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).

McElwee et al. Genome Biology 2007 8:R132   doi:10.1186/gb-2007-8-7-r132

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