Spots with a net intensity in both channels lower than the median signal background plus twice standard deviations were removed as low signal spots. Data were normalized by median global intensity and with LOWESS correction [41] using the Acuity 4.0 software (Axon Molecular Devices). Finally, only probes for which a valid data was obtained in at least 13 out of the 15 slides were considered for further analysis (13,722 spots; Table S1 ). Median, mean and standard deviations were calculated from each treatment (control, TEV-and TEV-At17-infected plants), and all data were normalized to the median of the expression in control samples. To detect differentially expressed genes in plants infected with TEV-At17 compared to TEV, data were analyzed with the SAM package [42] , using two-class comparison (TEV versus TEV-At17) with a false discovery rate (FDR) of 5.38% with no fold-change cut-off. Differentially over-and under-expressed genes were grouped in 262 self-organizing maps (SOMs) [43] using Acuity with Euclidean squared similarity metrics. Gene lists were further analyzed with FatiGO [33] to find differential distributions of gene ontology (GO) terms between statistically differential genes in each SOM and the rest of genes in the microarray, with P values adjusted after correcting for multiple testing [33] . SAM analysis at 1% FDR gave qualitatively identical results, confirming their robustness to changes in arbitrarily-chosen statistical thresholds. Figure S1 Representative plants showing the symptoms induced by several of the viral genotypes described in Table 1 Table S4 SOM clustering of significant genes, both up-and down-regulated, between TEV-and TEV-At17-infected plants. Genes belonging to each of the eight SOMs in Figure 3 are listed on different spreadsheets, along with their annotation and mean expression data in control and in TEV-and TEV-At17-infected plants. Found at: doi:10.1371/journal.pone.0002397.s005 (0.48 MB XLS) Table S5 Transcription factors differentially expressed after infection with TEV and TEV-At17. A. thaliana transcription factors and other transcription regulators were mainly downloaded from arabidopsis.med.ohio-state.edu/AtTFDB/index.jsp, and collapsed with the significantly up-regulated (Table S2 ) and downregulated (Table S3) Table S6 Differential GO categories among differential genes grouped by SOM. FatiGO analysis was carried out for each SOM in Figure 3 . Differential categories were identified for downregulated genes in SOMs B1 plus B2 and B3 ( Figure 3B ) and in up-regulated genes in SOM A3 ( Figure 3A ). List1 includes the differential genes (gene name, number and percentage) belonging to each GO category, while List2 include the rest of genes in the same GO category represented in the microarray. Unadjusted and adjusted P values after correcting for multiple-tests are also indicated.