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Table 2 Combinatorial relations of enrichment information in 128 reduced functional classes of GBM data

From: MGSEA – a multivariate Gene set enrichment analysis

Combinatorial Pattern Gene set
CNV MET MRNA CNV and MET MET and MRNA CNV and MRNA CNV and MET and MRNA
0 0 1 0 0 0 0 Actin based cell projection, Actin cytoskeleton, Antigen processing and presentation, Apoptotic signaling pathway, Bone development, Carbohydrate derivative catabolic process, Cell cycle arrest, Cell growth, Cell junction assembly, Cell substrate adhesion, Cell substrate junction, Cellular response to external stimulus, Cellular response to nitrogen compound, Coated vesicle, Covalent chromatin modification, Cytoplasmic side of membrane, Endocytosis, Endoplasmic reticulum lumen, Interaction with host, Membrane organization, Morphogenesis of a branching structure, Negative regulation of transferase activity, Organelle localization, Organic acid biosynthetic process, Poly a RNA binding, Positive regulation of cell proliferation, Positive regulation of cytoplasmic transport, Protein autophosphorylation, Protein dephosphorylation, Protein heterodimerization activity, Regulation of cell activation, Regulation of ossification, Regulation of peptide secretion, Regulation of protein stability, Regulation of synapse organization, Regulation of synaptic plasticity, Response to carbohydrate, Response to temperature stimulus, Second messenger mediated signaling, Somatodendritic compartment, Telencephalon development, Transferase activity transferring glycosyl groups, Transmembrane receptor protein tyrosine kinase signaling pathway, Tubulin binding, Ubiquitin like protein ligase binding, Vacuolar lumen, Vesicle membrane, Vesicle organization, Wound healing, Actin filament based process, Aging, Autophagy, Binding bridging, Biological adhesion, Calmodulin binding, Carbohydrate binding, Cell activation, Cell adhesion molecule binding, Cell body, Cell cortex, Cell death, Cell junction, Cell junction organization, Cell leading edge, Cell projection, Cell surface, Chromatin modification, Circulatory system development, Connective tissue development, Cysteine type peptidase activity, Cytokine production, Cytoplasmic region, Cytoskeletal protein binding, Endomembrane system organization, Enzyme binding, Excitatory synapse, Extracellular matrix component, Extracellular structure organization, Glycosaminoglycan binding, Growth, Growth factor binding, Homeostasis of number of cells, Identical protein binding, Immune system process, Kinase regulator activity, Locomotion, Macromolecular complex binding, Movement of cell or subcellular component, Multicellular organism metabolic process, Nuclear body, Organelle subcompartment, Ossification, Perinuclear region of cytoplasm, Plasma membrane organization, Positive regulation of proteolysis, Posttranscriptional regulation of gene expression, Protein complex binding, Protein dimerization activity, Protein domain specific binding, Protein folding, Receptor binding, Receptor complex, Receptor signaling protein activity, Regeneration, Regulation of autophagy, Regulation of gene expression epigenetic, Regulation of reactive oxygen species metabolic process, Regulation of stem cell differentiation, Regulation of synapse structure or activity, Respiratory system development, Response to biotic stimulus, Response to transition metal nanoparticle, Sarcolemma, Sh3 domain binding, Side of membrane, Site of polarized growth, Sphingolipid metabolic process, Sulfur compound biosynthetic process, Sulfur compound metabolic process, Symporter activity, Trans Golgi network, Transcription coactivator activity, Ubiquitin ligase complex, Vacuole, Allograft rejection, Angiogenesis, Apical junction, Apical surface, Apoptosis, Cholesterol homeostasis, Coagulation, Complement, Epithelial mesenchymal transition, G2M checkpoint, Hedgehog signaling, Hypoxia, Il2 stat5 signaling, Il6 JAK STAT3 signaling, Inflammatory response, Interferon gamma response, KRAS signaling up, Mitotic spindle, Myogenesis, P53 pathway, TNFa signaling via NFkB, Unfolded protein response, UV response down
