Skip to main content

Table 1 Combinatorial relations of enrichment information in 126 reduced functional classes of breast cancer 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 Carbohydrate biosynthetic process, Cellular response to DNA damage stimulus, Chromatin remodeling, Chromosome, Chromosome organization, DNA recombination, Epidermis development, Extracellular matrix, Heparin binding, Microtubule based movement, Morphogenesis of a branching structure, Nuclear chromosome segregation, Organic acid catabolic process, Pallium development, Positive regulation of growth, Regulation of neuron apoptotic process, Regulation of protein complex disassembly, Response to purine containing compound, Response to radiation, Second messenger mediated signaling, Sex differentiation, Signal release, Supramolecular fiber, Tubulin binding, Aminoglycan metabolic process, Anatomical structure homeostasis, Apical plasma membrane,Cell cycle, Cell division, Cell proliferation, Cellular response to acid chemical, Chromosome segregation, Digestive system development, DNA metabolic process, Gland development, Growth, Lyase activity, Mammary gland development, Microtubule based process, Midbody, Negative regulation of locomotion, Nuclear membrane, Organelle localization, Ossification, Protein homodimerization activity, Regulation of cell division, Regulation of ligase activity, Regulation of neurotransmitter levels, Regulation of ossification, Regulation of transmembrane receptor protein serine threonine kinase signaling pathway, Response to drug, Response to ketone, Response to toxic substance, Response to transition metal nanoparticle, Stem cell differentiation, Tube development, Apical surface, DNA repair, E2F targets, Estrogen response early, Estrogen response late, Fatty acid metabolism, G2M checkpoint, Glycolysis, Hedgehog signaling, Hypoxia, Mitotic spindle, MTORC1 signaling, MYC targets v1,MYC targets v2,Peroxisome, Spermatogenesis
0 1 0 0 0 0 0 Apoptotic signaling pathway, Cell substrate adhesion, Central nervous system neuron differentiation, Core promoter binding, ER to Golgi vesicle mediated transport, Interaction with host, Macromolecular complex disassembly, Negative regulation of phosphorylation, Peptidase inhibitor activity, Peptidyl Serine modification, Protein catabolic process, RAS protein signal transduction, Regulation of binding, Regulation of protein import, Response to carbohydrate, Response to endoplasmic reticulum stress, Small molecule biosynthetic process, Transcription corepressor activity, Transferase complex, Ubiquitin like protein ligase binding, WNT signaling pathway, Actin filament organization, Aging, Binding bridging, Cell cortex, Cell junction assembly, Cell junction organization, Cellular carbohydrate metabolic process, Cellular component disassembly, Cellular response to abiotic stimulus, Coenzyme binding, Cofactor binding, Cytoplasmic region, Energy derivation by oxidation of organic compounds, Establishment or maintenance of cell polarity, Heart morphogenesis, Hormone receptor binding, In utero embryonic development, Ligase activity, Lytic vacuole membrane, Macromolecule methylation, Mitochondrial matrix, Myelin sheath, Placenta development, Protein folding, Protein stabilization, Regulation of autophagy, Regulation of gene expression epigenetic, Regulation of protein stability, Regulation of response to extracellular stimulus, Regulatory region nucleic acid binding, RNA splicing, Transcription factor activity protein binding, Transcription factor binding, Transcription factor complex, Ubiquitin like protein transferase activity, Vacuole organization, Adipogenesis, Angiogenesis, Cholesterol homeostasis, Coagulation, Complement, Oxidative phosphorylation, TGF beta signaling, Unfolded protein response
0 1 1 0 1 0 0 Positive regulation of apoptotic signaling pathway, Magnesium ion binding, Negative regulation of protein serine threonine kinase activity, Positive regulation of cellular protein localization, Signal transduction by p53 class mediator, Telencephalon development, Notch signaling
1 0 0 0 0 0 0 Adaptive immune response, Anion transport, Cell-cell adhesion via plasma membrane adhesion molecules, Clathrin coated vesicle, Cognition, Excitatory synapse, Formation of primary germ layer, Growth factor receptor binding, GTPase activity, Hormone mediated signaling pathway, Muscle cell differentiation, Organic acid transmembrane transporter activity, Organic cyclic compound catabolic process, RAS guanyl nucleotide exchange factor activity, Regulation of body fluid levels, Regulation of cytokine production, Regulation of ion homeostasis, Regulation of stat cascade, Ribosome biogenesis, Transcriptional repressor activity RNA polymerase II transcription regulatory region sequence specific binding, Wound healing, Anterior posterior pattern specification, Cardiac chamber development, Cation channel complex, Cell activation, Cell adhesion molecule binding, Cell-cell signaling, Cell fate commitment, Cell junction, Cytosolic transport, G protein coupled receptor signaling pathway coupled to cyclic nucleotide second messenger, Intermediate filament cytoskeleton, Multi organism reproductive process, Muscle structure development, Muscle tissue development, Negative regulation of response to external stimulus, Organic acid transport, Receptor complex, Regulation of response to biotic stimulus, Regulation of transporter activity, Respiratory system development, Ribosome, rRNA metabolic process, Single organism behavior, Site of polarized growth, Skeletal system development, Synaptic signaling, Transmembrane receptor protein serine threonine kinase signaling pathway, Transporter complex, Androgen response, Epithelial mesenchymal transition, Il6 JAK STAT3 signaling, Pancreas beta cells, Reactive oxygen species pathway
1 0 1 0 0 1 0 Kidney epithelium development, Meiotic cell cycle process, Response to alcohol, Voltage gated ion channel activity, Lipid modification, Nuclear periphery, Positive regulation of cell division, Potassium ion transport, Regulation of organ morphogenesis, Urogenital system development, Bile acid metabolism
1 1 0 1 0 0 0 Core promoter proximal region DNA binding, Response to nutrient, RNA polymerase II transcription factor activity sequence specific DNA binding