Skip to main content

Table 2 Summary of top functions and corresponding enrichment scores from functional annotation clustering results by DAVID for gene lists (inducible genes at low concentrations of E2) from three different methods

From: A two-step hierarchical hypothesis set testing framework, with applications to gene expression data on ordered categories

Enrichment score Top functions by Coser et al. (2003)
4.11 Cell cycle, cell division, intracellular non-membrane-bounded organelle
2.48 DNA metabolic process, DNA repair, DNA recombination, cellular response to stress, disease mutation,
  response to DNA damage stimulus/ionizing radiation/abiotic stimulus
2.42 Chromosome organization, M phase of meiotic cell cycle
2.31 Microtubule-based process, centrosome cycle, microtubule cytoskeleton, enzyme binding
1.9 DNA replication, regulation of cell cycle, microtuble cytoskeleton, nuclear lumen, negative regulation
  of nucleobase/nitrogen compound/macromolecule metabolic process
  by Procedure 2 (Bonferroni)
4.56 DNA replication, DNA metabolic process, nucleoplasm
2.95 Response to DNA damage stimulus, cellular response to stress, DNA repair
2.72 Nucleoplasm, nuclear lumen, intracellular organelle lumen
2.16 Cholesterol biosynthesis and metabolic process, lipid synthesis and metabolic process, sterol biosynthesis
  and metabolic process, isoprenoid biosynthetic/metabolic process
2.01 Chromosome, intracellular non-membrane-bounded organelle
  by Procedure 3 (Holm)
5.85 Chromosome, intracellular non-membrane-bounded organelle
4.85 DNA replication, DNA metabolic process, DNA-dependent ATPase MCM, nucleoplasm, intracellular organelle
  lumen, purine nucleotide binding, adenyl robonucleotide binding
3.66 Response to DNA damage stimulus, DNA repair, cellular response to stress
3.13 Chromosome part, nuclear chromosome part
3.1 Cell cycle, cell division, mitosis, condensed chromosome, M phase, kinetochore, organelle fission