Reproducibility repo for Shashikadze et al. "Structural and proteomic repercussions of growth hormone receptor deficiency on the pituitary gland – lessons from a translational pig model".
Maxquant protein groups file was first processed with Perseus. Proteins with valid values in at least 70% of all replicates in at least one condition (genotype) were quantified. Missing values were imputed from a normal distribution using the Perseus default parameters (width - 0.3 and down-shift - 1.8). The volcano plot was generated with the Perseus, using Student’s t-test and permutation-based FDR cut-off of 0.05, alongside with an s0-parameter of 0.1. The imputed data with Perseus-generated statistics was used for downstream analysis in R. Figure 3 and figure 4 in the manuscript were generated with the following code.
Next, 2-way anova analysis was performed followed with Tukey's HSD - R code to reproduce the results
The proteomics dataset has been submitted to the ProteomeXchange Consortium via the PRIDE [1] partner repository (PXD035833).
- Perez-Riverol, Y., et al., The PRIDE database and related tools and resources in 2019: improving support for quantification data. Nucleic Acids Res, 2019. 47(D1): p. D442-d450.