Table S5.
Top 200 biogroups modulated by decitabine (DAC) in H1299 cells
| H1299 cells treated with 3 μM DAC (48 hours)
| |||
|---|---|---|---|
| Biogroup name | Direction | P value | |
| Cofactor binding | down | 4.70E-12 | |
| Lipid metabolic process | down | 5.10E-12 | |
| Cell differentiation | up | 2.50E-08 | |
| Coenzyme binding | down | 3.70E-08 | |
| Transcription | up | 1.00E-07 | |
| Inner ear development | up | 2.20E-07 | |
| Cell fate determination | up | 2.50E-07 | |
| Fatty acid metabolic process | down | 2.90E-07 | |
| Collagen binding | up | 4.90E-07 | |
| Oxidoreductase activity, acting on the CH–OH group of donors, NAD or NADP as acceptor | down | 1.20E-06 | |
| Enzyme inhibitor activity | up | 1.30E-06 | |
| Nucleosome | up | 1.30E-06 | |
| Aldehyde metabolic process | down | 1.40E-06 | |
| Sensory organ development | up | 2.30E-06 | |
| Oxidoreductase activity, acting on CH–OH group of donors | down | 2.50E-06 | |
| Response to external stimulus | up | 2.80E-06 | |
| Hormone biosynthetic process | up | 3.00E-06 | |
| CoA–ligase activity | down | 4.00E-06 | |
| Insulin-like growth factor binding | up | 4.20E-06 | |
| Response to stress | up | 4.40E-06 | |
| Mitochondrion | down | 5.20E-06 | |
| Acid–thiol ligase activity | down | 6.30E-06 | |
| Proteinaceous extracellular matrix | up | 7.40E-06 | |
| Transcription repressor activity | up | 7.90E-06 | |
| Extracellular matrix | up | 8.60E-06 | |
| Muscle cell differentiation | up | 9.40E-06 | |
| Response to wounding | up | 9.50E-06 | |
| Alcohol metabolic process | down | 9.90E-06 | |
| Enzyme regulator activity | up | 9.90E-06 | |
| Neurotransmitter metabolic process | up | 1.00E-05 | |
| Muscle fiber development | up | 1.10E-05 | |
| Skeletal muscle fiber development | up | 1.10E-05 | |
| Peroxisome | down | 1.10E-05 | |
| Microbody | down | 1.10E-05 | |
| Ligase activity, forming carbon-sulfur bonds | down | 1.40E-05 | |
| Regulation of epidermis development | up | 2.00E-05 | |
| Cell fate commitment | up | 2.20E-05 | |
| Hormone metabolic process | up | 2.20E-05 | |
| Sterol metabolic process | down | 2.30E-05 | |
| Inflammatory response | up | 2.30E-05 | |
| Oxidoreductase activity, acting on the CH–CH group of donors, NAD or NADP as acceptor | down | 2.60E-05 | |
| Death | up | 3.20E-05 | |
| Cell death | up | 3.20E-05 | |
| Steroid metabolic process | down | 3.50E-05 | |
| Lipid biosynthetic process | down | 3.80E-05 | |
| Lyase activity | down | 4.10E-05 | |
| Glycosaminoglycan binding | up | 4.50E-05 | |
| Polysaccharide binding | up | 5.30E-05 | |
| Pyridoxal phosphate binding | down | 5.50E-05 | |
| Muscle development | up | 6.70E-05 | |
| Nitrogen compound biosynthetic process | down | 6.90E-05 | |
| Protease inhibitor activity | up | 7.60E-05 | |
| Endopeptidase inhibitor activity | up | 7.60E-05 | |
| Phosphatase activator activity | up | 8.00E-05 | |
| Phenol metabolic process | up | 8.40E-05 | |
| Epidermis development | up | 8.50E-05 | |
| Regulation of neurotransmitter levels | up | 9.20E-05 | |
| Pattern binding | up | 9.60E-05 | |
| Cofactor catabolic process | down | 9.80E-05 | |
| Positive regulation of developmental process | up | 1.00E-04 | |
| Vitamin binding | down | 0.0001 | |
| Oxidoreductase activity, acting on the CH–CH group of donors | down | 0.0001 | |
| Amino acid derivative metabolic process | up | 0.0001 | |
| Chromatin assembly | up | 0.0001 | |
| Protein–DNA complex assembly | up | 0.0001 | |
| Amino acid derivative biosynthetic process | up | 0.0001 | |
| Positive regulation of cell differentiation | up | 0.0001 | |
