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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