Transcripts Representing Genes with Known Function Were Classified by Molecular Function

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Transcripts representing genes with known function were classified by Molecular Function (MF) and Biological Process (BP), according to the ontological definitions of the Gene Ontology Consortium (left column). A statistical test for non-random distribution of these functional groups (taking into account the total number of transcripts in each category) was performed on each combined cluster and each primary cluster using Onto-Express ( Only significant associations (corrected p<0.05) with either cluster are shown. Combined cluster = pooled groups of similar clusters from the 15 K-means set. Primary cluster = the individual cluster that best represents the combined cluster (the left hand cluster in column B Figure 4).

Significant ontological classifications within clusters / Combined clusters / Primary cluster
No.
genes / P
value / No.
genes / P
value
Inv 1 / set14: BP
rhodopsin mediated phototransduction / 1 / 3.55E-04
regulation of G-protein coupled receptor protein signaling pathway / 2 / 3.55E-04
sensory perception / 2 / 0.001187
sulfate transport / 1 / 0.043804
Inv1 / set14: MF
cytokine activity / 19 / 9.50E-05 / 9 / 7.84E-05
ionotropic glutamate receptor activity / 6 / 0.014553
glutamate-gated ion channel activity / 6 / 0.014553
GTPase inhibitor activity / 2 / 0.001187
UTP-hexose-1-phosphate uridylyltransferase activity / 1 / 0.01104
sulfate porter activity / 1 / 0.01104
leukemia inhibitory factor receptor ligand activity / 1 / 0.01104
interleukin-13 receptor ligand activity / 1 / 0.01104
UDP-glucose-hexose-1-phosphate uridylyltransferase activity / 1 / 0.01104
organic anion transporter activity / 1 / 0.043804
phosphoglycerate dehydrogenase activity / 1 / 0.043804
carnitine O-acetyltransferase activity / 1 / 0.043804
Inv2 / set6: BP
chloride transport / 6 / 0.006153
Inv2 / set6: MF
ribose-phosphate pyrophosphokinase activity / 2 / 0.022439
Inv3 / set7: BP
acetyl choline receptor signaling, muscarinic pathway / 4 / 0.003553 / 2 / 0.004524
transcription initiation / 3 / 0.0252
carbohydrate biosynthesis / 2 / 0.001928
long-chain fatty acid metabolism / 1 / 0.015894
IDP catabolism / 1 / 0.015894
spermine catabolism / 1 / 0.015894
ADP catabolism / 1 / 0.015894
response to superoxide / 1 / 0.015894
B-cell differentiation / 1 / 0.015894
actin cytoskeleton organization and biogenesis / 3 / 0.032474
Inv3 / set7: MF
hydrogen-translocating V-type ATPase activity / 5 / 0.001427
protein C-terminus binding activity / 3 / 0.0252
hydrogen-transporting two-sector ATPase activity / 8 / 0.040491
phospholipase A2 inhibitor activity / 2 / 0.001928
nucleoside diphosphatase activity / 1 / 0.015894
diamine N-acetyltransferase activity / 1 / 0.015894
acyl-CoA thioesterase I activity / 1 / 0.015894
ferroxidase activity / 1 / 0.015894
protein threonine/tyrosine kinase activity / 1 / 0.015894
uncoupling protein activity / 1 / 0.015894
actin monomer binding activity / 1 / 0.015894
phospholipase inhibitor activity / 1 / 0.015894
carboxypeptidase C activity / 1 / 0.015894
transcriptional elongation regulator activity / 1 / 0.015894
transferase activity, transferring hexosyl groups / 2 / 0.023515
apoptosis activator activity / 2 / 0.048967
Inv4 / set15: BP
humoral immune response / 18 / 1.34E-08 / 4 / 0.029886
immune response / 26 / 5.53E-05 / 14 / 3.15E-08
complement activation, alternative pathway / 4 / 5.11E-05
complement activation / 5 / 8.45E-05
cell wall catabolism / 2 / 5.11E-04
cholesterol transport / 2 / 0.001707
complement activation, classical pathway / 3 / 0.01197
antigen presentation, exogenous antigen / 2 / 0.013255
actin cortical patch assembly / 1 / 0.014502
phagocytosis / 1 / 0.014502
FGF receptor signaling pathway / 1 / 0.014502
inflammatory response / 5 / 0.015314
antigen processing, exogenous antigen via MHC class II / 2 / 0.020841
defense response / 7 / 0.032822
superoxide metabolism / 2 / 0.043427
Inv4 / set15: MF
antigen binding activity / 17 / 4.54E-08
