Unsupervised cluster analysis of BAL and urine proteins. BAL proteins from Additional file 7 and urine proteins from Additional file 10 were re-clustered for control and STAMPEDE subjects. Protein abundances were scaled by z-score, with green and red representing 1 standard deviation below and above the mean, respectively. The bar above the heatmap indicates controls (green) and disease (purple) subjects. The oval identified a subset of subjects who expressed a group of proteins in common, as discussed in the text. Gray indicates that a protein was not detected for that individual. Some individuals have multiple columns (e.g. D14 in 3B) which resulted from technical replicate analyses. These technical replicates clustered together.