Results/Discussion 
Adherence-Mediated Differential Expression We developed spotted oligonucleotide arrays of the S. pyogenes SF370 (an M1 serotype) genome [14] and compared the transcriptomes of streptococci that adhere to Detroit 562 human pharyngeal cells to non-adherent ("associated") streptococci within the same experiment.
Adherence assays were performed as described [15] with modifications to minimize eukaryotic cell disruption.
We replicated experiments independently and used dye-swaps to incorporate biological and technical variation [16,17].
Following filtering and normalization [18,19], we analyzed data from four biological replicates [16] with robust summary statistics [20], Bayesian statistics [21,22], and permutation algorithms [19] to identify genes differentially expressed with significance during pharyngeal cell adherence.
This analysis identified 79 genes (4% of the genome) exhibiting statistically significant fold changes in expression (PF value < 0.05) during adherence from 1,769 open reading frames represented on the array (Table 1).
We refer to such genes as "differentially expressed." We present the entire dataset from all experiments as Table S1.
Genes demonstrating upregulation (n = 45) and downregulation (n = 34) included virulence factors, prophage-encoded transcripts, metabolic genes, and transcriptional regulators (Table 2).
Undefined or hypothetical genes comprised 27% of differentially expressed genes (n = 21; 11 chromosomally encoded genes, ten phage-encoded genes).
