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ByrumLab / ProteoViz

Interactive tool for Phosphoproteomics
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ProteoViz

Interactive tool for Phosphoproteomics

Aaron J. Storey , Kevin Naceanceno , Renny Lan , Charity L. Washam, Lisa M. Orr , Samuel G. Mackintosh, Alan J. Tackett, Rick D. Edmondson, Zhengyu Wang, Hong-yu, Brendan Frett, Samantha Kendrick, Stephanie D. Byrum*. (2020) ProteoViz: A tool for the analysis and interactive visualization of phosphoproteomics data. Molecular Omics. DOI: 10.1039/c9mo00149b

Graphical output of motifx Sequence motif analysis

Set of R scripts for the analysis and visualization of Phosphoproteomics data sets.

Script 1: Creates metadata that links with the MaxQuant database search results
Script 2: Normalizes and runs limma differential expression on the protein lysate samples
Script 3: Normalizes phosphosites to the protein expression and runs limma differential expression
Script 4: Creates the input data file needed to run PTMsig analysis
Script 5: Runs PTMsig/ssGSEA
Script 6: Runs EGSEA gene set enrichment analysis
Script 7A-7C: Creates the interactive Shiny dashboard for visualization

MaxQuant txt files are saved in the txt folder
Scripts are in the src folder
Create a Sample_metadata.tsv and contrast_matrix.tsv file associated with your experiment to run the code

References:

  1. M. E. Ritchie, B. Phipson, D. Wu, Y. Hu, C. W. Law, W. Shi and G. K. Smyth, Nucleic Acids Research, 2015, 43, e47-e47. https://academic.oup.com/nar/article/43/7/e47/2414268

  2. K. Krug, P. Mertins, B. Zhang, P. Hornbeck, R. Raju, R. Ahmad, M. Szucs, F. Mundt, D. Forestier, J. Jane-Valbuena, H. Keshishian, M. A. Gillette, P. Tamayo, J. P. Mesirov, J. D. Jaffe, S. A. Carr and D. R. Mani, Mol Cell Proteomics, 2019, 18, 576-593. https://www.mcponline.org/content/18/3/576

  3. M. Alhamdoosh, C. W. Law, L. Tian, J. M. Sheridan, M. Ng and M. E. Ritchie, F1000Res, 2017, 6, 2010. https://f1000research.com/articles/6-2010