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

Kassahn, Karin S; Crozier, Ross H; Ward, Alister C; Stone, Glenn; Caley, M Julian

doi:10.1186/1471-2164-8-358

Table 1 Results of gene set analysis of gene expression responses to environmental stress in Pomacentrus moluccensis

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

Gene Ontology/GO ID	# of probes on array	# of genes on array	p-value (FDR-corrected)
			31°C 5 d	22°C 3 h	31°C 3 h	34°C 3 h sum.	34°C 3 h winter	Hypoxia	Hyposm.
Cell growth and Cytoskeleton
Actin cytoskeleton organization/GO:0030036	253	81	0.019	0.000	0.000	0.000	0.000	0.000	0.013
Anti-apoptosis/GO:0006916	76	72	0.017	0.000	0.079	0.033	0.025	0.000	0.065
Induction of apoptosis/GO:0006917	75	73	0.001	0.001	0.034	0.007	0.002	0.220	0.000
Cell growth/GO:0016049	65	63	0.044	0.000	0.454	0.000	0.001	0.075	0.167
Mitotic cell cycle/GO:0000278	30	30	0.106	0.082	0.572	0.127	0.027	0.069	0.417
Protein turnover
Regulation of translation/GO:0006445	82	81	0.000	0.000	0.002	0.005	0.000	0.001	0.012
Ubiquitin-dependent protein catabolism/GO:0006511	98	96	0.200	0.092	0.024	0.002	0.001	0.003	0.011
Protein folding/GO:0006457	75	74	0.000	0.191	0.005	0.000	0.002	0.000	0.446
Metabolism
Carbohydrate metabolism/GO:0005975	67	67	0.057	0.217	0.076	0.011	0.000	0.001	0.088
Lipid metabolism/GO:0006629	75	75	0.001	0.113	0.007	0.000	0.000	0.127	0.018
Glycolysis/GO:0006096	31	31	0.319	0.598	0.304	0.127	0.009	0.086	0.226
Gluconeogenesis/GO:0006094	21	21	0.644	0.408	0.353	0.154	0.013	0.087	0.430
Stress
Response to pest, pathogen or parasite/GO:0009613	92	89	0.000	0.000	0.000	0.000	0.000	0.000	0.024
Response to temperature stimulus/GO:0009266	57	52	0.023	0.148	0.001	0.000	0.010	0.163	0.225
Osmoregulation GO:0018987	16	16	0.272	0.136	0.162	0.035	0.067	0.457	0.178
Response to oxidative stress/GO:0006979	22	22	0.072	0.306	0.274	0.270	0.865	0.273	0.239
Other
DNA repair/GO:0006281	84	84	0.115	0.040	0.291	0.081	0.000	0.068	0.365
Hemoglobin complex/GO:0005833	16	11	0.017	0.651	0.227	0.027	0.050	0.151	0.446

For each gene ontology an aggregate score was computed based on the p-values for differential expression of the genes in that category. The significance of the resulting gene set score was determined by random sampling of the data using the software ermineJ [72]. P-values are FDR-corrected with values smaller than 0.1 indicated in bold. "3 h" indicates three hour exposure,"5 d" five day exposure to stressor, 'sum." refers to exposure experiments performed in summer, "Hyposm." refers to hyposmotic exposure experiments.

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ISSN: 1471-2164

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