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

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

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
  1. 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.