Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver

Identifying Differentially Abundant Phosphoproteome Sites With ProteomeRiver

Ignatius Pang (Childrens Medical Research Institute, Australia)

4:00 PM - 4:15 PM AEDT (Australian Eastern Daylight Time) on Friday, Dec. 2nd, 2022
LONG TALK

Identifying phosphorylation sites and how they change in abundance under different environmental conditions are important for elucidating the role of signal regulations in cellular processes. ProteomeRiver is a novel pipeline that facilitates the analysis of differential abundance of proteins and their phosphorylation events. The pipeline enables the batch analysis of many pairwise treatment versus control comparisons and subsequent pathways overrepresentation analysis. To enable differential abundance analysis of mono- and multi-phosphorylation events, ProteomeRiver incorporates missing values imputation (PhosR*, Kim et al. Cell Rep., 34(8), 108771), removal of unwanted variation (ruv*, Molania et al. 2019 Nucleic Acids Res. 47:6073 - 6083), linear models (limma*, Ritchie et al. 2015 Nucleic Acids Res. 43(7), e47), kinase-substrate enrichment (KinSwingR*), and pathways analysis (clusterProfiler*, Wu et al. The Innovation, 2(3), 100141). This pipeline uses modular components, which allows the modules to be substituted and/or extended with novel tools as they become available. This pipeline also uses a small set of configuration files and scripts to store all instructions necessary for data analysis, which could be shared publicly on code repositories to support reproducibility. The impact of applying remove unwanted variation and normalising the changes in abundance of phosphorylation events by the changes in host protein abundance was demonstrated through the re-analysis of a published dataset of synapses proteome and phosphoproteome during homeostatic up- and down-scaling (Desch et al. 2021 Cell Rep. 36:109583). Compared with the results from the original publication, the use of ProteomeRiver resulted in the identification of novel pathways and upstream kinases associated with homeostatic up- and down-scaling. The pipeline is currently under development and will be available as a R package via https://bitbucket.org/cmri-bioinforma.... (*) denotes R or Bioconductor packages.

Moderator: Peter Hickey (WEHI, Australia)