Table S4.
Top 200 biogroups modulated by azacitidine (AZA) in H1299 cells
| H1299 cells treated with 3 μM AZA (48 hours)
| ||
|---|---|---|
| Biogroup name | Direction | P value |
| Transcription | up | 1.90E-25 |
| Cell cycle | down | 7.60E-25 |
| Mitosis | down | 8.00E-24 |
| Cell division | down | 1.00E-22 |
| Cytoskeleton | down | 5.60E-14 |
| Microtubule | down | 1.30E-13 |
| Spindle | down | 1.80E-13 |
| Mitochondrion | down | 1.80E-12 |
| Sterol metabolic process | down | 1.40E-11 |
| Chromosome | down | 1.20E-10 |
| Alcohol metabolic process | down | 2.20E-10 |
| Ligase activity | up | 2.40E-10 |
| Lipid biosynthetic process | down | 2.70E-10 |
| Steroid biosynthetic process | down | 3.00E-10 |
| Mitotic sister chromatid segregation | down | 1.90E-09 |
| Steroid metabolic process | down | 2.50E-09 |
| Sister chromatid segregation | down | 2.90E-09 |
| Endoplasmic reticulum | down | 3.60E-09 |
| Envelope | down | 4.70E-09 |
| Lipid metabolic process | down | 2.60E-08 |
| Response to nutrient | down | 7.00E-08 |
| Collagen binding | down | 1.60E-07 |
| Centrosome | down | 1.70E-07 |
| Wound healing | down | 1.90E-07 |
| Response to nutrient levels | down | 2.00E-07 |
| Intramolecular oxidoreductase activity | down | 2.50E-07 |
| Response to extracellular stimulus | down | 2.70E-07 |
| Mitochondrial membrane | down | 2.80E-07 |
| Microtubule organizing center | down | 2.80E-07 |
| Acid–amino acid ligase activity | up | 3.10E-07 |
| Cell proliferation | down | 3.60E-07 |
| Blood coagulation | down | 3.70E-07 |
| Establishment of chromosome localization | down | 4.40E-07 |
| Coagulation | down | 4.90E-07 |
| Chromosome segregation | down | 5.00E-07 |
| Nitrogen compound catabolic process | down | 5.20E-07 |
| Kinase binding | up | 5.30E-07 |
| Beta-catenin binding | down | 5.50E-07 |
| Nucleoplasm | up | 6.10E-07 |
| Enzyme inhibitor activity | down | 8.80E-07 |
| Alcohol catabolic process | down | 9.80E-07 |
| Hemostasis | down | 1.10E-06 |
| Transcription cofactor activity | up | 1.10E-06 |
| Transcription repressor activity | up | 1.20E-06 |
| Midbody | down | 1.30E-06 |
| Ligase activity, forming carbon-nitrogen bonds | up | 1.70E-06 |
| Establishment of organelle localization | down | 2.00E-06 |
| Germ-line sex determination | down | 2.00E-06 |
| Oligosaccharyl transferase complex | down | 2.10E-06 |
| Response to external stimulus | down | 2.20E-06 |
| Oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor | down | 2.20E-06 |
| Amine catabolic process | down | 2.20E-06 |
| Cytoskeleton organization and biogenesis | down | 2.20E-06 |
| Cofactor binding | down | 2.30E-06 |
| Coenzyme binding | down | 2.70E-06 |
| Transcription corepressor activity | up | 3.00E-06 |
| Cell differentiation | up | 3.20E-06 |
| mRNA binding | down | 3.30E-06 |
| Meiotic chromosome segregation | down | 3.60E-06 |
| Homologous chromosome segregation | down | 3.60E-06 |
| Nuclear envelope-endoplasmic reticulum network | down | 3.90E-06 |
| Oxidoreductase activity, acting on the CH–CH group of donors, NAD or NADP as acceptor | down | 5.00E-06 |
| Intramolecular oxidoreductase activity, transposing C=C bonds | down | 5.30E-06 |
| Mitotic chromosome condensation | down | 5.50E-06 |
| Endoplasmic reticulum part | down | 5.50E-06 |
| Transcription factor binding | up | 5.60E-06 |
| Organic acid transport | up | 5.70E-06 |
| Carboxylic acid transport | up | 5.70E-06 |
