dphansti
commented
1 year ago That is great that you are using these tools. And thanks for reaching out. Unfortunately, these tools make use of data collected by previous researchers/publications. The data to make the CORALP tree was taken directly from Chen et al 2017 (https://www.science.org/doi/10.1126/scisignal.aag1796). The CORAL tree was taken directly from Manning et al and a tree drawn by Cell Signaling Technology (https://www.science.org/doi/full/10.1126/science.1075762). More info about which kinases and phosphatases are included can be found here (https://github.com/dphansti/CORAL/blob/master/Data/coral_dataframe.tsv) and here (https://github.com/PhanstielLab/coralp/blob/master/Data/PhosphataseTree.tsv).
We rely fully on those previous publications and don't have plans to incorporate new or other proteins.
Hello, I am a Postdoctoral researcher working in Angus Nairn’s lab, Department of Psychiatry, Yale University. We used a proximity labelling proteomics approach to identify the protein interactome of a brain phosphoprotein in rats. We identified 1945 proximal proteins (organism: rat) to this phosphoprotein. We used CORALP software to identify the phosphatases and kinases in the proximal protein interactome. Though the software identified and plotted PPIs with hierarchical information, there are lots of isoforms which are missing. For example, the software identified PPP2CB but not PPP2R2A, PPP2R5D, PPP1R9A. Like this many phosphatases were not identified. We believe that the proteins which were not identified are not in the phosphatase database of the software. The same happened with kinases as well.
We would like to know if there is an updated version of the software that could include these missing phosphatases and kinase isoforms? We would appreciate it if you could suggest some solutions. Thank you for your time. Boby