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Table 3 Comparison of the main Gene Ontology categories among the gene lists

From: A biological question and a balanced (orthogonal) design: the ingredients to efficiently analyze two-color microarrays with Confirmatory Factor Analysis

Gene Ontology: Level 3 A2780 vs. CP70 + C30 + C200 CP70 vs. C30 + C200  
  N° Genes (%) 1 N° Genes (%) 2 P
Biological Process    
   Cellular physiological process 60 (81) 39 (78) 0.82
   Metabolism 43 (58) 29 (58) 1
   Regulation of cellular process 24 (32) 15 (30) 0.85
   Organismal physiological process 23 (31) 10 (20) 0.22
   Regulation of physiological process 22 (30) 16 (32) 0.84
   Cell communication 20 (27) 13 (26) 1
   Localization 18 (24) 10 (20) 0.66
   Response to stress 13 (18) 5 (10) 0.30
   Response to biotic stimulus 10 (14) 5 (10) 0.78
   Cell adhesion 10 (14) 3 (6) 0.36
   Negative regulation of biological process 9 (12) 5 (10) 0.78
   Response to external stimulus 9 (12) 3 (6) 0.36
   Morphogenesis 7 (9) 3 (6) 0.73
   Organ development 6 (8) 5 (10) 0.75
Molecular Function    
   Protein binding 33 (40) 24 (40) 1
   Ion binding 27 (33) 15 (25) 0.35
   Nucleic acid binding 18 (22) 12 (20) 0.84
   Transferase activity 14 (17) 3 (5) 0.04 (1)3
   Transcription factor activity 8 (10) 3 (5) 0.36
   Receptor activity 7 (9) 11 (18) 0.12
   Nucleotide binding 7 (9) 4 (7) 0.76
   Hydrolase activity 6 (7) 9 (15) 0.17
   Enzyme inhibitor activity 6 (7) 4 (7) 1
   Receptor binding 5 (6) 5 (8) 0.74
  1. 1 74 genes with Gene Ontology annotation for biological process and 82 for molecular function; 2 50 genes with Gene Ontology annotation for biological process and 60 for molecular function; 3 FDR adjusted p-value.