Computational protocol: Transcriptional Analysis of Arabidopsis thaliana Response to Lima Bean Volatiles

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Protocol publication

[…] Affymetrix microarrays (Arabidopsis ATH1 genome array) containing 22,810 probe sets were used in our experiments. Labeling and hybridization on the ATH1 microarrays (one sample per chip) were performed according to the manufacturer's instructions (www.affymetrix.com/support/technical/manual/expression_manual.affx). Global analysis of temporal gene expression was performed by subjecting the absolute expression values for scaling using Affymetrix MAS5.0. The probe arrays were further analyzed with GENESPRING Version 5.0 (Silicon Genetics). Normalization of every gene and chip was performed to allow comparisons of two or three independent replicates performed for each set of experiment. SAM analysis (Significance Analysis of Microarrays software package) was conducted for A. thaliana triplicate samples between treatment and control plants using a q value ≤0.05 and a fold change cutoff ≥2 to identify the genes differentially expressed in the treatments . We searched GO enrichment information for the differently expressed probe sets using EasyGO (http://bioinformatics.cau.edu.cn/easygo/category_treeBrowse.html). We applied χ 2 analysis for the biological process search, and the cutoff for false discovery rate (FDR) was adjusted using a p value of 0.0001. Cluster 3.0 and TreeView were used (http://rana.Stanford.EDU/software/) to group and display genes with similar expression profiles . We used the default options of hierarchical clustering with uncentered correlation similarity metrics. All GeneChip data sets are available in a MIAME-compliant format through GEO (accession no. GSE33505). […]

Pipeline specifications

Software tools GeneSpring GX, SAM, EasyGO, TreeView
Application Gene expression microarray analysis
Organisms Arabidopsis thaliana, Drosophila melanogaster