| Acute inflammatory response | up | 0.0001 | |
| Dopamine metabolic process | up | 0.0001 | |
| Growth factor binding | up | 0.0002 | |
| Endothelial cell development | down | 0.0002 | |
| Transcription corepressor activity | up | 0.0002 | |
| Keratinocyte differentiation | up | 0.0002 | |
| Ectoderm development | up | 0.0002 | |
| Cellular respiration | down | 0.0002 | |
| RNA polymerase II transcription elongation factor activity | up | 0.0002 | |
| Angiogenesis | up | 0.0003 | |
| Calcium-dependent phospholipid binding | down | 0.0003 | |
| Suckling behavior | down | 0.0003 | |
| Oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor | down | 0.0003 | |
| Germ-line sex determination | down | 0.0003 | |
| RNA polymerase II transcription factor activity | up | 0.0003 | |
| Protein kinase inhibitor activity | up | 0.0004 | |
| Translation activator activity | up | 0.0004 | |
| Regulation of Notch signaling pathway | up | 0.0004 | |
| Fatty acid biosynthetic process | down | 0.0004 | |
| Kinase inhibitor activity | up | 0.0004 | |
| Regulation of cell differentiation | up | 0.0004 | |
| ER-Golgi intermediate compartment | up | 0.0005 | |
| UDP-glycosyltransferase activity | down | 0.0005 | |
| Cell maturation | up | 0.0005 | |
| Cell surface | down | 0.0005 | |
| Inner ear receptor cell fate commitment | up | 0.0005 | |
| Organic acid biosynthetic process | down | 0.0005 | |
| Negative regulation of signal transduction | up | 0.0006 | |
| Hydro–Lyase activity | down | 0.0006 | |
| Epidermal cell differentiation | up | 0.0007 | |
| Inner ear morphogenesis | up | 0.0007 | |
| Regulation of cell growth | up | 0.0007 | |
| Response to bacterium | up | 0.0007 | |
| Blood vessel morphogenesis | up | 0.0007 | |
| Carbohydrate metabolic process | down | 0.0007 | |
| Lipoprotein binding | down | 0.0007 | |
| Multicellular organismal movement | down | 0.0008 | |
| Aromatic compound metabolic process | up | 0.0008 | |
| Amine biosynthetic process | down | 0.0008 | |
| tRNA binding | down | 0.0008 | |
| Cell migration | up | 0.0008 | |
| Transcription elongation factor complex | up | 0.0009 | |
| Glutathione peroxidase activity | up | 0.0009 | |
| Oxidoreductase activity, acting on the CH–NH group of donors, NAD or NADP as acceptor | down | 0.0009 | |
| Primary sex determination | down | 0.0009 | |
| Negative regulation of cell differentiation | up | 0.001 | |
| Defense response to bacterium | up | 0.001 | |
| Nuclear envelope | down | 0.001 | |
| Ear morphogenesis | up | 0.0011 | |
| Ligase activity, forming carbon–oxygen bonds | down | 0.0011 | |
| Ligase activity, forming aminoacyl–tRNA and related compounds | down | 0.0011 | |
| Generation of precursor metabolites and energy | down | 0.0011 | |
| Developmental maturation | up | 0.0011 | |
| Peripheral nervous system development | down | 0.0011 | |
| Extracellular matrix structural constituent | up | 0.0012 | |
| Oxidoreductase activity, acting on the aldehyde or oxo group of donors | down | 0.0012 | |
| Biogenic amine metabolic process | up | 0.0012 | |
| Epidermis morphogenesis | up | 0.0013 | |
| Endothelial cell differentiation | down | 0.0013 | |
| Endoplasmic reticulum | down | 0.0013 | |
| Carbon–oxygen lyase activity | down | 0.0013 | |
| Germ cell development | up | 0.0014 | |
| Cell proliferation | down | 0.0015 | |
| Peroxidase activity | up | 0.0015 | |
| Oxidoreductase activity, acting on peroxide as acceptor | up | 0.0015 | |
| Specific RNA polymerase II transcription factor activity | up | 0.0015 | |
| Positive regulation of programmed cell death | up | 0.0016 | |
