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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
  1. Class Ontology: MF = molecular function, BP = biological process, CC = cellular component, PIR = protein information resource. Count: Number of genes in ontology. Total: Number of genes in ontology cluster. Terms: number of ontology terms in ontology cluster.