extracellular matrix structural constituent conferring tensile strength activity / 12 / 1.04E-04
complement activity / 7 / 0.046152 / 5 / 6.38E-05
bacteriolytic toxin activity / 2 / 5.11E-04
antimicrobial peptide activity / 2 / 0.007747
cysteine dioxygenase activity / 1 / 0.014502
cathepsin S activity / 1 / 0.014502
oncostatin-M receptor activity / 1 / 0.014502
lysozyme activity / 1 / 0.014502
legumain activity / 1 / 0.014502
15-hydroxyprostaglandin dehydrogenase (NAD+) activity / 1 / 0.014502
caspase-1 activity / 1 / 0.014502
cytokine binding activity / 1 / 0.014502
acute-phase response protein activity / 1 / 0.014502
macrophage elastase activity / 1 / 0.014502
actin modulating activity / 1 / 0.014502
phosphoribosylamine-glycine ligase activity / 1 / 0.014502
apoptotic protease activator activity / 1 / 0.014502
stromelysin 1 activity / 1 / 0.014502
hemoglobin binding activity / 1 / 0.014502
thioether S-methyltransferase activity / 1 / 0.014502
MHC class II receptor activity / 2 / 0.020841
L1 / set13: BP
purine nucleotide biosynthesis / 4 / 0.040075
oxidative phosphorylation, NADH to ubiquinone / 3 / 0.014195
CTP biosynthesis / 3 / 0.028632
UTP biosynthesis / 3 / 0.028632
GTP biosynthesis / 3 / 0.028632
L1 / set13: MF
NADH dehydrogenase (ubiquinone) activity / 7 / 0.007465 / 5 / 0.003449
NADH dehydrogenase activity / 6 / 0.038105 / 4 / 0.03197
acyl carrier activity / 2 / 0.022733
nucleoside-diphosphate kinase activity / 3 / 0.028632
L2 / set1: BP
cellular morphogenesis during differentiation / 2 / 0.00902 / 1 / 0.013408
acetyl-CoA biosynthesis / 2 / 0.00902 / 1 / 0.013408
sterol biosynthesis / 3 / 0.009196
polyamine biosynthesis / 2 / 0.029821 / 1 / 0.030004
metabolism / 14 / 0.045604
N-acetylneuraminate metabolism / 1 / 0.00337
UDP-N-acetylglucosamine metabolism / 1 / 0.00337
succinyl-CoA metabolism / 1 / 0.00337
mechanosensory behavior / 1 / 0.013408
hair cell differentiation / 1 / 0.013408
inner ear morphogenesis / 1 / 0.030004
glutathione metabolism / 1 / 0.030004
lipopolysaccharide biosynthesis / 1 / 0.030004
steroid biosynthesis / 2 / 0.048152
L2 / set1: MF
acetate-CoA ligase activity / 2 / 0.00902 / 2 / 7.27E-05
prostaglandin-endoperoxide synthase activity / 2 / 0.029821 / 1 / 0.030004
3-oxoacid CoA-transferase activity / 1 / 0.00337
adhesive extracellular matrix constituent activity / 1 / 0.00337
CoA-transferase activity / 1 / 0.00337
fumarylacetoacetase activity / 1 / 0.00337
acetyl-CoA transporter activity / 1 / 0.00337
isopentenyl-diphosphate delta-isomerase activity / 1 / 0.00337
iron ion transporter activity / 1 / 0.00337
UDP-N-acetylglucosamine 2-epimerase activity / 1 / 0.00337
glucocorticoid receptor activity / 1 / 0.00337
glycine N-methyltransferase activity / 1 / 0.00337
binding activity / 4 / 0.006065
gamma-glutamyl transferase activity / 1 / 0.013408
sodium-dependent phosphate transporter activity / 1 / 0.013408
transferrin receptor activity / 1 / 0.013408
beta-galactosamide alpha-2,6-sialyltransferase activity / 1 / 0.013408
ornithine decarboxylase activity / 1 / 0.013408
enzyme activity / 7 / 0.025045
aldo-keto reductase activity / 1 / 0.030004
integrin binding activity / 1 / 0.030004
long-chain-fatty-acid-CoA-ligase activity / 1 / 0.030004
isomerase activity / 4 / 0.03146
L3 / set2: BP
regulation of muscle contraction / 3 / 0.011783
binding/fusion of sperm to egg plasma membrane / 1 / 0.012447
peptide metabolism / 1 / 0.04937
negative regulation of Wnt receptor signaling pathway / 1 / 0.04937
ceramide metabolism / 1 / 0.04937
behavior / 1 / 0.04937
dopamine receptor, adenylate cyclase activating pathway / 1 / 0.04937
L3 / set2: MF
thiopurine S-methyltransferase activity / 1 / 0.012447
inorganic phosphate transporter activity / 1 / 0.012447
glial cell line-derived neurotrophic factor receptor ligand activity / 1 / 0.012447
mu-opioid receptor activity / 1 / 0.012447
ceramide kinase activity / 1 / 0.012447
geranyltranstransferase activity / 1 / 0.04937
tryptase activity / 1 / 0.04937
phosphatidylcholine-sterol O-acyltransferase activity / 1 / 0.04937
interleukin-1, Type II, blocking receptor activity / 1 / 0.04937
chemoattractant activity / 1 / 0.04937