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In most cases, transcripts with high sequence homology responded similarly to a specific biotic stress (Supporting Information Table?S3), so averaging the fold-change data across similar genes was not likely to influence the results. Data sets were subjected to hierarchical average-linkage clustering with Cluster software (Eisen et?al. 1998) and displayed with TreeView version 1.60 (http://rana.lbl.gov/EisenSoftware.htm). http://www.selleck.cn/products/Imatinib(STI571).html The output from the clustering algorithm provided a graphical display of the similarity of expression data as well as similarity among the response of different forms of biotic stress. Shades of green and magenta represent genes that were downregulated and upregulated, respectively, and the intensity of colour represents the magnitude of the fold-change relative to controls. No ��mask�� was applied to the graphical output, so all significant genes were displayed regardless of the magnitude of the response; the same ��image contrast�� was applied to each analysis, so the fold-change values represented by the colour intensity were consistent across figures. The black colour represented the genes with no significant transcript change for the studies performed with Arabidopsis. For species other than Arabidopsis, dark grey represented the absence of the gene on the microarray or the inability to identify sequence homologs to Arabidopsis (Figs?1�C4, Supporting Information Table?S2). The http://www.selleckchem.com/products/AZD6244.html cluster analysis of photosynthesis light reaction, carbon fixation, photorespiration, ROS scavenging network and starch and sucrose metabolism genes showed co-expression patterns. The protein sequences of these co-expressed genes were obtained from TAIR and subcellular localization of each gene was determined by ChloroP 1.1 (Emanuelsson, Nielsen & von Heijne 1999; http://www.cbs.dtu.dk/services/ChloroP/). Within co-expressed clusters the genes were grouped according to their subcellular localization as chloroplast targeted or not. To determine the enriched DNA motifs that might be co-regulating elements in co-expressed gene clusters, the 2?kb upstream sequences of co-expressed and chloroplast targeted and non-targeted genes were obtained from Matt http://www.selleckchem.com/products/SP600125.html Hudson Lab Bioinformatics and Plant Genomics database (Hudson & Quail 2003; http://stan.cropsci.uiuc.edu/index.php). The enriched DNA motifs in these upstream sequences were determined with the same database. The number of occurrences of each motif was compared with the frequency of that element in the sequence of the promoters for the whole genome by a version of one-degree-of-freedom chi squared test. The over-represented elements with P?