Table 1

The four gene lists analyzed by Kayo et al. [24] along with the total time needed for initial analysis are shown for the manual and EASE analyses

Total time for analysis

Themes of genes downregulated with caloric restriction

Themes of genes upregulated with caloric restriction

Themes of genes downregulated with aging

Themes of genes upregulated with aging


Manual analysis by Kayo et al. [24]

Approximately 200 hours

Energy metabolism, mitochondrial bioenergetics

Structural proteins, cytoskeletal proteins

Energy metabolism, mitochondrial electron transport, oxidative phosphorylation

[Inflamation/immune function], [oxidative stress]

EASE

Approximately 15 minutes

Mitochondrion, electron transport, mitochondrial membrane, inner membrane, primary active transporter, mitochondrial electron transport chain, oxidoreductase, hydrogen ion transporter, mitochondrial inner membrane, monovalent inorganic cation transporter, energy pathways, [carrier], ion transporter, [cytoplasm]

Extracellular matrix, [calmodulin binding], [morphogenesis], structural molecule, [development], microfibril, cytoskeleton

Inner membrane, hydrogen ion transporter, [intracellular], monovalent inorganic cation transporter, metabolism, mitochondrial membrane, mitochondrial inner membrane, primary active transporter, energy pathways, mitochondrion, ion transporter, [carrier], cation transporter

[Gas transport], [oxygen transport]


For each list, the major biological themes as determined by Kayo et al. [24] are shown, as well as all significant (p < 0.05) gene categories as determined by EASE score corrected for multiplicity with the bootstrap function using 10,000 random trials. The time shown for EASE represents initial analysis before running the bootstrap analysis. Bootstrap analysis took an additional 2 hours. Themes that differ between Kayo et al.'s themes and the EASE results are in square brackets.

Hosack et al. Genome Biology 2003 4:R70   doi:10.1186/gb-2003-4-10-r70

Open Data