Table 2 Enriched ontologies that were not present in the original EDGE selection, but appeared when examining the subset that did not pass LOOCV after EDGE, and the subset that passed both LOOCV and EDGE.
From: Assessing and selecting gene expression signals based upon the quality of the measured dynamics
| a | |
|---|---|
| GDS599 | |
| Rejected by LOOCV | Accepted by LOOCV |
| actin polymerization or depolymerization | cellular carbohydrate metabolic process |
| amino acid biosynthetic process | cellular alcohol metabolic process |
| coenzyme biosynthetic process | response to external stimulus |
| ER to Golgi vesicle-mediated transport | response to stress |
| fat-soluble vitamin metabolic process | response to stimulus |
| nucleobase, nucleoside, nucleotide and nucleic acid transport | generation of precursor metabolites and energy |
| defense response | |
| inflammatory response | |
| response to wounding | |
| acute inflammatory response | |
| acute-phase response | |
| b | |
| GDS253 | |
| Rejected by LOOCV | Accepted by LOOCV |
| blood vessel remodeling | acute-phase response |
| cholesterol transport | alcohol biosynthetic process |
| endothelial cell proliferation | coenzyme biosynthetic process |
| keratinocyte differentiation | cofactor biosynthetic process |
| positive regulation of epithelial cell proliferation | DNA damage response, signal transduction |
| regulation of heart contraction | gluconeogenesis |
| regulation of muscle contraction | hexose biosynthetic process |
| response to hydrogen peroxide | monosaccharide biosynthetic process |
| sterol transport | purine ribonucleotide biosynthetic process |
| regulation of circadian rhythm | |
| ribonucleotide biosynthetic process | |
| translational initiation | |
| c | |
| GDS972 | |
| Rejected by LOOCV | Accepted by LOOCV |
| ameboidal cell migration | activation of immune response |
| base-excision repair | activation of plasma proteins during acute inflammatory response |
| DNA-dependent DNA replication | aging |
| ER to Golgi vesicle-mediated transport | alcohol catabolic process |
| fatty acid beta-oxidation | ATP synthesis coupled electron transport |
| fatty acid oxidation | B cell mediated immunity |
| germ cell migration | bile acid metabolic process |
| Golgi vesicle transport | carbohydrate catabolic process |
| I-kappaB kinase/NF-kappaB cascade | cellular aromatic compound metabolic process |
| modification-dependent macromolecule catabolic process | cellular carbohydrate catabolic process |
| modification-dependent protein catabolic process | cofactor biosynthetic process |
| proteasomal ubiquitin-dependent protein catabolic process | complement activation |
| protein amino acid N-linked glycosylation | complement activation, classical pathway |
| regulation of cellular biosynthetic process | DNA damage response, signal transduction |
| regulation of DNA replication | DNA damage response, signal transduction by p53 class mediator |
| regulation of protein import into nucleus | gas transport |
| ubiquitin-dependent protein catabolic process | glucose catabolic process |
| glutamine family amino acid catabolic process | |
| glycolysis | |
| heterocycle metabolic process | |
| hexose catabolic process | |
| humoral immune response mediated by circulating immunoglobulin | |
| immunoglobulin mediated immune response | |
| lipid biosynthetic process | |
| lymphocyte mediated immunity | |
| mitochondrial ATP synthesis coupled electron transport | |
| monosaccharide catabolic process | |
| oxidative phosphorylation | |
| protein targeting to mitochondrion | |
| response to toxin | |
| S-adenosylhomocysteine metabolic process | |
| steroid biosynthetic process | |
| sulfur compound biosynthetic process | |