| Acyl-CoA binding | down | 5.70E-06 |
| DNA-directed RNA polymerase II, holoenzyme | up | 5.80E-06 |
| Interphase of mitotic cell cycle | down | 6.00E-06 |
| Primary sex determination | down | 6.00E-06 |
| Cell-matrix adhesion | down | 6.20E-06 |
| Hormone activity | down | 6.30E-06 |
| Organic acid transmembrane transporter activity | up | 6.30E-06 |
| Mitochondrial inner membrane | down | 7.30E-06 |
| Cell-substrate adhesion | down | 7.60E-06 |
| Transcription activator activity | up | 7.70E-06 |
| Mitotic spindle organization and biogenesis | down | 7.90E-06 |
| Lyase activity | down | 8.10E-06 |
| Sterol transport | down | 8.70E-06 |
| Arginine metabolic process | down | 8.70E-06 |
| Chromatin assembly | down | 1.00E-05 |
| Nitrogen compound biosynthetic process | down | 1.10E-05 |
| RNA polymerase II transcription factor activity | up | 1.10E-05 |
| Transaminase activity | up | 1.20E-05 |
| Meiotic spindle organization and biogenesis | down | 1.30E-05 |
| Organelle localization | down | 1.40E-05 |
| Isomerase activity | down | 1.40E-05 |
| Interphase | down | 1.40E-05 |
| Urea cycle intermediate metabolic process | down | 1.50E-05 |
| Fatty acid biosynthetic process | down | 1.70E-05 |
| Receptor binding | down | 1.70E-05 |
| Regulation of body fluids | down | 1.80E-05 |
| Condensin complex | down | 1.80E-05 |
| Regulation of coagulation | down | 1.90E-05 |
| Nuclear envelope | down | 2.20E-05 |
| Caveola | down | 2.30E-05 |
| Organic acid biosynthetic process | down | 2.30E-05 |
| Meiotic cell cycle | down | 2.30E-05 |
| Amino acid transport | up | 2.50E-05 |
| NADP binding | down | 2.80E-05 |
| Protein dimerization activity | up | 2.90E-05 |
| Spindle pole | down | 3.40E-05 |
| Ubiquitin–protein ligase activity | up | 3.50E-05 |
| Transferase activity, transferring nitrogenous groups | up | 3.60E-05 |
| Nucleoside metabolic process | down | 3.80E-05 |
| Structural constituent of cytoskeleton | down | 3.90E-05 |
| Carbohydrate catabolic process | down | 4.10E-05 |
| Endoplasmic reticulum membrane | down | 4.30E-05 |
| Nucleosome | down | 4.40E-05 |
| Nucleotide catabolic process | down | 4.60E-05 |
| Cellular chemical homeostasis | down | 4.70E-05 |
| Cellular ion homeostasis | down | 4.70E-05 |
| Cytokinesis | down | 4.90E-05 |
| Muscle cell differentiation | up | 5.00E-05 |
| Myeloid cell differentiation | up | 5.20E-05 |
| Catabolic process | down | 5.20E-05 |
| Oxygen and reactive oxygen species metabolic process | down | 5.20E-05 |
| Chromatin | down | 5.30E-05 |
| Epidermis development | down | 5.40E-05 |
| Oxidoreductase activity, acting on the CH–NH group of donors | down | 5.60E-05 |
| SNARE complex | up | 5.60E-05 |
| Ligase activity, forming carbon–oxygen bonds | up | 5.70E-05 |
| Ligase activity, forming aminoacyl–tRNA and related compounds | up | 5.70E-05 |
| Soluble fraction | up | 5.80E-05 |
| Endopeptidase inhibitor activity | down | 5.90E-05 |
| Protease inhibitor activity | down | 5.90E-05 |
| Small protein conjugating enzyme activity | up | 6.00E-05 |
| AP-type membrane coat adaptor complex | down | 6.40E-05 |
| Cell–cell signaling | down | 6.70E-05 |
| Amine transport | up | 6.80E-05 |
| Response to DNA damage stimulus | up | 7.20E-05 |
| Male sex determination | down | 7.20E-05 |
| Cell–cell adhesion | down | 8.00E-05 |
| Protein heterodimerization activity | down | 8.00E-05 |
| Enzyme binding | up | 8.40E-05 |
| Oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen | down | 9.10E-05 |
| Ectoderm development | down | 9.40E-05 |
| Positive regulation of progression through cell cycle | down | 0.0001 |
| One-carbon compound metabolic process | down | 0.0001 |
| Heterogeneous nuclear ribonucleoprotein complex | down | 0.0001 |
| Response to stress | down | 0.0001 |
| Response to endogenous stimulus | up | 0.0001 |
| Cell death | up | 0.0001 |
| Death | up | 0.0001 |
| Meiosis | down | 0.0001 |
| Dioxygenase activity | up | 0.0001 |
| Oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen | up | 0.0001 |
| Isoprenoid biosynthetic process | down | 0.0001 |
| Carbon–carbon lyase activity | down | 0.0001 |
| Lipid digestion | down | 0.0001 |
| Nitric oxide metabolic process | down | 0.0001 |
| Nitric oxide biosynthetic process | down | 0.0001 |
| Cellular homeostasis | down | 0.0001 |
| Positive regulation of locomotion | down | 0.0001 |
| Positive regulation of cell motility | down | 0.0001 |
| Sulfur compound biosynthetic process | up | 0.0001 |
| Proton-transporting ATP synthase complex, catalytic core F(1) | down | 0.0001 |
| Mitochondrial proton-transporting ATP synthase complex | down | 0.0002 |
| Muscle development | up | 0.0002 |
| Integrator complex | up | 0.0002 |
| Caspase inhibitor activity | down | 0.0002 |
| Fatty acid binding | down | 0.0002 |
| Isoprenoid metabolic process | down | 0.0002 |
| Blood vessel morphogenesis | up | 0.0002 |
| Vasculogenesis | up | 0.0002 |
| Kinetochore | down | 0.0002 |
| Low-density lipoprotein binding | down | 0.0002 |
| Cell structure disassembly during apoptosis | up | 0.0002 |
| Endoplasmic reticulum lumen | down | 0.0002 |
| Negative regulation of multicellular organismal process | down | 0.0002 |
| Intestinal absorption | down | 0.0002 |
| Organelle outer membrane | down | 0.0002 |
| Proton-transporting two-sector ATPase complex, catalytic domain | down | 0.0002 |
| Regulation of transforming growth factor beta receptor signaling pathway | down | 0.0002 |
| Clathrin adaptor complex | down | 0.0002 |
| Fatty acid metabolic process | down | 0.0003 |
| Replication fork | down | 0.0003 |
| Lipoprotein binding | down | 0.0003 |
| Insemination | up | 0.0003 |
| Behavior | down | 0.0003 |
| Leukocyte differentiation | up | 0.0003 |
| Single-stranded RNA binding | down | 0.0003 |
| Histone acetyltransferase complex | up | 0.0003 |
| Oxidoreductase activity, acting on single donors with incorporation of molecular oxygen | up | 0.0003 |
| Hemopoiesis | up | 0.0003 |
| Outer kinetochore of condensed | down | 0.0003 |
| chromosome | ||
| Response to virus | up | 0.0003 |
| Vasculature development | up | 0.0003 |
| DNA-directed RNA polymerase complex | up | 0.0003 |
| Perinuclear region of cytoplasm | down | 0.0003 |
| Sterol binding | down | 0.0003 |
| Generation of precursor metabolites and energy | down | 0.0003 |
| Copulation | up | 0.0004 |
| Spindle localization | down | 0.0004 |
| Establishment of mitotic spindle localization | down | 0.0004 |
| Establishment of spindle localization | down | 0.0004 |
| Neural crest cell development | down | 0.0004 |
| GTPase inhibitor activity | down | 0.0004 |
Notes: Functional groupings of the modulated genes were determined using Gene Ontology classifications in NextBio. The top 200 biogroups most significantly regulated by AZA (at 3 µM) are shown.