Gibberella_zeae 13k Microarray Expression profiling was conducted with the Gibberella zeae (anamorph Fusarium graminearum) 13k Microarray. The 13k Microarray was designed from the F. graminearum sequencing assembly released Mar. 2007 (http://www.broad.mit.edu/annotation/genome/fusarium_group/MultiDownloads.html). The assembly contained 13,382 transcripts. Ten 60-nt long probes were designed from each gene starting 250 bp ahead the end of stop codon and with shifting 10 bp so 10 probes cover 150 bp in the 3' region of the gene. Mitochondrial genes (50) and selection markers such as gfp, gus, hyg, bar, and kan were included. Probes were duplicated in 2 blocks. In total, 267,324 probes were designed. The average size of probe is 60-nt long with adjusting its Tm value 75 to 85 °C. The microarray was manufctured at NimbleGen inc (http://www.nimblegen.com/). Random GC probes (40,000) to monitor the hybridization efficiency and four corner fiducial controls (225) were included to assist with overlaying the grid on the image. Multiple analysis was performed with limma package in R computing environment (Smyth, G. K. (2004). Linear models and empirical Bayes methods for assessing differential expression in microarray experiments. Statistical Applications in Genetics and Molecular Biology, Vol. 3, No. 1, Article 3). The package adopts the linear modeling approach implemented by lmFit and the empirical Bayes statistics implemented by eBayes. Genes of which adj.P.Value or false discovery below 0.05 were collected and further selected for those gene expressions were higher than 1 or less than -1 at least at one stage compared to that at stage1. Multivariate statistical tests such as clustering, principal component analysis, and multidimensional scaling were performed with Acuity 3.1 (Axon Instruments). Hierarchical clustering was performed with similarity metrics based on squared Euclidean correlation and average linkage clustering was used to calculate the distance of genes. Hybridization Genes on microarray