Table S2.
Top 200 biogroups modulated by azacitidine (AZA) in A549 cells
| A549 cells treated with 3 μM AZA (48 hours)
| ||
|---|---|---|
| Biogroup name | Direction | P value |
| Proteinaceous extracellular matrix | down | 3.40E-18 |
| Extracellular matrix | down | 4.70E-18 |
| Transcription | up | 2.50E-16 |
| Extracellular matrix structural constituent | down | 4.90E-16 |
| Glycosaminoglycan binding | down | 7.30E-15 |
| Polysaccharide binding | down | 9.60E-15 |
| Pattern binding | down | 2.80E-14 |
| Lipid biosynthetic process | down | 3.60E-14 |
| Fibrillar collagen | down | 1.60E-13 |
| Calcium ion binding | down | 2.20E-13 |
| Fibrinogen complex | down | 7.20E-13 |
| Humoral immune response | down | 8.90E-12 |
| Protein binding, bridging | down | 9.00E-12 |
| Collagen | down | 1.70E-11 |
| Response to wounding | down | 6.00E-11 |
| Response to external stimulus | down | 1.50E-10 |
| Platelet activation | down | 2.20E-10 |
| Ligase activity, forming aminoacyl-tRNA and related compounds | up | 3.30E-10 |
| Ligase activity, forming carbon-oxygen bonds | up | 3.30E-10 |
| Response to nutrient | up | 3.70E-10 |
| Carbohydrate binding | down | 3.80E-10 |
| Basement membrane | down | 1.00E-09 |
| Lipid metabolic process | down | 2.20E-09 |
| Response to nutrient levels | up | 2.30E-09 |
| Steroid biosynthetic process | down | 2.30E-09 |
| Collagen binding | down | 2.40E-09 |
| Response to extracellular stimulus | up | 3.70E-09 |
| Inflammatory response | down | 7.80E-09 |
| Nucleoplasm | up | 8.70E-09 |
| Acute inflammatory response | down | 1.30E-08 |
| Response to stress | down | 1.50E-08 |
| Blood pressure regulation | down | 1.50E-08 |
| RNA binding | up | 1.60E-08 |
| Cell motility | down | 3.40E-08 |
| Localization of cell | down | 3.40E-08 |
| Epithelial cell differentiation | down | 4.70E-08 |
| tRNA binding | up | 4.80E-08 |
| Steroid metabolic process | down | 7.20E-08 |
| Endoplasmic reticulum | down | 8.00E-08 |
| Translation | up | 1.30E-07 |
| Fatty acid biosynthetic process | down | 1.90E-07 |
| Parturition | down | 2.50E-07 |
| Sterol metabolic process | down | 2.50E-07 |
| Blood coagulation | down | 2.90E-07 |
| Coagulation | down | 3.10E-07 |
| Humoral immune response mediated by circulating immunoglobulin | down | 3.60E-07 |
| Hemostasis | down | 3.60E-07 |
| Organic acid biosynthetic process | down | 4.40E-07 |
| Regulation of body fluids | down | 6.70E-07 |
| Wound healing | down | 6.90E-07 |
| ER-Golgi intermediate compartment | down | 8.00E-07 |
| Actin binding | down | 9.70E-07 |
| Anion transport | down | 1.10E-06 |
| Extracellular structure organization and biogenesis | down | 1.10E-06 |
| Transaminase activity | up | 1.10E-06 |
| Complement activation | down | 1.20E-06 |
| Extracellular matrix organization and biogenesis | down | 1.20E-06 |
| Calmodulin binding | down | 1.90E-06 |
| Circulation | down | 1.90E-06 |
| Female pregnancy | down | 2.50E-06 |
| Cellular homeostasis | down | 2.60E-06 |
| Morphogenesis of an epithelium | down | 2.70E-06 |
| Cell proliferation | down | 3.10E-06 |
| Alkene metabolic process | down | 3.10E-06 |
| Ribosome biogenesis and assembly | up | 3.20E-06 |
| Complement activation, classical pathway | down | 3.50E-06 |
| Ribonucleoprotein complex biogenesis and assembly | up | 4.90E-06 |
