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Table 1 Distribution of Ontology terms within Gene Clusters. The gene clusters identified in Figure 1d were analyzed for asymmetric distribution of ontology terms using the Gominer Software [16]. The top 40 gene ontology terms for each cluster ranked by significance scoring (Fishers exact T-test) are shown. Total numbers of genes in each cluster are indicated in parentheses. Statistical ranking of asymmetrically distributed gene ontology terms is represented by an estimated p-value (Fisher's Exact T-test).

From: Human promoter genomic composition demonstrates non-random groupings that reflect general cellular function

  Cluster One (1187)
P-Value Ontology Term
0.0003 DNA dependent DNA replication
0.0003 mitotic cell cycle
0.0008 DNA replication
0.001 structural constituent of cytoskeleton
0.0014 metabolism
0.0015 proteolysis and peptidolysis
0.0016 cell cycle
0.0016 hydrolase activity
0.0016 S phase of mitotic cell cycle
0.0021 protein metabolism
0.0024 protein catabolism
0.0028 DNA replication and chromosome cycle
0.0029 small ribosomal subunit
0.0031 intracellular
0.0031 extracellular
0.004 DNA replication factor C complex
0.0059 nucleic acid binding activity
0.0059 ATP dependent helicase activity
0.006 transmembrane receptor protein phosphatase activity
0.006 transmembrane receptor protein tyrosine phosphatase activity
0.0061 cell proliferation
0.0063 mitochondrial inner membrane
0.0065 extracellular space
0.0065 macromolecule catabolism
0.0071 protein phosphatase activity
0.0073 nucleobase, nucleoside, nucleotide and nucleic acid metabolism
0.0074 replication fork
0.0078 protein amino acid dephosphorylation
0.0078 dephosphorylation
0.0078 protein-ligand dependent protein catabolism
0.0081 mitochondrial ribosome
0.009 inner membrane
0.0092 mitochondrion
0.0095 cellular_component unknown
0.0111 helicase activity
0.0113 organellar ribosome
0.0123 N-linked glycosylation
0.0123 di-, tri-valent inorganic cation homeostasis
0.014 proton-transporting ATP synthase complex
0.014 spindle
  Cluster Nine (724)
P-Value Ontology Term
0.0003 mitochondrion
0.0005 metabolism
0.0008 intracellular
0.0018 biosynthesis
0.0022 complement activation, alternative pathway
0.003 complement activation
0.0044 complement activity
0.0047 sugar binding activity
0.0047 carbohydrate binding activity
0.006 humoral defense mechanism (sensu Vertebrata)
0.0067 plasma membrane
0.007 cell adhesion molecule activity
0.0071 1-phosphatidylinositol 3-kinase complex
0.0071 membrane attack complex
0.0071 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances
0.0071 phosphatidylinositol 3-kinase activity
0.0079 ATP-binding cassette (ABC) transporter activity
0.0098 cell adhesion
0.0099 chemotaxis
0.0099 taxis
0.0125 cell-cell adhesion
0.013 mitochondrial membrane
0.0151 lectin
0.0156 G-protein coupled receptor protein signaling pathway
0.0176 cellular_component unknown
0.0187 P-P-bond-hydrolysis-driven transporter activity
0.02 thyroid hormone generation
0.02 lipid raft
0.02 ethanol oxidation
0.02 ethanol metabolism
0.02 flowering
0.02 thyroid hormone metabolism
0.02 aldo-keto reductase activity
0.02 alcohol dehydrogenase activity, iron-dependent
0.02 alcohol dehydrogenase activity, metal ion-independent
0.02 T-cell differentiation
0.02 negative regulation of Wnt receptor signaling pathway
0.02 fluid secretion
0.022 homophilic cell adhesion
0.0266 humoral immune response
  Cluster Four (271)
P-Value Ontology Term
0.0002 cytoplasm
0.001 transcription
0.0012 regulation of transcription, DNA-dependent
0.0013 regulation of transcription
0.0015 transcription, DNA-dependent
0.0029 immune response
0.0029 nucleus
0.0034 transferase activity, transferring sulfur-containing groups
0.0034 solute:sodium symporter activity
0.005 defense response
0.0051 phenol metabolism
0.0051 catecholamine metabolism
0.0051 organic acid transporter activity
0.0053 cell communication
0.0055 response to biotic stimulus
0.0059 protein modification
0.0063 protein kinase CK2 activity
0.0069 solute:cation symporter activity
0.0071 response to external stimulus
0.0084 negative regulation of transcription
0.0093 biogenic amine metabolism
0.0093 adherens junction
0.0096 cAMP-dependent protein kinase activity
0.0096 cyclic-nucleotide dependent protein kinase activity
0.0096 casein kinase activity
0.0097 transcription from Pol II promoter
