Figure 5

Clustering analysis of differentially regulatedgenes in PPV-infected Arabidopsis protoplasts. (A) Hierarchical clustering and changes in gene expression of 411 significantly (Q ≤ 0.05) differentially regulated genes in PPV-infected Arabidopsis protoplasts at 3, 6 and 12 hours post transfection (hpt). Gene tree map generated from 411 significantly differentially regulated Arabidopsis genes are derived from 263 upregulated and 304 downregulated genes. (B) Using k-mean clustering, the gene expression profiles were grouped into twelve major cluster groups. The expression pattern of a gene in a cluster group is indicated in parentheses. Expression levels are color coded with red indicating upregulation by PPV infection; green indicating downregulation by PPV infection; and black indicating no change in expression. The intensity of color represents the degree of gene expression levels. List of genes induced or repressed at each time point in different cluster groups along with their expression levels and putative functions is provided in [Additional file 8].