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Table 3 Exclusive gene ontology terms of demethylated gene promoters at late passages of hBM-MSCs

From: From cytogenomic to epigenomic profiles: monitoring the biologic behavior of in vitro cultured human bone marrow mesenchymal stem cells

Category GO terms
Development and differentiation GO:0007275 multicellular organismal development
  GO:0048468 cell differentiation/cell development
  GO:0007399 nervous system development
  GO:0032501 multicellular organismal process
  GO:0009887 multicellular organismal development/system development/organ development/organ morphogenesis
  GO:0030182 generation of neurons/neuron differentiation
  GO:0048699 generation of neurons
  GO:0022008 nervous system development/neurogenesis
  GO:0009790 multicellular organismal development/embryonic development
  GO:0048598 multicellular organismal development/embryonic development/embryonic morphogenesis
  GO:0048666 generation of neurons/neuron differentiation/neuron development
  GO:0009880 embryonic pattern specification
  GO:0048646 anatomic structure morphogenesis/anatomic structure formation
  GO:0000904 cell differentiation/cell development/cellular morphogenesis during differentiation
  GO:0031175 generation of neurons/neuron differentiation/neuron development/neurite development
  GO:0045597 positive regulation of cell differentiation
  GO:0048667 generation of neurons/neuron differentiation/neuron development/neuron morphogenesis during differentiation
  GO:0048812 generation of neurons/neuron differentiation/neuron development/neuron morphogenesis during differentiation/neurite morphogenesis
  GO:0007389 multicellular organismal development/pattern-specification process
  GO:0007417 nervous system development/central nervous system development
  GO:0045165 cell differentiation/cell-fate commitment
Metabolic process GO:0016071 mRNA metabolic process
  GO:0009056 catabolic process
  GO:0044248 cellular catabolic process
  GO:0043285 biopolymer catabolic process
  GO:0006401 RNA catabolic process
  GO:0007005 mitochondrion organization and biogenesis
  GO:0009057 macromolecule catabolic process
  GO:0007584 response to nutrient
  GO:0016072 rRNA metabolic process
  GO:0031667 response to nutrient levels
  GO:0009310 amine catabolic process
  GO:0030163 protein catabolic process
  GO:0044270 nitrogen compound catabolic process
  GO:0044265 cellular macromolecule catabolic process
  GO:0006839 mitochondrial transport
  GO:0048878 chemical homeostasis
  GO:0009063 amino acid catabolic process
  GO:0045792 negative regulation of cell size
Cell cycle and growth GO:0042127 regulation of cell proliferation
  GO:0045786 negative regulation of progression through cell cycle
  GO:0007088 regulation of mitosis
  GO:0000082 G1/S transition of mitotic cell cycle
  GO:0051329 interphase of mitotic cell cycle
  GO:0051325 interphase
  GO:0030308 negative regulation of cell growth
Cell signaling GO:0007242 intracellular signaling cascade
  GO:0007169 transmembrane receptor protein tyrosine kinase signaling pathway
  GO:0048015 phosphoinositide-mediated signaling
  GO:0019932 second-messenger-mediated signaling
  GO:0045859 regulation of protein kinase activity
  GO:0043085 positive regulation of catalytic activity
  GO:0007167 enzyme-linked receptor protein signaling pathway
  GO:0007219 Notch signaling pathway
  GO:0045860 positive regulation of protein kinase activity
  GO:0033674 positive regulation of kinase activity
  GO:0007243 protein kinase cascade
  GO:0007200 G-protein signaling, coupled to IP3 second messenger (phospholipase C activating)
  GO:0000079 regulation of cyclin-dependent protein kinase activity
  GO:0007165 signal transduction
  GO:0043549 regulation of kinase activity
Apoptosis and cell death GO:0008219 cell death
  GO:0016265 death
  GO:0006915 apoptosis
  GO:0043067 programmed cell death/regulation of programmed cell death
  GO:0043069 negative regulation of programmed cell death
  GO:0042981 regulation of apoptosis
  GO:0043066 negative regulation of apoptosis
  GO:0008632 apoptosis/apoptotic program
  GO:0006916 antiapoptosis
  GO:0043068 positive regulation of programmed cell death
  GO:0012501 programmed cell death
  GO:0012502 induction of programmed cell death
Gene expression GO:0010467 gene expression
  GO:0006396 RNA processing
  GO:0006397 mRNA processing
  GO:0008380 RNA splicing
  GO:0006364 rRNA processing
  GO:0040029 regulation of gene expression, epigenetic
  GO:0000377 RNA splicing, via transesterification reactions with bulged adenosine as nucleophile
  GO:0000398 nuclear mRNA splicing, via spliceosome
  GO:0000375 RNA splicing, via transesterification reactions
Response to stimulus GO:0042221 response to chemical stimulus
  GO:0006950 response to stress
  GO:0009605 response to external stimulus
  GO:0009991 response to extracellular stimulus;
  GO:0006955 immune response
  GO:0010035 response to inorganic substance
  GO:0009628 response to abiotic stimulus
  GO:0042060 wound healing
Exclusive GO terms of methylated gene promoters at LATE passages of hBM-MSCs
Category GO term
Development and differentiation GO:0016043 cellular component organization and biogenesis
  GO:0008361 cell morphogenesis/regulation of cell size
  GO:0007276 gamete generation
  GO:0007283 spermatogenesis
  GO:0048232 male gamete generation
Metabolic process GO:0006512 ubiquitin cycle
  GO:0031323 regulation of cellular metabolic process
  GO:0044255 cellular lipid metabolic process
  GO:0006629 lipid metabolic process
  GO:0006631 fatty acid metabolic process
  GO:0032787 monocarboxylic acid metabolic process
  GO:0043412 biopolymer modification
  GO:0006464 protein modification process
  GO:0043687 posttranslational protein modification
  GO:0008610 lipid biosynthetic process
Cell cycle and growth GO:0000075 cell-cycle checkpoint
  GO:0016049 cell growth
  GO:0040008 growth/regulation of growth
  GO:0001558 regulation of cell growth
Response to stimulus GO:0006974 response to DNA-damage stimulus
  GO:0006281 DNA repair
  1. GO, gene ontology.