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Table 3 Gene Ontology categories and KEGG metabolic pathways that have been found significantly enriched in more than 2 expression studies on RMS by the meta-analysis.

From: Defining the gene expression signature of rhabdomyosarcoma by meta-analysis

Gene Ontology Class description§ W$ B DP K SA SF # studies
Biological Process Cell killing   x x x x x 5
  Muscle contraction x x x   x x 5
  Biosynthesis x    x x x 4
  Appendage morphogenesis x   x   x x 4
  Macromolecule metabolism x x    x x 4
  Myoblast differentiation   x   x x x 4
  Endothelial cell differentiation x    x x x 4
  Regulation of organismal physiological process   x x   x x 4
Molecular Functions ↓ Oxidoreductase activity, acting on the CH-NH group of donors x x x x x x 6
  ↓ AMP deaminase activity   x x x x x 5
  Thioredoxin-disulfide reductase activity x x   x x x 5
  Cytoskeletal protein binding x x x   x x 5
  Primary active transporter activity x x x   x x 5
  ↑ Phospholipid-hydroperoxide glutathione peroxidase activity x x   x x x 5
  RNA binding x   x   x x 4
  4-alpha-glucanotransferase activity   x   x x x 4
  Amylo-alpha-1,6-glucosidase activity   x   x x x 4
  ↑ Glutathione peroxidase activity   x   x x x 4
  Protein C-terminus binding   x x   x x 4
  Ornithine decarboxylase inhibitor activity   x   x x x 4
  Heme-copper terminal oxidase activity x x    x x 4
  ↓ Oxidoreductase activity, acting on NADH or NADPH x x    x x 4
  ↓ Oxidoreductase activity, acting on sulfur group of donors   x   x x x 4
  ↓ Oxidoreductase activity, acting on heme group of donors x x    x x 4
  Hydrolase activity, acting on ether bonds   x x   x x 4
  Intramolecular oxidoreductase activity x x    x x 4
  ↑ Phosphatase activator activity   x x   x x 4
  ↓ Electron transporter, transferring electrons from coqh2-cytochrome c reductase complex and cytochrome c oxidase complex activity x x   x   x 4
Cellular Component ↓ Proton-transporting ATP synthase complex (sensu Eukaryota) x   x x x   4
  ↓ Proton-transporting ATP synthase complex, catalytic core F(1) (sensu Eukaryota) x   x   x x 4
  ↓ Transcription factor TFIIH complex    x x x x 4
  Cytoplasm x x    x x 4
  ↓ Proton-transporting ATP synthase, catalytic core (sensu Eukaryota) x   x x x   4
  Cytosolic small ribosomal subunit (sensu Eukaryota) x    x x x 4
  Cytoskeleton   x x   x x 4
  Isoamylase complex   x   x x x 4
  ↓ Proton-transporting ATP synthase complex x   x   x x 4
  ↓ Proton-transporting ATP synthase complex, catalytic core F(1) x   x x x   4
  ↓ Proton-transporting ATP synthase, catalytic core x   x x x   4
  ↓ Respiratory chain complex III x x    x x 4
Metabolic Pathways Energy Metabolism
  ↓ Reductive carboxylate cycle (CO2 fixation) x x x x x x 6
  ↓ Oxidative phosphorylation x x x   x   4
  ↓ ATP synthesis x   x   x   3
  ↓ Carbon fixation   x    x   2
  Carbohydrate Metabolism
  Glyoxylate and dicarboxylate metabolism x x x   x   4
  ↓ Inositol metabolism x x    x x 4
  Glycolysis/Gluconeogenesis   x    x   2
  ↓ Pentose phosphate pathway   x    x   2
  Biosynthesis and secondary metabolism
  Streptomycin biosynthesis   x   x x   3
  Alkaloid biosynthesis I and II x x x x x x 6
  Other
  Ribosome x   x   x x 4
  Apoptosis   x   x   x 3
  Chondroitin/Heparan sulfate biosynthesis x   x x    3
  D-Arginine and D-ornithine metabolism x    x x   3
  Prion disease x   x x    3
  Protein export    x   x x 3
  1. $ W, B, K, DP, SA and SF stand respectively for Wachtel, Baer, Khan, De Pittà, Schaaf Adult and Schaaf Foetal datasets. Cells with an x represent enriched classes in the correspondent dataset.
  2. § The presence of arrows (↑ up or ↓ down regulation) in the category name indicates the expression levels of genes belonging to the class.