• Mitochondrial OxPhos · 15 genes

Stress (10)

• BMP-ID Stress Response · 18 genes
• ER Stress UPR · 15 genes
• Heat Shock Response · 14 genes
• Hypoxia Metabolic Stress · 12 genes
• Hypoxia Response · 17 genes
• Hypoxia-driven EMT · 16 genes
• Integrated Stress Response · 18 genes
• Lysosomal Stress Response · 12 genes
• Proteotoxic Stress Survival · 9 genes
• Unfolded Protein Response · 14 genes

Vesicular traficking (5)

• ER Protein Processing · 14 genes
• ER-Golgi Trafficking · 15 genes
• ER-Golgi Trafficking · 15 genes
• Lysosomal Biogenesis · 14 genes
• Lysosomal Cytoskeletal · 10 genes

Wound healing (3)

• Activated Myofibroblast State · 16 genes
• Myofibroblast Subtype · 9 genes
• Repair Cytokine Secretion · 15 genes