Table 1.
Study subjects with racial and complication status.
Table 2.
Patient characteristics and concomitant medications.
Figure 1.
Identifying gene signatures in sarcoidosis. Panel A. Enriched pathways among complicated sarcoidosis-associated genes.
The top ranking KEGG pathways are listed for each population. The red line indicates the cutoff of significance (adjusted p-value<0.05). The number of genes in each pathway is shown beside the pathway name. Panel B. Heatmap of patients with complicated sarcoidosis and healthy controls. Red represents increased gene expression; Blue represents down-regulation. “++”: patients with complicated sarcoidosis; “−”: healthy controls. Panel C. Principal component analysis on expression values of the 20-gene signature. X-axis: principal component 1 with eigenvalue; Y-axis: principal component 2 with eigenvalue. Left panel: patients with complicated sarcoidosis and healthy controls; middle panel: patients with complicated sarcoidosis, uncomplicated sarcoidosis and healthy controls; and right panel: patients with complicated sarcoidosis and uncomplicated sarcoidosis. HC: healthy controls; US: patients with uncomplicated sarcoidosis; and CS: patients with complicated sarcoidosis. Panel D. Comparison between the 20-gene signature and the TCR/JS/CCR signaling pathway gene signature. The distribution of prediction accuracy is based on 1,000 times of five-fold cross-validation. The dashed lines indicate the average classification accuracy for the 20-gene signature or the TCR/JS/CCR signaling pathway gene signature. Left panel: all sarcoidosis patients versus healthy controls; and right panel: patients with complicated sarcoidosis versus patients with uncomplicated sarcoidosis.
Table 3.
The unbiased 20-gene signature for complicated sarcoidosis.
Table 4.
The 31 differentially-expressed TCR/JS/CRR signaling pathway genes in sarcoidosis.
Figure 2.
Validation in independent datasets.
The upper panels show the comparison between the 20-gene signature and the TCR/JS/CCR signaling pathway gene signature. The distribution of prediction accuracy is based on 1,000 times of five-fold cross-validation. The dashed lines indicate the average classification accuracy for the 20-gene signature or the TCR/JS/CCR signaling pathway gene signature. The lower panels show the results of principal component analysis on expression values of the 20-gene signature. X-axis: principal component 1 with eigenvalue; Y-axis: principal component 2 with eigenvalue.
Table 5.
SNPs significantly associated with sarcoidosis within the unbiased 20 signature genes (P<0.01).
Table 6.
PubMatrix search results for the 20-gene signature against sarcoidosis-related search terms.
Figure 3.
Boxplot of expression of the 20 signature genes.
The dark grey points and lines indicate the geometric mean of expression in each category. HC: healthy controls; US: patients with uncomplicated sarcoidosis; and CS: patients with complicated sarcoidosis. Y-axis: log2-transformed expression values.