Table 2. Highlighted gene ontologies significantly over-represented in genes significantly altered in CP.

Gene Ontology	GO#	Category	Observed	Expected	p-value
Biological Process	Increased in CP
extracellular matrix organization	0030198	86	20	3.57	1.55e-07
collagen metabolic process	0032963	38	8	1.58	0.0044
actin cytoskeleton organization	0030036	213	22	8.85	0.0044
Molecular Function
calcium ion binding	0005509	680	64	28.22	3.91e-08
collagen binding	0005518	32	8	1.33	0.0005
growth factor binding	0019838	97	14	4.02	0.0006
Cellular Component
collagen	0005581	31	12	1.31	4.60e-08
cytoskeleton	0005856	1008	75	42.73	1.58e-05
basal lamina	0005605	15	6	0.64	0.0003
Biological Process	Decreased in CP
ubiquitin-dependent protein catabolic process	0006511	190	33	12.18	9.76e-06
glucose metabolic process	0006006	116	19	7.43	0.0041
skeletal muscle contraction	0003009	15	6	0.96	0.0073
Molecular Function
ligase activity	0016874	281	43	18.12	6.48e-06
ubiquitin-protein ligase activity	0004842	107	23	6.90	1.39e-05
zinc ion binding	0008270	1447	128	93.32	0.0028
Cellular Component
proteasome complex	0000502	54	11	3.35	0.0047
cis-Golgi network	0005801	12	5	0.74	0.0056
nuclear lumen	0031981	1203	101	74.65	0.0081

(Category) is the number of genes on the reference list or in this case on the microarray that fall under the ontology. (Observed) is the number of genes on either the significantly up or down-regulated in CP list. (Expected) is the number of genes expected to be in the significantly altered list based on the relative sizes of lists.