Table 4 Annotated functions of ten most downregulated genes by ginsenoside

WSB1

Phosphorylation, protein ubiquitination, intracellular signal transduction

Intracellular

Protein binding, kinase activity

PSME4

MAPK cascade, activation of MAPKK activity, protein polyubiquitination, mitotic cell cycle, stimulatory C-type lectin receptor signaling pathway, antigen processing and presentation of peptide antigen via MHC class I, antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent, DNA repair, regulation of cellular amino acid metabolic process, polyamine metabolic process, apoptotic process, cellular response to DNA damage stimulus, DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest, epidermal growth factor receptor signaling pathway, small GTPase mediated signal transduction, Ras protein signal transduction, multicellular organismal development, spermatogenesis, axon guidance, insulin receptor signaling pathway, fibroblast growth factor receptor signaling pathway, gene expression, proteasomal ubiquitin-independent protein catabolic process, positive regulation of peptidase activity, programmed cell death, viral process, cell differentiation, anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process, tumor necrosis factor-mediated signaling pathway, cellular nitrogen compound metabolic process, spermatogenesis, exchange of chromosomal proteins, NIK/NF-kappaB signaling, Fc-epsilon receptor signaling pathway, antigen processing and presentation of exogenous peptide antigen via MHC class I, regulation of apoptotic process, negative regulation of apoptotic process, regulation of mRNA stability, small molecule metabolic process, innate immune response, vascular endothelial growth factor receptor signaling pathway, neurotrophin TRK receptor signaling pathway, T cell receptor signaling pathway, positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition, regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle, negative and positive regulation of canonical Wnt signaling pathway

Proteasome complex, nucleus, cytoplasm, cytosol, spermatoproteasome complex

Protein binding, peptidase activator activity, lysine-acetylated histone binding

DCAF7

Multicellular organismal development, protein ubiquitination, protein ubiquitination

Nucleus, cytoplasm, cytoplasm, nuclear matrix, protein complex, Cul4-RING E3 ubiquitin ligase complex

Protein binding

ETV1

Transcription, regulation of transcription, transcription from RNA polymerase, axon guidance, muscle organ development, mechanosensory behavior, cell differentiation, positive regulation of transcription, positive regulation of transcription from RNA polymerase II promoter, peripheral nervous system neuron development

Nucleus

RNA polymerase II core promoter proximal region sequence-specific DNA binding, transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding, DNA binding, transcription factor activity, sequence-specific DNA binding, protein binding, sequence-specific DNA binding

SMAD5

Ossification, ureteric bud development, Mullerian duct regression, osteoblast fate commitment, transcription, regulation of transcription, protein phosphorylation, signal transduction, transforming growth factor beta receptor signaling pathway, germ cell development, embryonic pattern specification, erythrocyte differentiation, BMP signaling pathway, intracellular signal transduction, positive regulation of osteoblast differentiation, positive regulation of transcription, positive regulation of transcription from RNA polymerase II promoter, cartilage development, cardiac muscle contraction, bone development, SMAD protein signal transduction, cellular response to organic cyclic compound, cellular response to BMP stimulus, positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus

Intracellular, nucleus, nucleoplasm, nucleoplasm, transcription factor complex, cytoplasm, cytosol, integral component of membrane, protein complex, SMAD protein complex

RNA polymerase II core promoter sequence-specific DNA binding, DNA binding, transcription factor activity, sequence-specific DNA binding, receptor signaling protein activity, protein binding, transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity, ubiquitin protein ligase binding, metal ion binding

DMXL2

–

Extracellular space, synaptic vesicle, membrane, cell junction, synaptic vesicle membrane, cytoplasmic vesicle, synapse

Protein binding, Rab GTPase binding

CD47

Cell adhesion, integrin-mediated signaling pathway, blood coagulation, opsonization, positive regulation of cell proliferation, response to bacterium, positive regulation of cell-cell adhesion, extracellular matrix organization, positive regulation of inflammatory response, positive regulation of phagocytosis, positive regulation of T cell activation, leukocyte migration

Plasma membrane, integral component of plasma membrane, membrane, integral component of membrane, extracellular exosome

protein binding, thrombospondin receptor activity

GIT2

Regulation of G-protein coupled receptor protein signaling pathway, phosphorylation, positive regulation of GTPase activity, behavioral response to pain

Nucleoplasm, focal adhesion

GTPase activator activity, protein binding, kinase activity, protein complex binding, metal ion binding

SCRN1

Proteolysis, exocytosis

Cell, nucleus, cytoplasm, nuclear membrane

Protein binding, dipeptidase activity

NCOR1

Negative regulation of transcription from RNA polymerase II promoter, regulation of thyroid hormone mediated signaling pathway, CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation, chromatin organization, regulation of transcription, transcription initiation from RNA polymerase II promoter, transforming growth factor beta receptor signaling pathway, Notch signaling pathway, circadian rhythm, gene expression, negative regulation of phosphatidylinositol 3-kinase signaling, chromatin modification, thalamus development, positive regulation of histone deacetylation, circadian regulation of gene expression, regulation of multicellular organism growth, cholesterol homeostasis, cellular lipid metabolic process, small molecule metabolic process, negative regulation of JNK cascade, spindle assembly, definitive erythrocyte differentiation, regulation of glycolytic process, regulation of lipid transport, cellular response to thyroglobulin triiodothyronine, regulation of fatty acid transport

Histone deacetylase complex, nuclear chromatin, nucleus, nucleoplasm, transcription factor complex, cytoplasm, spindle microtubule, membrane, Sin3 complex, transcriptional repressor complex

RNA polymerase II activating transcription factor binding, DNA binding, chromatin binding, transcription factor activity, transcription corepressor activity, protein binding, ligand-dependent nuclear receptor binding, histone deacetylase regulator activity, nuclear hormone receptor binding, histone deacetylase binding, retinoic acid receptor binding, sequence-specific DNA binding, transcription regulatory region DNA binding, retinoid X receptor binding, thyroid hormone receptor binding