Computational protocol: A Transcriptomic Analysis of Xylan Mutants Does Not Support the Existence of a Secondary Cell Wall Integrity System in Arabidopsis

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Protocol publication

[…] Data analysis was done using the R-based FlexArray software (Blazejczyk et al., ). For the background correction of raw data, Gene Chip—Robust Multi-array Analysis (GC-RMA) was used (Wu and Irizarry, ). Arrays were normalized using quantile normalization (Bolstad et al., ) and probeset summarization used median polish (Berger and Carlon, ). Arrays were analyzed for significance using the Significance Analysis of Microarrays test (Tusher et al., ), and probesets with a p-value ≤ 0.05 and at least 2-fold change of their log values were retained for further analysis. Gene annotations for the probesets were obtained from the Affymetrix website (http://www.affymetrix.com) and Gene Ontology (GO) was done using Classification Superviewer tool from the Bio-Analytic Resource for Plant Biology (http://bar.utoronto.ca) (Provart and Zhu, ). Data is presented as log2(abundance in mutant/abundance in WT), as described in (Vanholme et al., ). […]

Pipeline specifications

Software tools GC–RMA, SAM
Application Gene expression microarray analysis
Organisms Saccharomyces cerevisiae, Arabidopsis thaliana