Table 3.

Simulation of expected number of differentially expressed ortholog sets: probability of the observed number of differentially expressed orthologs

Category (orthologous pairs or sets)	Expected DE orthologs	Observed DE orthologs	p value
Fly-Ames, up-regulated	27.7	23	0.85
Fly-Ames, down-regulated	7.4	5	0.86
Fly-worm, up-regulated	13.8	9	0.94
Fly-worm, down-regulated	3	0	1
Worm-Ames, up-regulated	11.4	9	0.81
Worm-Ames, down-regulated	6.9	5	0.83
Fly-Little, up-regulated	20.9	34	0.004
Fly-Little, down-regulated	5.2	3	0.9
Worm-Little, up-regulated	8.6	9	0.5
Worm-Little, down-regulated	5	1	0.99
Worm-fly-Ames, up-regulated	0.9	0	1
Worm-fly-Ames, down-regulated	0.5	0	1
Worm-fly-Little, up-regulated	0.6	4	0.003
Worm-fly-Little, down-regulated	0.2	0	1

The number of differentially expressed (DE) ortholog pairs/sets expected by chance and actually observed for each indicated comparison. In all cases, the orthologs were significantly differentially expressed in each microarray dataset (q < 0.1), and showed the same direction of change (either up- or down-regulated). The number of expected DE orthologs was determined by simulation in silico, and the probability of identifying at least the number of observed orthologs was calculated from the simulation and is represented by the p value (see Materials and methods for p value calculations).