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

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