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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
  1. It is evident that in all cases the subset that passed both LOOCV and EDGE introduced more additional ontologies. Furthermore, one of the interesting observations is that through the rejection of a population of genes, we are better able to see evidence of biological processes that are associated with inflammation, the immune response, metabolism, and injury (red) which are hallmarks of our experiments associated with the anti-inflammatory effects of corticosteroids or the response to a significant burn injury.