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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.