Computational protocol: Plasma membrane lipid–protein interactions affect signaling processes in sterol-biosynthesis mutants in Arabidopsis thaliana

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Protocol publication

[…] A combined score for definition of lipid–protein correlations was calculated by multiplying lipid log2 fold changes in mutant versus wildtype with scores from comparative DRM/DSF protein abundance analysis (Unicorn scores). Thereby, only significantly altered proteins were included. Significance of lipid–protein dependence was defined by a false discovery threshold <1%. This threshold was calculated from randomized sampling of lipid ratios and protein Unicorn scores. Networks were visualized using the “igraph” (Han et al., , ) R-package. Protein subcellular localizations were obtained from SUBA3 (Tanz et al., ). Phosphorylation data was obtained from PhosPhat database (Durek et al., ; Zulawski et al., ). Myristoylation data was taken from TAIR and was based on work from Thierry Meinnel's group. Protein palmitoylation was predicted using CSS-Palm software 3.0 (Ren et al., ). GPI-anchoring of proteins was predicted using Arabidopsis specific predictions obtained from GPI-DB (Poisson et al., ). Palmitoylation and GPI-anchoring predictions were FDR (FDR <0.05%) controlled, running both algorithms with randomized sequences from analyzed proteins in parallel. […]

Pipeline specifications

Software tools Igraph, CSS-Palm
Databases TAIR SUBA3 PhosPhAt
Application PTM analysis
Organisms Arabidopsis thaliana