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).

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


McNutt et al. BMC Bioinformatics 2005 6:259   doi:10.1186/1471-2105-6-259

Open Data