Table 3

Two group comparisons examined for each of the GEO datasets
Dataset
 Condition 1
 Condition 2
 No. of samples in condition 1
 No. of samples in condition 2
 Significant dataset
GSE3320
 Non smokers
 Smokers
 5
 6
 *
GSE2302
 Control
 Smoke 15 min, 24 hr recovery
 9
 5
 **
GSE2302
 Control
 Smoke 15 min, 4 and 24 hr recovery
 9
 9
 *
GSE2302
 Control
 Smoke 15 min, 4 hr recovery
 9
 4
 **
GSE1276
 Untreated, 2 and 4 h S9+CSCA/CSCB
 8 and 12 h S9+CSCA/CSCB
 10
 8
 *
GSE1276
 S9 2, 4, 8 and 12 h
 S9+CSCA 2, 4, 8, 12 h
 8
 8
GSE1276
 S9 2, 4, 8 and 12 h
 S9+CSCB 2, 4, 8, 12 h
 8
 8
GSE1815
 Untreated 8 and 24 h
 INF-gamma treated 24 h
 9
 5
 **
GSE1815
 Untreated 8 and 24 h
 INF-gamma treated 8 and 24 h
 9
 9
 *
GSE2111
 Control
 Zinc sulfate
 4
 4
 *
GSE2111
 Control
 Vanadium
 4
 4
GSE5264
 Days 0 through 8
 Days 10 through 28
 14
 16
 *
GSE620
 Control
 4-PBA 12 and 24 h
 5
 6
 *
GSE620
 Control
 4-PBA 24 h
 5
 3
 **
GSE3397
 Control
 RSV 24 h
 4
 4
GSE3397
 Control
 RSV 4 and 24 h
 4
 8
 *
GSE3183
 Control
 IL13 4, 12, and 24 h
 6
 9
GSE3183
 Control
 IL13 24 h
 6
 3
GSE3183
 Control + IL13 4 h
 IL13 12 and 24 h
 9
 6
 *
GSE3004
 Pre-allergen challenge
 Post-allergen challenge
 5
 5

The GEO series accessions as well as the description and numbers of samples in each of the conditions are listed for each comparison. Datasets where genes differentially expressed between condition 1 and condition 2 demonstrated similarity to genes differentially expressed between current and never smokers in our dataset are indicated by the presence of one or two asterisks. Only comparisons indicated by a single asterisk are shown in Figure 5. S9, rat S9 microsomal fraction; CSC, cigarette smoke condensate; INF-gamma, interferon gamma; 4-PBA, 4-phenylbutyrate; RSV, respiratory syncytial virus; IL13, interleukin 13.

Beane et al. Genome Biology 2007 8:R201   doi:10.1186/gb-2007-8-9-r201

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