Toxicogenomic analysis of susceptibility to inhaled urban particulate matter in mice with chronic lung inflammation

Table 1 Number of differentially expressed probes for all pair-wise analyses as determined by MAANOVA or fold-change cut-off.

Pairwise Comparison		Significant probes (# above background)^a	Probes with > 1.5 FC^b
Treatment	WT,0 h (Air vs. EHC)	4 (2)	147
	TNF, 0 h (Air vs. EHC)	2 (2)	211
	WT, 24 h (Air vs. EHC)	1 (0)	147
	TNF, 24 h (Air vs. EHC)	1 (0)	117
Time	WT, Air (0 vs. 24 h)	279 (277)	440
	TNF, Air (0 vs. 24 h)	34 (34)	269
	WT, EHC (0 vs. 24 h)	177 (175)	486
	TNF, EHC (0 vs. 24 h)	57 (56)	349
Genotype	0 h, Air (WT vs. TNF)	3303 (3208)	2424
	24 h, Air (WT vs. TNF)	2332 (2328)	2279
	0 h, EHC (WT vs. TNF)	2447 (2438)	2557
	24 h, EHC (WT vs. TNF)	2285 (2282)	2232
Summary^c
Treatment	Union	8 (4)	572
	Intersection	0 (0)	0
Time	Union	291 (286)	1055
	Intersection	21 (21)	46
Genotype	Union	3331 (3238)	3024
	Intersection	1864 (1863)	1327

^aNumber of statistically significant probes for each comparison after analysis of three-way and two-way interactions and all main effects. Numbers in parentheses indicate probes that have been declared present in at least 4 out of 5 arrays in the group showing a significant effect.
^bList of all probes with fold-change (FC) > 1.5; no statistical filtering.
^cSummary of pair-wise comparisons. Union refers to the number of probes present in any comparison for a given factor. Intersection refers to the number of probes commonly affected in all comparisons for a given factor.

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