Computational protocol: Arabidopsis flower specific defense gene expression patterns affect resistance to pathogens

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Protocol publication

[…] Analyses were performed on sepal data (Voelckel et al., ) and publicly available microarray data from the AtGenExpress developmental series (Schmid et al., ) for flowers and pollen (GSE5632) and leaves (GSE5630) for sepal (stage 15, GSM131603-GSM131605), petal (stage 15, GSM131606-GSM131608), rosette (GSM131510-GSM131512), leaf 1+2 GSM131498-GSM131500) and senescent leaf (GSM131537-GSM131539) samples were downloaded from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/, Edgar et al., ; Barrett et al., ). Arrays were normalized using Robust Multi-Array Averaging (RMA) in the Bioconductor affylmGUI package (Smyth, ; Smyth et al., ; Wettenhall et al., ) before a linear fit model was applied and the following contrasts (differentials) calculated: sepal vs. petal, sepal vs. rosette, sepal vs. leaf (not shown), sepal vs. senescent leaf, petal vs. senescent leaf. The top 25 most up-regulated genes in each contrast were then selected according to descending B-statistics. GO analyses were performed on each up-regulated gene list using AgriGO (http://bioinfo.cau.edu.cn/agriGO/, Du et al., ). The data from the transcriptional analyses are in Table . […]

Pipeline specifications

Software tools affylmGUI, agriGO
Databases GEO
Application Gene expression microarray analysis
Organisms Arabidopsis thaliana, Botrytis cinerea
Chemicals Salicylic Acid