Table 1 Over-represented ontologies of each gene cluster
From: Transcriptional regulation of gene expression clusters in motor neurons following spinal cord injury
Ontology Term | Class | Count | Total | Terms |
|---|---|---|---|---|
Cluster 1: 574 transcripts | ||||
Cell-cell adhesion | BP | 18 | 34 | 9 |
Ensheathment of neurons | BP | 7 | 7 | 4 |
Zinc finger, C2H2-type | INTERPRO | 11 | 11 | 4 |
L-amino acid transmembrane transporter activity | MF | 7 | 9 | 8 |
Solute:cation symporter activity | MF | 6 | 9 | 6 |
Nucleosome assembly | BP | 6 | 14 | 10 |
Cluster 2: 244 transcripts | ||||
Ribonucleoprotein complex | CC | 31 | 54 | 16 |
Translation | BP | 23 | 54 | 16 |
Intracellular part | CC | 143 | 162 | 8 |
RNA splicing | BP | 9 | 14 | 9 |
Ribonucleoprotein complex biogenesis | BP | 10 | 14 | 4 |
Macromolecule metabolic process | BP | 95 | 110 | 4 |
Mitochondrial ribosome | CC | 4 | 4 | 4 |
Regulation of apoptosis | BP | 16 | 37 | 12 |
Cluster 3: 494 transcripts | ||||
Cell-cell adhesion | BP | 22 | 44 | 11 |
Metal ion binding | MF | 97 | 98 | 4 |
Cellular metabolic process | BP | 198 | 217 | 4 |
Regulation of biosynthetic process | BP | 12 | 19 | 4 |
Macromolecule biosynthetic process | BP | 37 | 52 | 4 |
Ribosome | KEGG | 12 | 38 | 9 |
Cell part | CC | 294 | 294 | 8 |
Peptidase M, neutral zinc metallopeptidase, zinc binding | INTERPRO | 5 | 8 | 4 |
Zinc finger, C2H2-type | INTERPRO | 10 | 10 | 4 |
Ligase activity, forming carbon-nitrogen bonds | MF | 13 | 19 | 6 |
Cytosolic large ribosomal subunit | CC | 6 | 11 | 5 |
Cluster 4: 254 transcripts | ||||
RNA metabolic process | BP | 43 | 85 | 14 |
Cellular metabolic process | BP | 108 | 117 | 4 |
Monooxygenase activity | MF | 5 | 9 | 7 |
Cluster 5: 358 transcripts | ||||
Inflammatory response | BP | 21 | 50 | 4 |
Adaptive immune response | BP | 8 | 12 | 16 |
Pancreatitis-associated protein | INTERPRO | 4 | 7 | 6 |
Chemokine activity | MF | 5 | 10 | 10 |
Ras | INTERPRO | 10 | 20 | 8 |
GTP binding | MF | 19 | 19 | 8 |
Biopolymer modification | BP | 5 | 6 | 5 |
Immunoglobulin subtype | INTERPRO | 9 | 12 | 8 |
Cytokine production | BP | 6 | 10 | 8 |
Cluster 6: 186 transcripts | ||||
Glycosyltransferase | PIR | 8 | 10 | 12 |
Ribonucleotide binding | MF | 32 | 37 | 8 |
Contractile fiber part | CC | 4 | 4 | 4 |
Ras | INTERPRO | 6 | 10 | 8 |
Tyrosine-specific protein kinase | PIR | 4 | 10 | 9 |
Kinase activity | MF | 18 | 25 | 19 |
Hydrolase activity, hydrolysing O-glycosyl compounds | MF | 5 | 9 | 4 |
Biopolymer modification | BP | 28 | 60 | 6 |
Cluster 7: 178 transcripts | ||||
Positive regulation of transcription from RNA polymerase II | BP | 7 | 45 | 25 |
Cluster 8: 238 transcripts | ||||
EGF-like | INTERPRO | 7 | 7 | 10 |
Anatomical structure development | BP | 43 | 66 | 6 |
Membrane part | CC | 75 | 75 | 4 |
Transporter activity | MF | 32 | 35 | 8 |
Transcription coactivator activity | MF | 8 | 14 | 4 |
Intracellular transport | BP | 23 | 26 | 8 |
Integral to endoplasmic reticulum membrane | CC | 5 | 8 | 7 |
Coated vesicle | CC | 9 | 11 | 6 |
Cluster 9: 335 transcripts | ||||
Protein amino acid phosphorylation | BP | 28 | 64 | 14 |
Plasma membrane part | CC | 31 | 53 | 4 |
Protein kinase, core | INTERPRO | 16 | 22 | 6 |
Immunoglobulin-like | INTERPRO | 13 | 13 | 5 |
Neurotransmitter transporter activity | MF | 5 | 12 | 14 |
System development | BP | 52 | 72 | 5 |
Gated channel activity | MF | 13 | 28 | 28 |
Neurological system process | BP | 29 | 30 | 4 |
ATP binding | MF | 37 | 45 | 8 |
Cation transmembrane transporter activity | MF | 19 | 39 | 8 |
Negative regulation of fibroblast proliferation | BP | 4 | 10 | 11 |
Axogenesis | BP | 9 | 18 | 14 |
Regulation of neurotransmitter levels | BP | 9 | 14 | 6 |
Cluster 10: 263 transcripts | ||||
Membrane part | CC | 98 | 111 | 4 |
Glycolysis | BP | 13 | 37 | 25 |
Transporter activity | MF | 40 | 40 | 6 |
Purine ribonucleotide binding | MF | 45 | 48 | 9 |
Positive regulation of nucleobase, nucleoside, nucleotide | BP | 13 | 15 | 5 |
Synaptic transmission | BP | 17 | 31 | 5 |
Phosphorylation activity | BP | 24 | 49 | 25 |
Active transmembrane transporter activity | MF | 16 | 31 | 47 |
Phosphorylation activity | MF | 22 | 35 | 6 |
Neuron differentation | BP | 14 | 20 | 14 |
Cell development | BP | 34 | 37 | 11 |
Monovalent inorganic cation homeostasis | BP | 5 | 12 | 10 |
Amine transport | BP | 7 | 12 | 4 |
Ion exchanger activity | BP | 10 | 10 | 11 |
Cluster 11: 251 transcripts | ||||
Calycin | INTERPRO | 10 | 10 | 6 |
Synaptic transmission | BP | 18 | 27 | 5 |
DNA repair | BP | 10 | 21 | 4 |
Neuron projection development | BP | 11 | 24 | 17 |
Developmental process | BP | 61 | 61 | 4 |
Glycealdehyde-3-phosphate dehydrogenase () | MF | 5 | 20 | 21 |
Activation of adenylatecyclase activity by G-protein signaling pathway | BP | 4 | 9 | 7 |
Cluster 12: 333 transcripts | ||||
Mitochondrial ATP synthesis coupled electron transport | BP | 10 | 19 | 9 |
Mitochondrial part | CC | 31 | 44 | 8 |
Oxidative phosphorylation | KEGG | 21 | 28 | 5 |
Primary active transmembrane transporter activity | MF | 15 | 26 | 13 |
Tricarboxylic acid cycle | BP | 6 | 9 | 11 |
Ion transmembrane transporter activity | MF | 23 | 37 | 10 |
ATPase activity, coupled to transmembrane movement of substances | MF | 12 | 23 | 39 |
Alkali metal ion binding (K+) | MF | 8 | 14 | 23 |
Anion channel activity | MF | 5 | 14 | 23 |