Transcriptional profiling differences for articular cartilage and repair tissue in equine joint surface lesions

BMC Medical Genomics

Table 3 Overrepresented ontological categories for transcripts with >2-fold difference in repair tissue versus normal articular cartilage.

GO System	Gene Category	List Hits	List Total	Population Hits	Population Total	EASE Score
Biological Process	immune response	23	270	98	2575	0.00032
Biological Process	defense response	23	270	103	2575	0.00066
Cellular Component	cytoskeleton	39	275	216	2556	0.00095
Cellular Component	actin cytoskeleton	18	275	73	2556	0.00133
Biological Process	response to biotic stimulus	26	270	130	2575	0.00148
Biological Process	organelle organization and biogenesis	21	270	96	2575	0.00162
Biological Process	cytoskeleton organization and biogenesis	16	270	65	2575	0.00216
Cellular Component	extracellular matrix	21	275	100	2556	0.00368
Biological Process	histogenesis	7	270	16	2575	0.00398
Biological Process	cell motility	18	270	84	2575	0.00492
Biological Process	response to external stimulus	36	270	220	2575	0.00569
Molecular Function	calcium ion binding	25	279	134	2611	0.00627
Biological Process	protein complex assembly	10	270	34	2575	0.00646
Biological Process	cell adhesion (3)	26	270	145	2575	0.00685
Molecular Function	hydrogen ion transporter activity (2)	13	279	53	2611	0.00808

Redundant or similar categories were removed. When present, the number of redundant or similar categories are indicated in parentheses within the listed "gene category." "GO System" represents the major gene ontological system (i.e., cellular component, biological process, or molecular function). "Gene category" shows a descriptive term shared by a group of genes. "List hits" are the numbers of differentially abundant transcripts that belong to the gene category. "List total" is the number of differentially expressed genes within the corresponding cellular component, biological process, or molecular function system. "Population hits" represent the total number of genes found on the microarray possessing that specific gene category annotation (e.g., extracellular, skeletal development, etc.). "Population Total" represents the total number of genes found on the microarray possessing that ontological system annotation. "EASE score" is a measure of overrepresentation that scales the results of a statistical analysis (Fisher's exact test) by biasing against categories supported by few genes.

ISSN: 1755-8794