0 1 0 0 0 0 0 Anion transmembrane transport, Calcium ion transmembrane transporter activity, Cellular response to inorganic substance, Cilium, Epidermis development, Hindbrain development, Negative regulation of cell growth, Negative regulation of secretion, Nephron development, Post synapse, RAS guanyl nucleotide exchange factor activity, Regulation of lipid biosynthetic process, Regulation of muscle cell differentiation, Regulation of reproductive process, Response to ketone, Sensory perception of mechanical stimulus, Signaling receptor activity, Skeletal system morphogenesis, Ameboidal type cell migration, Amide biosynthetic process, Ammonium ion metabolic process, Anchored component of membrane, Cation channel complex, Cell maturation, G protein coupled receptor signaling pathway, Growth factor activity, GTPase binding, Intrinsic component of plasma membrane, Membrane protein complex, Membrane region, Mitochondrial transport, Multi multicellular organism process, Multicellular organismal signaling, Pattern specification process, Positive regulation of cell division, Regionalization, Regulation of camp metabolic process, Regulation of membrane potential, Regulation of transmembrane receptor protein serine threonine kinase signaling pathway, Response to estrogen, Response to light stimulus, Response to starvation, Stem cell differentiation, Structural molecule activity, Transporter complex, Urogenital system development, UV response up
0 1 1 0 1 0 0 Cell part morphogenesis, Cytokine receptor binding, Extrinsic component of plasma membrane, Inositol lipid mediated signaling, Negative regulation of nervous system development, Regulation of epithelial cell proliferation, Regulation of wound healing, Vasculature development, Extracellular matrix, Extrinsic component of membrane, Membrane microdomain, Peptidyl tyrosine modification, Positive regulation of peptidase activity, Protein tyrosine kinase activity, Regulation of chemotaxis, Regulation of extrinsic apoptotic signaling pathway, Regulation of receptor activity, Synapse organization, Interferon alpha response, Notch signaling, WNT beta catenin signaling
1 0 0 0 0 0 0 Cell cycle phase transition, Chromosomal region, Circadian rhythm, Hexose metabolic process, MRNA metabolic process, Negative regulation of cellular catabolic process, Negative regulation of hydrolase activity, Peptidase inhibitor activity, Positive regulation of DNA metabolic process, Positive regulation of homeostatic process, Regulation of cation transmembrane transport, Regulation of protein modification by small protein conjugation or removal, Regulatory region nucleic acid binding, RNA splicing via transesterification reactions, Sex differentiation, Adenylate cyclase modulating g protein coupled receptor signaling pathway, B cell activation, Coenzyme metabolic process, Cofactor metabolic process, Cytosolic part, Endocrine system development, Hemostasis, Hepaticobiliary system development, Hormone metabolic process, Hormone receptor binding, Iron ion binding, Lipid localization, Metallopeptidase activity, Methylation, ncRNA metabolic process, Nucleic acid binding transcription factor activity, Organic hydroxy compound biosynthetic process, Oxidoreductase activity acting on paired donors with incorporation or reduction of molecular oxygen, Positive regulation of WNT signaling pathway, RAS protein signal transduction, Response to calcium ion, Response to drug, Rhythmic process, Tetrapyrrole binding, Transcription factor complex, Transferase activity transferring acyl groups, Transferase complex transferring phosphorus containing groups, Bile acid metabolism, Protein secretion
1 0 1 0 0 1 0 Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains, Positive regulation of binding, Regulation of endocytosis, Negative regulation of cell-cell adhesion, Negative regulation of cellular response to growth factor stimulus, Phosphatase binding, Regulation of leukocyte proliferation
1 1 0 1 0 0 0 Cell fate commitment, G protein coupled receptor signaling pathway coupled to cyclic nucleotide second messenger, Mesenchymal cell differentiation, Negative regulation of canonical WNT signaling pathway
1 1 1 1 1 1 1 Pancreas beta cells, TGF beta signaling