Table 4 Gene cluster analysis of differentially expressed genes
From: Transcriptome analysis of egg viability in rainbow trout, Oncorhynchus mykiss
Cluster | Number of genes | Cluster enrichment | Maximum number of GOs in biological process | Maximum number of GOs in molecular function | Major involvement | ||
|---|---|---|---|---|---|---|---|
GO description | P-value | GO description | P-value | ||||
Cluster 1 | 164 | 8.43 | ribosome biogenesis | 1.01E-130 | structural constituent of ribosome | 4.07E-159 | Ribosome biogenesis |
Cluster 2 | 74 | 5.82 | transport | 5.81E-03 | transporter activity | 2.56E-02 | Mitochondrion related transporter |
Cluster 3 | 55 | 2.09 | autophagosome assembly | 9.55E-04 | protein binding | 1.09E-05 | Protein transport and modification |
Cluster 4 | 48 | 2.44 | proteolysis | 9.53E-02 | protein binding | 1.09E-05 | Protein transport |
Cluster 5 | 32 | 3.22 | metabolic process | 4.74E-02 | GTP binding | 1.29E-04 | Translation |
Cluster 6 | 30 | 2.39 | phosphorylation | 4.84E-02 | ATP binding | 9.37E-03 | Phosphorylation |
Cluster 7 | 29 | 2.68 | regulation of transcription, DNA-templated | 7.14E-03 | zinc ion binding | 4.92E-02 | Transcription |
Cluster 8 | 22 | 13.4 | rRNA processing | 3.43E-07 | nucleic acid binding | 2.32E-02 | Ribosome processing |
Cluster 9 | 22 | 10.73 | metabolic process | 4.74E-02 | metal ion binding | 5.60E-02 | Transcription |
Cluster 10 | 20 | 10.7 | oxygen transport | 8.43E-20 | iron ion binding | 5.84E-07 | Oxygen transport |
Cluster 11 | 17 | 2.35 | metabolic process | 4.74E-02 | zinc ion binding | 4.92E-02 | Zinc ion binding |
Cluster 12 | 13 | 5.26 | hydrogen ion transmembrane transport | 6.72E-10 | NADH dehydrogenase (ubiquinone) activity | 5.13E-14 | NADH dehydrogenase (ubiquinone) activity |
Cluster 13 | 13 | 10.9 | cellular iron ion homeostasis | 1.69E-12 | ferric iron binding | 1.69E-16 | Iron ion homeostasis and oxidation reduction |
Cluster 14 | 12 | 2.96 | ATP synthesis coupled proton transport | 1.42E-11 | proton-transporting ATP synthase activity | 4.16E-09 | ATP generation |
Cluster 15 | 11 | 1.74 | G-protein coupled receptor signaling pathway | 1.22E-02 | structural molecule activity | 1.40E-02 | structural molecule activity |
Cluster 16 | 10 | 1.56 | regulation of transcription from RNA polymerase II promoter | 1.35E-01 | nucleic acid binding | 2.32E-02 | Transcription |
Cluster 17 | 10 | 5.65 | oxidation-reduction process | 2.83E-04 | glutathione peroxidase activity | 1.93E-06 | Protect from oxidative damage |
Cluster 18 | 9 | 1.7 | signal transduction | 7.68E-04 | transposase activity | 8.42E-07 | Immune response, |
Cluster 19 | 9 | 5.28 | positive regulation of RNA polymerase II transcriptional preinitiation | 4.86E-05 | TBP-class protein binding | 3.31E-04 | Cell division |
Cluster 20 | 8 | 1.86 | regulation of cell proliferation | 7.20E-02 | calcium ion binding | 6.47E-04 | Regulate cell proliferation |
Cluster 21 | 8 | 1.67 | midbrain-hindbrain boundary structural organization | 4.06E-04 | transcription factor activity, sequence-specific DNA binding | 1.32E-02 | Transcription regulation |
Cluster 22 | 7 | 4.46 | multicellular organism development | 2.96E-02 | nucleic acid binding | 2.32E-02 | Cell cycle and division |
Cluster 23 | 7 | 3.39 | proton transport | 1.63E-05 | NADH dehydrogenase (ubiquinone) activity | 5.13E-14 | Mitochondrial electron transport |
Cluster 24 | 6 | 1.76 | interstrand cross-link repair | 3.82E-03 | metal ion binding | 5.60E-02 | Transcription regulation |
Cluster 25 | 6 | 1.92 | transmembrane transport | 1.35E-02 | ATP binding | 9.37E-03 | Regulate apoptosis |
Cluster 26 | 6 | 5.01 | heart contraction | 1.13E-02 | metal ion binding | 5.60E-02 | Transcription regulation |
Cluster 27 | 6 | 1.52 | microtubule-based movement | 1.03E-01 | metal ion binding | 5.60E-02 | Transcription regulation |
Cluster 28 | 6 | 1.97 | proteolysis | 9.53E-02 | zinc ion binding | 4.92E-02 | Regulate cell cycle and apoptosis |
Cluster 29 | 5 | 1.7 | metabolic process | 4.74E-02 | metal ion binding | 5.60E-02 | ATP binding |
Cluster 30 | 4 | 2.96 | regulation of transcription, DNA-templated | 7.14E-03 | DNA binding | 5.37E-04 | Transcription regulation |
Cluster 31 | 4 | 10.23 | neurotrophin TRK receptor signaling pathway | 2.92E-07 | structural constituent of ribosome | 4.07E-159 | Transcription regulation |