0.0099 secretin-like receptor activity
0.0099 neurotransmitter:sodium symporter activity
0.0099 neurotransmitter transporter activity
0.0099 biogenic amine biosynthesis
0.0103 protein amino acid phosphorylation
0.0106 G-protein coupled receptor activity
0.0112 neurogenesis
0.0119 transmembrane receptor protein serine/threonine kinase signaling pathway
0.0128 phosphorylation
0.0139 small GTPase mediated signal transduction
0.0141 protein kinase activity
0.0151 brain development
0.016 frizzled receptor signaling pathway
0.016 frizzled receptor activity
  Cluster Ten (815)
P-Value Ontology Term
<.0001 nucleobase, nucleoside, nucleotide and nucleic acid metabolism
<.0001 nucleus
<.0001 intracellular
<.0001 extracellular space
<.0001 extracellular
<.0001 RNA binding activity
<.0001 nucleic acid binding activity
0.0001 plasma glycoprotein
0.0001 oxidoreductase activity, acting on the CH-NH2 group of donors, oxygen as acceptor
0.0003 oxidoreductase activity, acting on the CH-NH2 group of donors
0.0003 molecular_function
0.0003 alpha-type channel activity
0.0004 response to external stimulus
0.0004 channel/pore class transporter activity
0.0005 chymotrypsin activity
0.0005 RNA metabolism
0.0007 trypsin activity
0.0011 metabolism
0.0014 immune response
0.0015 defense response
0.0016 RNA processing
0.0025 response to biotic stimulus
0.0028 cell surface receptor linked signal transduction
0.0028 integral to membrane
0.0031 regulation of transcription
0.0032 transcription
0.0037 signal transducer activity
0.0039 translation regulator activity
0.004 regulation of transcription, DNA-dependent
0.004 membrane
0.0042 voltage-gated ion channel activity
0.0044 ligand-dependent nuclear receptor activity
0.0044 potassium channel activity
0.0044 steroid hormone receptor activity
0.0045 ion transport
0.005 small GTPase mediated signal transduction
0.0051 nucleoplasm
0.0052 cation channel activity
0.0054 digestion
0.0058 ligand-regulated transcription factor activity
  Cluster Six (474)
P-Value Ontology Term
0.0002 development
0.0002 extracellular matrix structural constituent
0.0003 muscle development
0.0004 muscle contraction
0.0007 intramolecular isomerase activity
0.0013 cell differentiation
0.0014 mitochondrion
0.002 cellular process
0.002 organogenesis
0.0022 cell adhesion
0.0027 cytoskeleton
0.0032 oncogenesis
0.0032 structural constituent of cytoskeleton
0.0033 cell communication
0.0036 morphogenesis
0.0037 troponin complex
0.0037 NGF/TNF (6 C-domain) receptor activity
0.0042 circulation
0.0046 structural molecule activity
0.0048 actin cytoskeleton
0.0049 cell motility
0.005 muscle fiber
0.0056 photoreceptor activity
0.0056 G-protein coupled photoreceptor activity
0.0056 collagen type I
0.011 intermediate filament cytoskeleton
0.011 intermediate filament
0.0125 transcription cofactor activity
0.0128 extracellular matrix structural constituent conferring tensile strength activity
0.0128 sarcomere
0.0128 myofibril
0.0128 collagen
0.0139 response to stress
0.0149 hydrolase activity
0.016 intramolecular isomerase activity, interconverting aldoses and ketoses
0.016 phosphagen metabolism
0.016 neurofilament
0.016 galactose binding lectin
0.016 inactivation of MAPK
0.0176 striated muscle thin filament
  Cluster Twelve (619)
P-Value Ontology Term
<.0001 cell communication
0.0001 signal transduction
0.0078 development
0.0103 phosphate metabolism
0.0103 phosphorus metabolism
0.0159 neurogenesis
0.016 cell adhesion
0.0179 intracellular signaling cascade
0.0196 amino acid transport
0.0311 small GTPase mediated signal transduction
0.0384 coreceptor activity
0.0464 heme-copper terminal oxidase activity
0.0464 acute-phase response
0.0464 regulation of metabolism
0.0476 cell-cell signaling
0.085 beta3-adrenergic receptor activity
0.085 purine ribonucleoside catabolism
0.085 purine ribonucleoside metabolism
0.085 pentose catabolism
0.085 pentose metabolism
0.085 ribose catabolism
0.085 adenosine metabolism
0.085 manganese ion transport
0.085 ADP-sugar diphosphatase activity
0.085 bile acid biosynthesis
0.0858 cellular respiration
0.094 organelle organization and biogenesis
0.0966 alcohol catabolism
0.1096 xenobiotic metabolism
0.1096 neuropeptide signaling pathway
0.1105 meiosis
0.1136 deaminase activity
0.1198 synaptic transmission
0.1215 transmission of nerve impulse
0.1314 monovalent inorganic cation transporter activity
