TABLE 3.

Number of genes within each of the 28 patterns of expression

	No. of genes differentially expressed
Pattern	By ≥1.5-fold	By ≥2-fold
E	436	315
M	177	95
L	937	657
EM	1799	1328
EL	1033	633
ML	841	634
Coch	59	34
V	824	225
Yng-M	195	75
Old-M	218	82
E10.5-Up	71	33
E10.5-Down	202	80
E11-UP	57	17
E11-Down	182	91
Both-M	—	420
C	106	60
U	188	115
S	241	109
CS	43	31
CU	215	65
US	211	97
Yng-L	142	34
Old-L	188	84
E14-Up	171	43
E14-Down	499	151
Both-L	—	720
IE-Up	—	1410a
—	—	384b
IE-Down	—	226a
—	—	66b

The number of genes that change by ≥1.5-fold or ≥2-fold (with an estimated FDR of at most 0.5%) are shown for each type of pattern according to the abbreviations in Table 2. In EML analysis, the lowest boundary of fold changes was 1.5-fold after taking error into account. In M and L analyses, the number of genes indicated are those that were able to meet the two-way ANOVA P-value cutoff of 0.005 (see text and supplemental Materials and Methods for details). These had a lowest boundary of fold changes of 1.4-fold after taking error into account. Genes within expression patterns Both-M and Both-L do not have an expression ratio associated with them.

^aGenes that were either up- or downregulated in at least one-tenth of all IE samples relative to at least one NIE sample.

^bGenes that were either up- or downregulated in at least one-third of all IE samples relative to at least one NIE sample.