Classification analysis.

<p>Panel A shows the heat map of the 10 genes isolated by the USC algorithm to classify the samples with regards to infectious strain. The samples are denoted by their ID number and the euthanasia day, and are sorted according to strain (and dose for A/Cal/07 infected animals). The asterisks denote gene expression verified by qRT-PCR. Panel B shows the 7 genes that were used to classify the samples based on the cumulative histopathology score. The samples are denoted with ID number and euthanasia day, and are sorted according to cumulative histopathology score (given as numbers under the sample names). Panel C displays the 31 genes required to classify the samples based on infectious strain and histopathology score. The samples are denoted with ID number and euthanasia day, and are sorted according to strain and cumulative histopathology score (given as numbers under the heat map). All samples were correctly classified with regards to strain. The samples used to train the classification algorithm is denoted in black, correctly classified samples in the test set in green and incorrectly classified samples in red.</p

Global gene expression changes.

<p>Panel A shows a heat map of the 25% (7685 probes) most variable genes in the dataset for all samples. Each sample day represents three individual animals, except the control group (CTRL, n = 6). HD and LD indicate high dose and low dose, respectively. D1 through D7 designates the day of euthanasia. Panel B illustrates gene expression profiles of 1997 significantly changed probes with a fold change larger than +/−2 in at least one group when compared to the control group. The average fold change from the three animals within each group is shown. Red designate up-regulated genes, blue down regulated genes, where a more intense color illustrates a more pronounced fold change. The Venn diagram in panel C shows the number of probes up or down regulated after infection by any of the three strains (177 genes), by two of the three strains (228, 131 and 29 genes) and the number of probes aberrantly expressed in a strain specific pattern.</p