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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