Figure 1. Real-time qRT-PCR validation of c-DNA hybridization method. BALF samples from all patients were tested for qRT-PCR (n = 15) as for macroarray (n = 10). Expression levels were measured by SYBR Green binding during PCR. Results are shown as medians and quartiles of fold induction in TB patients vs. non-TB patients.

Figure 2. IFN-γ and TNF-α in the lung of TB and control patients. Comparison of IFN-γ and TNF-α mRNAs between TB (n = 10) and non-TB (n = 5) patients by qRT-PCR. Cytokine mRNAs were normalized using the L34 gene and expressed as relative to the level seen for the lowest expressing patient. Results are medians plus 25Th and 75th percentile (boxes) with the range indicated by single lines of relative levels. Median levels of cytokine that were significantly different between groups are indicated (*p < 0.05).

Figure 3. IFN-γ and TNF-α transcripts levels and the radiological score in the lung of TB patients. Cytokines mRNAs relative levels were determined by real-time PCR, using L34 mRNA as a normalization control. Expression for each gene was calculated relative to the level seen for the lowest expressing patient (n = 10). Radiological score and TNF-α transcripts level (A) and IFN-gamma transcripts (B) are presented. mRNAs levels are medians plus 25^th and 75^th percentile (boxes) with the range indicated by single lines. Median levels of cytokine that were significantly different between groups are indicated (* = p < 0.05).

Figure 4. Correlation of IFN-γ  and IFN-γ pathway genes transcripts levels in the lung of TB patients. Comparison of gene messages within the TB patient group. mRNA levels of all molecules were determined by real-time PCR, normalizing against the L34 gene. Expression for each gene was calculated relative to the level seen for the lowest expressing patient. Correlations between IFN-γ transcripts and STAT-1, IRF-1, and IFN-γ-R2 mRNA levels were calculated using the Pearson correlation test. Values of *p < 0.05 were considered to be significant.

Differential gene expression between the lung of TB and control patients by macroarray

List of functional categories of genes up-regulated (A) and down-regulated (B) in TB (n = 10) vs. non-TB (n = 5) patients is shown. Statistical analysis was performed on the normal density values using the Mann–Whitney test. Values of p < 0.05 were considered to be significant. All fold differences are significant. The fold change for each gene was generated by comparing medians of signal densities of TB vs. non-TB.