Variable numbers of sequential blood samples were available from critically ill patients. Comparisons of TLRs did not show any distinguishable pattern (data not shown). For evaluating gene expressions, a separate cluster analysis was carried out for the sequential PBMC samples of critically ill patients (Figure 3b ). Samples formed two distinct clusters. Samples from S1, S2, S3 and S4 formed a single cluster (cluster 1) showing significant Figure 2 . TLR levels in the blood lymphocytes and monocytes. TLR levels of peripheral blood from the patients and healthy controls were determined separately by either surface staining or intracellular staining of the cells using TLR specific antibodies followed by FACS analysis. Scatter dot plots and histograms: A representative sample each from different categories, a) healthy individual, b) mild case, c) critically ill case, d) TLR levels: Expressed as median fluorescence intensities (MFI) for different categories of patients. doi:10.1371/journal.pone.0013099.g002 downregulation of most of the immune function genes. Cluster 2 contained all sequential samples from the seasonal flu case (S21) and one pH1N1 case (S7). Though most of the gene expression levels were similar to survived case, S7 did not survive. Genes formed four clusters, A, B, C and D. Cluster C contained majority of the analyzed genes (73/87) and all were downregulated in the cluster 1.