Skip to main content

Table 2 Results of over-representation analysis of gene ontologies

From: From transcriptome to biological function: environmental stress in an ectothermic vertebrate, the coral reef fish Pomacentrus moluccensis

Gene Ontology GO ID Number of probes on array Number of genes on array Number of genes in gene cluster Raw p-value FDR-corrected p-value
Cluster I-Immune Function and Development
MHC class I protein binding GO:0042288 7 7 2 0.0000 0.0561
Neurite morphogenesis GO:0048812 62 60 3 0.0032 0.1289
Cell fate determination GO:0001709 59 45 2 0.0106 0.1807
Cluster II-Cell Growth
Vesicle transport along actin filament GO:0030050 181 9 2 0.0000 0.0251
SWR1 complex GO:0000812 182 10 2 0.0000 0.0119
Cortical actin cytoskeleton GO:0030864 183 11 2 0.0000 0.0122
Condensed nuclear chromosome GO:0000794 13 13 2 0.0001 0.0168
Histone acetylation GO:0016573 186 14 2 0.0001 0.0178
Actin filament GO:0005884 187 15 2 0.0001 0.0190
Meiosis GO:0007126 51 51 3 0.0002 0.0269
M phase of mitotic cell cycle GO:0000087 97 96 3 0.0024 0.0779
Cluster III-Metabolism
Sterol metabolism GO:0016125 12 12 3 0.0000 0.0001
Trypsin activity GO:0004295 14 14 3 0.0000 0.0001
Positive regulation of protein metab. GO:0051247 18 18 3 0.0000 0.0002
Cholesterol metabolism GO:0008203 18 18 3 0.0000 0.0002
Cluster IV-Stress
Lytic vacuole GO:0000323 42 42 3 0.0001 0.2378
Lysosome GO:0005764 54 54 3 0.0004 0.3168
Response to UV GO:0009411 6 5 1 0.0004 0.1620
Replicative cell aging GO:0001302 5 5 1 0.0004 0.1296
Response to water deprivation GO:0009414 5 5 1 0.0004 0.1080
Response to reactive oxygen species GO:0000302 7 7 1 0.0008 0.1349
  1. We tested for significant over-representation of gene ontologies of genes within a cluster compared to the total complement of genes represented on the microarray. Gene clusters were identified by hierarchical clustering of significant gene responses across stressors (see Figure 3 for cluster identification)