0.1491 chloride transport
0.1627 internalization receptor activity
0.1627 regulation of mitotic cell cycle
0.1627 cAMP metabolism
0.1627 regulation of cell volume
  Cluster Thirteen (1208)
P-Value Ontology Term
0.0002 mitochondrion
0.0004 intracellular
0.0008 metabolism
0.0012 extracellular
0.0026 DNA repair
0.0031 immune response
0.0041 extracellular space
0.0045 phosphatidylinositol transporter activity
0.0061 cytosolic large ribosomal subunit (sensu Eukarya)
0.0065 defense response
0.0069 nucleobase, nucleoside, nucleotide and nucleic acid metabolism
0.0071 RNA binding activity
0.0078 large ribosomal subunit
0.0083 heme biosynthesis
0.0083 sex determination
0.0095 G-protein coupled receptor protein signaling pathway
0.0097 integral to membrane
0.0098 biosynthesis
0.0101 integral to plasma membrane
0.0109 mitotic cell cycle
0.0147 pigment biosynthesis
0.0147 post Golgi transport
0.015 nucleus
0.0157 cyclohydrolase activity
0.0157 protein amino acid methylation
0.0157 RNA-nucleus export
0.0157 transferase activity, transferring pentosyl groups
0.0169 porphyrin biosynthesis
0.0169 chromatin remodeling complex
0.0169 heme metabolism
0.0178 plasma membrane
0.0192 S phase of mitotic cell cycle
0.0193 coenzymes and prosthetic group biosynthesis
0.0209 cell surface receptor linked signal transduction
0.021 ion transport
0.0233 trypsin activity
0.0234 pigment metabolism
0.0236 inorganic anion transport
0.0266 apoptosis regulator activity
0.0268 nucleic acid binding activity
  Cluster Fifteen (725)
P-Value Ontology Term
0.0007 blood vessel development
0.0007 angiogenesis
0.001 phosphotransferase activity, alcohol group as acceptor
0.0013 nuclear localization sequence binding activity
0.0017 protein kinase activity
0.002 response to pest/pathogen/parasite
0.0023 protein serine/threonine kinase activity
0.0024 kinase activity
0.0025 cellular process
0.0028 cell migration
0.0038 actin polymerization and/or depolymerization
0.0048 spermatid development
0.0048 NLS-bearing substrate-nucleus import
0.0048 galactosyltransferase activity
0.0051 signal transduction
0.0053 protein tyrosine kinase activity
0.0059 embryogenesis and morphogenesis
0.006 neurogenesis
0.007 immune response
0.0073 cell-matrix adhesion
0.0073 nucleotide binding activity
0.0077 Golgi apparatus
0.0079 transferase activity, transferring phosphorus-containing groups
0.0088 phosphate metabolism
0.0088 phosphorus metabolism
0.0091 protein amino acid phosphorylation
0.0097 response to wounding
0.0097 response to biotic stimulus
0.0106 phosphorylation
0.0111 RAN protein binding activity
0.0112 morphogenesis
0.0113 development
0.0113 purine nucleotide binding activity
0.012 actin filament-based process
0.0121 importin, beta-subunit
0.0121 actin modulating activity
0.0121 actin monomer binding activity
0.0121 regulation of actin polymerization and/or depolymerization
0.0124 cytoskeleton organization and biogenesis
0.0137 cell communication
  Cluster Sixteen (1266)
P-Value Ontology Term
0.0004 immune response
0.0008 oncogenesis
0.0009 defense response
0.0042 ionic insulation of neurons by glial cells
0.0125 inflammatory response
0.0245 histogenesis and organogenesis
0.0261 sarcomere alignment
0.0261 phagocytosis, engulfment
0.0261 negative regulation of osteoclast differentiation
0.0261 regulation of osteoclast differentiation
0.0261 negative regulation of cell differentiation
0.0261 NO mediated signal transduction
0.0326 activation of NF-kappaB-inducing kinase
0.0327 oogenesis
0.0453 cell activation
0.0483 humoral immune response
0.0491 protein modification
0.0575 regulation of cell differentiation
0.0673 cell cycle
0.07 biotin metabolism
0.0806 phosphate metabolism
0.0806 phosphorus metabolism
0.0888 sensory organ development
0.0888 G-protein signaling, adenylate cyclase activating pathway
0.1073 pattern specification
0.1111 gametogenesis
0.119 peptide receptor activity
0.1221 microtubule-based process
0.1251 phosphate transport
0.1251 glutathione conjugation reaction
0.1251 G-protein chemoattractant receptor activity
0.1256 phagocytosis
0.1256 carbohydrate kinase activity
0.1299 regulation of transcription
0.1309 fatty acid metabolism
0.1435 antimicrobial humoral response (sensu Invertebrata)
0.1435 protein amino acid phosphorylation
0.1454 NIK-I-kappaB/NF-kappaB cascade
0.1507 protein phosphatase type 2C activity
0.1507 heavy metal ion transport