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Table 1 Gene ontology clusters in the mouse retina upregulated at various time points after I/R injury

From: Progressive morphological changes and impaired retinal function associated with temporal regulation of gene expression after retinal ischemia/reperfusion injury in mice

Time   Ontology Enrichment score P value (P < 0.05)
0 day   No significant changes   
6 hr BP eye development 4.82 3.20E-04
inflammatory response 4.49 2.20E-05
apoptosis 1.76 8.40E-03
blood Bessel morphogenesis 0.67 4.00E-02
MF structural constituent of eye lens 4.82 7.80E-09
cytokine activity 3.15 3.80E-04
CC extracellular space 3.15 1.80E-04
1 day BP eye development 8.99 2.10E-09
inflammatory response 3.51 2.20E-03
cell death 1.37 1.10E-02
MF structural constituent of eye lens 8.99 1.80E-15
transcriptional factor activity 1.52 1.80E-02
CC extracellular region part 2.71 1.30E-05
3 day BP inflammatory response 8.12 3.30E-08
eye development 5.29 1.30E-04
cell death 2.21 9.60E-04
MF structural molecule activity 5.29 3.30E-04
CC extracellular region 3.1 5.30E-04
7 day BP defense response 2.83 7.00E-09
eye development 1.59 2.10E-02
MF peptide antigen binding 2.83 1.20E-02
CC extracellular region part 3.62 1.90E-04
antigen processing and presentation 2.83 1.60E-03
14 day BP chemotaxis 3.2 3.90E-03
cell-cell signaling 2.51 1.90E-03
inflammatory response 1.96 6.50E-02
cell death 1.73 3.40E-03
tissue regeneration 1.51 5.60E-03
myelination 1.51 4.90E-02
neuron differentiation 1.35 3.80E-02
MF glutamate receptor activity 3.13 4.80E-04
CC extracellular region 6.58 6.60E-04
neuron projection 4.31 3.30E-06
synapse 3.13 1.20E-05
postsynaptic membrane 3.13 2.80E-03
gap junction 1.64 3.60E-02
21 day BP defense response 1.73 1.10E-02
inflammatory response 1.73 3.00E-02
hemopoiesis 1.3 4.00E-02
MF no significant changes   
CC extracellular region part 4.57 1.60E-07
extracellular region 4.57 1.50E-06
proteinaceous extracellular matrix 1.56 2.10E-04
28 day BP immune response 2.46 2.20E-04
protein maturation 2.46 4.50E-02
complement activation 2.46 7.10E-03
MF glycosaminoglycan binding 1.02 5.70E-02
CC extracellular region 3.48 3.90E-04
proteinaceous extracellular matrix 1.36 3.70E-03
  1. After normalization to control eyes, microarray data were filtered to select genes upregulated higher than 1.5 fold (log2). Data were further analyzed using DAVID (Database for Annotation, Visualization and Integrated Discovery) for gene clustering based on gene ontology to identify potential enrichment of genes. Gene clusters were identified into 3 categories, biological process (BP), molecular function (MF) and cellular component (CC) at 8 time points (0 hr, 6 hr, 1, 3, 7, 14, 21 and 28 days) after I/R injury.