| Response to nutrient levels | down | 0.0016 | |
| Myeloid cell differentiation | up | 0.0016 | |
| Lung development | up | 0.0017 | |
| Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | down | 0.0017 | |
| Vasculature development | up | 0.0017 | |
| Respiratory tube development | up | 0.0018 | |
| Oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen | down | 0.0018 | |
| Dioxygenase activity | down | 0.0018 | |
| Negative regulation of enzyme activity | up | 0.0019 | |
| Odontogenesis | up | 0.0019 | |
| Positive regulation of locomotion | down | 0.0019 | |
| Positive regulation of cell motility | down | 0.0019 | |
| Cell cycle | up | 0.0019 | |
| Anatomical structure formation | up | 0.002 | |
| Cell growth | up | 0.0021 | |
| Regulation of cell size | up | 0.0021 | |
| NAD binding | down | 0.0021 | |
| Steroid biosynthetic process | down | 0.0022 | |
| Response to extracellular stimulus | down | 0.0022 | |
| Endocytosis | down | 0.0023 | |
| Membrane invagination | down | 0.0023 | |
| Oxidoreductase activity, acting on single donors with incorporation of molecular oxygen | down | 0.0025 | |
| Musculoskeletal movement | down | 0.0025 | |
| Brain development | up | 0.0026 | |
| Immune system development | up | 0.0027 | |
| Negative regulation of cell growth | down | 0.0028 | |
| Negative regulation of cell size | down | 0.0028 | |
| Envelope | down | 0.0029 | |
| Negative regulation of developmental process | up | 0.0029 | |
| Chromatin | up | 0.003 | |
| mRNA binding | up | 0.0032 | |
| Antioxidant activity | up | 0.0033 | |
| Selenium binding | up | 0.0035 | |
| Receptor signaling protein serine/threonine kinase activity | down | 0.0036 | |
| Outer membrane-bounded periplasmic space | down | 0.0036 | |
| Cell envelope | down | 0.0036 | |
| Axon | up | 0.0036 | |
| Transferase activity, transferring hexosyl groups | down | 0.0038 | |
| Energy derivation by oxidation of organic compounds | down | 0.0038 | |
| Response to reactive oxygen species | up | 0.0038 | |
| Meiosis | up | 0.0038 | |
| Meiotic cell cycle | up | 0.0038 | |
| Enzyme activator activity | up | 0.0039 | |
| Hemopoiesis | up | 0.0043 | |
| Positive regulation of biosynthetic process | up | 0.0043 | |
| Regulation of transforming growth factor beta receptor signaling pathway | down | 0.0043 | |
| FAD binding | down | 0.0044 | |
| Negative regulation of growth | down | 0.0045 | |
| Defense response to Gram-positive bacterium | up | 0.0048 | |
| Sensory perception of light stimulus | down | 0.0048 | |
| Catabolic process | down | 0.0049 | |
| Hemopoietic or lymphoid organ development | up | 0.005 | |
| Positive regulation of protein metabolic process | up | 0.0051 | |
| Intermediate filament | up | 0.0051 | |
| Ras GTPase activator activity | down | 0.0052 | |
| Response to nutrient | down | 0.0053 | |
| Protein kinase regulator activity | up | 0.0053 | |
| Carbohydrate binding | up | 0.0054 | |
| Calcium ion binding | down | 0.0055 | |
| Oxidoreductase activity, acting on sulfur group of donors | down | 0.0056 | |
| Response to hypoxia | down | 0.0057 | |
| Transferase activity, transferring aldehyde or ketonic groups | up | 0.0058 | |
| Positive regulation of multicellular organismal process | up | 0.0059 | |
| Xenobiotic transporter activity | up | 0.0063 | |
| Xenobiotic-transporting ATPase activity | up | 0.0063 | |
| Phospholipase inhibitor activity | up | 0.0064 | |
Notes: Functional groupings of the modulated genes were determined using Gene Ontology classifications in NextBio. The top 200 biogroups most significantly regulated by DAC (at 3 µM) are shown.