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Table 3 Driving signatures and ontologies of gene clusters on different matrixes

From: Analysis of the interaction of extracellular matrix and phenotype of bladder cancer cells

Cluster Driving signature Ontology
Matrigel_1 J82 underexpressed negative regulation of biological process
Matrigel_2 JP underexpressed mRNA processing
Matrigel_3 HUC & JB overexpressed mismatch repair; transcription factor activity
Matrigel_4 HUC underexpressed anti-apoptosis; induction of apoptosis by extracellular signals; protein binding; protein serine/threonine kinase activity
Matrigel_5 JB underexpressed regulation of cyclin dependent protein kinase activity; mitotic control; negative regulation of cell proliferation
Matrigel_6 JB & J82 underexpressed  
Matrigel_7 J82 & JP overexpressed regulation of cyclin dependent protein kinase activity; anti-apoptosis; negative regulation of cell proliferation; positive regulation of cell proliferation; extracellular space
Plastic_1 JP underexpressed induction of apoptosis
Plastic_2 JP underexpressed
RT4 overexpressed
immune response
Plastic_3 TCCSUP & J82 overexpressed negative regulation of cell cycle
Plastic_4 TCCSUP underexpressed protein kinase cascade; meiotic recombination; cell cycle arrest; anti-apoptosis; induction of apoptosis by extracellular signals; protein ubiquitination; nucleotide-excision repair; protein binding; nucleus
Plastic_5   mitotic cell cycle; chromosome
Plastic_6 J82 underexpressed cell cycle arrest; nucleus
Plastic_7 HUC underexpressed negative regulation of cellular process; antioxidant activity; extracellular matrix
SISgel_1 J82 & JP overexpressed cell cycle; induction of apoptosis; extracellular matrix
SISgel_2 HUC underexpressed
J82 overexpressed
regulation of cell cycle; negative regulation of cell proliferation; inflammatory response
SISgel_3 JB underexpressed induction of apoptosis by extracellular signals; DNA replication; purine nucleotide biosynthesis; ligase activity, forming carbon-nitrogen bonds; cytoskeleton
SISgel_4 JB overexpressed  
SISgel_5 RT4 underexpressed negative regulation of cell cycle
SISgel_6 J82 underexpressed cell division; protein complex assembly