| Sodium:potassium-exchanging ATPase complex | down | 5.20E-06 |
| Transferase activity, transferring nitrogenous groups | up | 5.80E-06 |
| Cell activation | down | 6.10E-06 |
| Endoplasmic reticulum lumen | down | 6.60E-06 |
| Fatty acid metabolic process | down | 6.90E-06 |
| Vesicular fraction | down | 8.20E-06 |
| Cellular ion homeostasis | down | 1.10E-05 |
| Cellular chemical homeostasis | down | 1.10E-05 |
| Positive regulation of immune system process | down | 1.10E-05 |
| Positive regulation of immune response | down | 1.10E-05 |
| Phosphoinositide binding | down | 1.40E-05 |
| Activation of immune response | down | 1.50E-05 |
| Positive regulation of multicellular organismal process | down | 1.60E-05 |
| Cofactor transporter activity | up | 1.60E-05 |
| Soluble fraction | up | 1.70E-05 |
| Enzyme inhibitor activity | down | 1.70E-05 |
| Development of primary sexual characteristics | up | 1.80E-05 |
| NAD binding | down | 1.90E-05 |
| Amine biosynthetic process | up | 1.90E-05 |
| Cytoskeleton | down | 2.20E-05 |
| Lymphocyte mediated immunity | down | 2.40E-05 |
| Receptor binding | down | 2.50E-05 |
| Transcription corepressor activity | up | 2.50E-05 |
| Response to DNA damage stimulus | up | 2.60E-05 |
| Cartilage development | down | 2.70E-05 |
| SNARE complex | up | 2.80E-05 |
| Gastrulation | up | 3.20E-05 |
| mRNA transport | up | 3.50E-05 |
| Epidermis development | down | 3.80E-05 |
| Cell migration | down | 4.20E-05 |
| Immune effector process | down | 4.20E-05 |
| Response to hypoxia | down | 4.30E-05 |
| Leukocyte mediated immunity | down | 4.50E-05 |
| Adaptive immune response | down | 4.90E-05 |
| Adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains | down | 4.90E-05 |
| Endopeptidase inhibitor activity | down | 5.00E-05 |
| Protease inhibitor activity | down | 5.00E-05 |
| Oxidoreductase activity, acting on heme group of donors | down | 5.30E-05 |
| Oxidoreductase activity, acting on heme group of donors, oxygen as acceptor | down | 5.30E-05 |
| Cytochrome-c oxidase activity | down | 5.30E-05 |
| Heme-copper terminal oxidase activity | down | 5.30E-05 |
| Germ cell migration | up | 6.00E-05 |
| Coenzyme binding | down | 6.20E-05 |
| Regulation of translation | up | 6.90E-05 |
| Cytokine biosynthetic process | up | 7.30E-05 |
| Neurotransmitter:sodium symporter activity | up | 7.40E-05 |
| Ectoderm development | down | 7.50E-05 |
| Establishment of RNA localization | up | 8.00E-05 |
| RNA transport | up | 8.00E-05 |
| Nucleic acid transport | up | 8.00E-05 |
| Transcription factor binding | up | 8.30E-05 |
| Regulation of immune response | down | 8.50E-05 |
| Regulation of immune system process | down | 8.50E-05 |
| Ligase activity | up | 8.60E-05 |
| RNA localization | up | 9.10E-05 |
| Neurotransmitter transporter activity | up | 9.30E-05 |
| RNA export from nucleus | up | 9.80E-05 |
| Phospholipid binding | down | 9.90E-05 |
| Cell cycle | up | 0.0001 |
| Cytosol | down | 0.0001 |
| Cytoskeletal protein binding | down | 0.0001 |
| Response to endogenous stimulus | up | 0.0001 |
| Gonad development | up | 0.0001 |
| Nucleobase, nucleoside, nucleotide and nucleic acid transport | up | 0.0001 |
| Nucleolus | up | 0.0001 |
