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Table 4 Differentially expressed gene sets for gestational age under 27 weeks versus 27 to 28 weeks

From: Perturbation of gene expression of the chromatin remodeling pathway in premature newborns at risk for bronchopulmonary dysplasia

Gene set/pathway

NTk q value

NEk q value

Coenzyme metabolism (GO:0006731)

0.0

0.0

Mitochondrial inner membrane (GO:0005740)

0.0

0.0

Ribonucleotide biosynthesis processing (GO:0009260)

0.0

0.0

Mitochondrial matrix (GO:0005759)

0.0

0.08

Citrate cycle TCA cycle (GO:0006099)/Oxidative phosphorylation (KEGG)

0.0

0.1

  1. Shown here are the pathways (with redundant pathways removed) that were ranked at the top of the list of those differentially expressed by two measures of false discovery: the NTk q value and the NEk q value. The NTk q value corresponds to the degree to which genes within a set/pathway are more predictive of the phenotype than the genes outside that set, and the NEk q value corresponds to the degree to which genes within that set are predictive of the phenotype. Only those pathways with an NTk q value below 10-4 and a NEk q value below 1 are shown above. The relatively high NEk q value with respect to NTk q value values shows that these gene sets are not as significantly predictive of outcome, because they demonstrate significant differential expression with respect to the other gene sets. This illustrates the limitations of the sample size and nature of the current data set. Each pathway is annotated by ontology source (Gene Ontology [GO] or Kyoto Encyclopedia of Genes and Genomes [KEGG]). TCA, tricarboxylic acid.