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Table 3 Annotated functions of ten most upregulated genes by ginsenoside

From: Ginsenosides induce extensive changes in gene expression and inhibit oxidative stress-induced apoptosis in human lens epithelial cells

Gene SymbolBiological ProcessCellular ComponentMolecular Function
FOXN2Transcription, regulation of transcription, skeletal muscle cell differentiationNucleus, nucleoplasm, intracellular membrane-bounded organelleDNA binding, transcription factor activity, sequence-specific DNA binding
APPResponse to yeast, suckling behavior, platelet degranulation, mRNA polyadenylation, regulation of translation, protein phosphorylation, proteolysis, cellular copper ion homeostasis, post-Golgi vesicle-mediated transport, endocytosis, apoptotic process, response to oxidative stress, cell adhesion, regulation of epidermal growth factor-activated receptor activity, Notch signaling pathway, nervous system development, axonogenesis, blood coagulation, mating behavior, locomotory behavior, axon cargo transport, cholesterol metabolic process, adult locomotory behavior, visual learning, negative regulation of peptidase activity, regulation of gene expression, negative regulation of endopeptidase activity, positive regulation of G2/M transition of mitotic cell cycle, axon midline choice point recognition, neuron remodeling, dendrite development, antibacterial humoral response, antifungal humoral response, platelet activation, extracellular matrix organization, forebrain development, neuron projection development, ionotropic glutamate receptor signaling pathway, nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway, regulation of multicellular organism growth, regulation of protein binding, cellular protein metabolic process, innate immune response, negative regulation of neuron differentiation, positive regulation of mitotic cell cycle, positive regulation of transcription from RNA polymerase II promoter, collateral sprouting in absence of injury, regulation of synapse structure or activity, defense response to Gram-negative and Gram-positive bacterium, neuromuscular process controlling balance, synaptic growth at neuromuscular junction, neuron apoptotic process, smooth endoplasmic reticulum calcium ion homeostasis, membrane organizationExtracellular region, extracellular space, nuclear envelope lumen, cytoplasm, endosome, smooth endoplasmic reticulum, Golgi apparatus, cytosol, plasma membrane, coated pit, cell-cell junction, cell surface, membrane, ER to Golgi transport vesicle, axon, platelet alpha granule lumen, cytoplasmic vesicle, neuromuscular junction, endosome lumen, trans-Golgi network membrane, ciliary rootlet, neuron projection, terminal bouton, dendritic spine, dendritic shaft, intracellular membrane-bounded organelle, receptor complex, membrane raft, apical part of cell, synapse, spindle midzone, extracellular exosomeDNA binding, serine-type endopeptidase inhibitor activity, receptor binding, protein binding, heparin binding, peptidase activity, peptidase activator activity, enzyme binding, peptidase inhibitor activity, acetylcholine receptor binding, metal ion binding, PTB domain binding, growth factor receptor binding,
RAD23BNucleotide-excision repair, DNA damage recognition, spermatogenesis, regulation of proteasomal ubiquitin-dependent protein catabolic processProteasome complex, nucleus, nucleoplasm, cytoplasm, XPC complexDamaged DNA binding, single-stranded DNA binding, protein binding, polyubiquitin binding
LMNB1Apoptotic process, cellular component disassembly involved in execution phase of apoptosis, programmed cell deathNucleus, nuclear envelope, nuclear inner membrane, lamin filament, nucleoplasm, intermediate filament, membrane, nuclear matrix, nuclear membraneStructural molecule activity, phospholipase binding
MAPK8MAPK cascade, ossification, neuron migration, toll-like receptor signaling pathway, MyD88-dependent toll-like receptor signaling pathway, DNA repair, protein phosphorylation, apoptotic process, response to stress, JNK cascade, JUN phosphorylation, response to UV, regulation of gene expression, positive regulation of gene expression, programmed cell death, phosphorylation, peptidyl-serine phosphorylation, peptidyl-threonine phosphorylation, regulation of histone deacetylation, positive regulation of cyclase activity, negative regulation of protein binding, regulation of protein localization, toll-like receptor 2, 3, 4, 5, 9, and 10 signaling pathway, TRIF-dependent toll-like receptor signaling pathway, Fc-epsilon receptor signaling pathway, toll-like receptor TLR1:TLR2 and TLR6:TLR2 signaling pathway, regulation of circadian rhythm, positive and negative regulation of apoptotic process, innate immune response, response to cadmium ion, neurotrophin TRK receptor signaling pathway, rhythmic process, dendrite morphogenesis, regulation of sequence-specific DNA binding transcription factor activity, positive regulation of protein metabolic process, stress-activated MAPK cascade, cellular response to hydrogen peroxide, lipopolysaccharide, mechanical stimulus, and nitric oxide, positive regulation of deacetylase activity, apoptotic signaling pathway, intrinsic apoptotic signaling pathway, programmed necrotic cell death, positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway, positive regulation of determination of dorsal identityIntracellular, nucleus, nucleoplasm, cytoplasm, mitochondrion, cytosolNucleotide binding, protein kinase activity, protein serine/threonine kinase activity, JUN kinase activity, MAP kinase activity, protein binding, ATP binding, kinase activity, transferase activity, transferring phosphorus-containing groups, enzyme binding, histone deacetylase regulator activity, histone deacetylase binding
FBXL17Protein ubiquitination, SCF-dependent proteasomal ubiquitin-dependent protein catabolic processCytoplasm, SCF ubiquitin ligase complexProtein binding, ubiquitin protein ligase activity
TLK2Regulation of chromatin assembly or disassembly, protein phosphorylation, cellular response to DNA damage stimulus, cell cycle, chromosome segregation, negative regulation of autophagy, phosphorylation, chromatin modification, peptidyl-serine phosphorylation, negative regulation of proteasomal ubiquitin-dependent protein catabolic process, intracellular signal transduction, cellular response to gamma radiationNucleus, cytoplasm, cytoskeleton, intermediate filament, cell junction, perinuclear region of cytoplasmNucleotide binding, protein kinase activity, protein serine/threonine kinase activity, protein binding, ATP binding, kinase activity, transferase activity, transferring phosphorus-containing groups
PSD3Vesicle-mediated transport, neuron differentiation, regulation of ARF protein signal transduction, positive regulation of GTPase activityTrans-Golgi network, plasma membrane, postsynaptic density, membrane, cell junction, synapse, postsynaptic membraneGuanyl-nucleotide exchange factor activity, ARF guanyl-nucleotide exchange factor activity, phospholipid binding
LIMK1Protein phosphorylation, signal transduction, small GTPase mediated signal transduction, Rho protein signal transduction, nervous system development, axon guidance, actin cytoskeleton organization, positive regulation of actin filament bundle assembly, Fc-gamma receptor signaling pathway involved in phagocytosis, innate immune response, positive regulation of axon extension, ephrin receptor signaling pathway, negative regulation of ubiquitin-protein transferase activity, positive regulation of stress fiber assemblyNucleus, nucleoplasm, cytoplasm, cytosol, focal adhesion, membrane, neuron projectionNucleotide binding, protein kinase activity, protein serine/threonine kinase activity, protein binding, ATP binding, zinc ion binding, transferase activity, transferring phosphorus-containing groups, heat shock protein binding, metal ion binding, protein heterodimerization activity