Computational protocol: Pichia pastoris regulates its gene-specific response to different carbon sources at the transcriptional, rather than the translational, level

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Protocol publication

[…] In-house P. pastoris DNA microarrays (Agilent platform, AMAD-ID: 034821, design and general processing as described by []) were used. cRNA synthesis, hybridization and scanning were done according to the Agilent protocol for 2-color expression arrays. Each sample was hybridized against an RNA reference pool sample in dye swap. The microarray data were not background normalized. Within the arrays, loess-normalization was done for the color-effect. Quantile normalization was done between the arrays, the limma package (R-project) was used to calculate fold-changes, and p-value correction was done for multiple testing using the false discovery rate controlling method of []. Raw microarray data are provided in Additional file . Venn diagrams were created using the web-based tool Venny [] and gene ontology (GO) term enrichment analysis was conducted with GO term finder and Saccharomyces Genome Database (SGD) annotations.Principal component analysis was performed with the Excel plug-in XLSTAT.Synonymous codon usage order (SCUO) analysis was performed online using the CondonO platform [].The statistical analysis was done in R using the standard functions fisher.test, chisq.test, and lm for the regression []. The implementation of the Fisher test obtains the p-values directly if a 2 by 2 table is present [], otherwise a network implementation based on FEXACT was used []. For the group comparisons a test on normality was performed (Shapiro-Wilk-test) and Wilcoxon-Rank tests were performed since normality was not given. […]

Pipeline specifications

Software tools limma, VENNY, GO::TermFinder
Databases SGD
Application Gene expression microarray analysis
Organisms Komagataella pastoris, Saccharomyces cerevisiae
Chemicals Methanol, Carbon, Glucose, Glycerol