Computational protocol: The Arabidopsis LRR-RLK, PXC1, is a regulator of secondary wall formation correlated with the TDIF-PXY/TDR-WOX4 signaling pathway

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Protocol publication

[…] Microarray expression data sets were explored for the predicted AtLRR-RLK genes using the Arabidopsis Affymetrix GeneChip® average data available on the GENEVESTIGATOR analysis tool site (http://www.genevestigator.ethz.ch) []. The Gene Co-expression Analysis (GeneCAT) Toolbox at http://genecat.mpg.de/cgi-bin/Ainitiator.py[] was used to generate the Expression Tree which clustered genes by the similarity of their expression profiles and visualized those similarities using a dendogram. To minimize the effects of experimental artifacts, data were renormalized, and Pearson’s correlation coefficient between genes was weighted in ATTED-II []. […]

Pipeline specifications

Software tools Genevestigator, GeneCAT
Databases ATTED-II
Application Transcription analysis
Organisms Arabidopsis thaliana