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

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
Cellular Component extracellular 69 380 244 2556 2.01E-08
Biological Process skeletal development 21 379 55 2575 0.00005
Molecular Function receptor activity 53 385 218 2611 0.00012
Cellular Component extracellular matrix 30 380 100 2556 0.00015
Biological Process development 82 379 394 2575 0.00036
Molecular Function signal transducer activity 81 385 393 2611 0.00059
Molecular Function calcium ion binding 34 385 134 2611 0.00129
Biological Process regulation of transcription (3) 82 379 410 2575 0.00134
Molecular Function glycosaminoglycan binding 12 385 31 2611 0.00318
Molecular Function endopeptidase inhibitor activity (2) 11 385 27 2611 0.00341
Molecular Function protease inhibitor activity 11 385 27 2611 0.00341
Cellular Component membrane (2) 148 380 842 2556 0.00553
Molecular Function steroid hormone receptor activity 7 385 13 2611 0.00668
Biological Process transcription 83 379 441 2575 0.00764
Molecular Function insulin-like growth factor binding 6 385 10 2611 0.00893
  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.