| Regulation of cytokine biosynthetic process | up | 0.0001 |
| Rhythmic process | up | 0.0001 |
| Reproductive structure development | up | 0.0002 |
| Mitochondrion organization and biogenesis | up | 0.0002 |
| Structural constituent of cytoskeleton | down | 0.0002 |
| Sex differentiation | up | 0.0002 |
| Transcription repressor activity | up | 0.0002 |
| Peroxidase activity | down | 0.0002 |
| Oxidoreductase activity, acting on peroxide as acceptor | down | 0.0002 |
| Laminin-1 complex | down | 0.0002 |
| Transcription cofactor activity | up | 0.0002 |
| Female sex differentiation | up | 0.0002 |
| Development of primary female sexual characteristics | up | 0.0002 |
| Oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor | down | 0.0002 |
| Nitrogen compound biosynthetic process | up | 0.0002 |
| Cell structure disassembly during apoptosis | up | 0.0003 |
| Amino acid transport | up | 0.0003 |
| Acyl-CoA binding | down | 0.0003 |
| Response to dsRNA | up | 0.0003 |
| Neuron development | down | 0.0003 |
| Integrator complex | up | 0.0003 |
| Immune response | down | 0.0003 |
| Protein dimerization activity | up | 0.0004 |
| Laminin complex | down | 0.0004 |
| Cofactor binding | down | 0.0004 |
| Germ-line sex determination | down | 0.0004 |
| Intramolecular oxidoreductase activity | down | 0.0004 |
| DNA repair | up | 0.0004 |
| Cell soma | down | 0.0004 |
| Cellular morphogenesis during differentiation | down | 0.0004 |
| RNA polymerase II transcription factor activity | up | 0.0005 |
| Regulation of epithelial cell proliferation | down | 0.0005 |
| Regulation of biosynthetic process | up | 0.0005 |
| UDP-glycosyltransferase activity | up | 0.0005 |
| Pyridoxal phosphate binding | up | 0.0005 |
| Lipid binding | down | 0.0005 |
| Positive regulation of programmed cell death | up | 0.0005 |
| Helicase activity | up | 0.0006 |
| Cell redox homeostasis | down | 0.0006 |
| Cell death | up | 0.0006 |
| Death | up | 0.0006 |
| Epithelial cell proliferation | down | 0.0006 |
| Mesenchymal cell development | down | 0.0006 |
| Ovulation | up | 0.0006 |
| Positive regulation of locomotion | down | 0.0006 |
| Positive regulation of cell motility | down | 0.0006 |
| DNA catabolic process | up | 0.0006 |
| Cell differentiation | down | 0.0006 |
| Basal lamina | down | 0.0007 |
| Insulin-like growth factor binding mesenchymal cell differentiation | Down down |
0.0007 0.0007 |
| Sequestering of metal ion | down | 0.0007 |
| Neurotransmitter transport | up | 0.0007 |
| Specific RNA polymerase II transcription factor activity | up | 0.0007 |
| Intramolecular oxidoreductase activity, transposing C=C bonds | down | 0.0007 |
| Cellular component disassembly | up | 0.0008 |
| Heme binding | down | 0.0008 |
| Tetrapyrrole binding | down | 0.0008 |
| Presynaptic active zone | up | 0.0008 |
| Amine transport | up | 0.0009 |
| Sequestering of calcium ion | down | 0.0009 |
| Cell recognition | down | 0.0009 |
| Endoplasmic reticulum part | down | 0.0009 |
| Oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor | down | 0.001 |
| Myosin binding | down | 0.001 |
| Lyase activity | up | 0.001 |
| Transferase activity, transferring hexosyl groups | down | 0.001 |
| Neuron differentiation | down | 0.001 |
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.