Table 1.
Gene Number (Percentage) That Met Selection Criteria for Analysis
| Gene selection method | Infection-related change | Treatment-related change | Infected vehicle∗ | Anti-Ang2 antibody∗ | Anti-TNF antibody∗ | Antibody combination∗ |
|---|---|---|---|---|---|---|
| Method No. 1 | ||||||
| Condition A | Increase | Decrease | 4129 (54) | 116 (30) | 904 (69) | 1006 (54) |
| Condition B | Increase | Increase | 134 (34) | 126 (10) | 383 (21) | |
| Condition C | Decrease | Increase | 3512 (46) | 46 (12) | 268 (20) | 416 (22) |
| Condition D | Decrease | Decrease | 96 (24) | 12 (1) | 61 (3) | |
| Total | 7641 (100) | 392 (100) | 1310 (100) | 1866 (100) | ||
| Method No. 2 | ||||||
| Condition A | Increase | Decrease | 3864 (46) | 119 (14) | 855 (50) | 946 (39) |
| Condition B | Increase | Increase | 239 (29) | 154 (9) | 482 (20) | |
| Condition C | Decrease | Increase | 4497 (54) | 76 (9) | 523 (31) | 711 (29) |
| Condition D | Decrease | Decrease | 396 (48) | 178 (10) | 299 (12) | |
| Total | 8361 (100) | 830 (100) | 1710 (100) | 2438 (100) |
Values from Affymetrix GeneChip arrays were obtained from tracheas of five groups of mice: pathogen-free, infected with Mycoplasma pulmonis for 7 days and treated with vehicle, and infected and treated with anti-Ang2 antibody, anti-TNF antibody, or both antibodies (antibody combination) (N = 4 to 5 mice per group). Method 1 was used to assess the overall effect of the treatments, identify genes that underwent large or small changes in expression during infection and treatment, and analyze changes in signaling pathways by the Database for Annotation, Visualization and Integrated Discovery (DAVID). Probe sets were selected that had at least 25% increase or decrease in expression in the infected vehicle group relative to the pathogen-free group; then, the subset of these probe sets was selected for each treatment group that had 50% or more suppression or amplification in expression compared with the infected vehicle group. Selected probe sets in infected vehicle group met the first criterion, and those in the three treatment groups met both criteria. The direction of the two changes defined conditions A, B, C, and D. Method 2 was used to analyze changes in signaling pathways by Ingenuity Pathway Analysis (IPA). As described in Materials and Methods, probe sets selected for analysis by IPA satisfied multiple criteria, including >10% difference from the pathogen-free group and 50% or greater change in any treatment group from the infected vehicle group.
Ang2, angiopoietin-2; TNF, tumor necrosis factor.
Data are given as number (percentage).