A Curated Resource for Phosphosite-specific Signature Analysis

著者: Karsten Krug, Philipp Mertins, Bin Zhang, Peter Hornbeck, Rajesh Raju, Rushdy Ahmad, Matthew J. Szucs, Filip Mundt, Dominique Forestier, Judit Jané‐Valbuena, Hasmik Keshishian, Michael A. Gillette, Pablo Tamayo, Jill P. Mesirov, Jacob D. Jaffe, StevenA. Carr, D.R. Mani - Molecular & Cellular Proteomics 2018 被引用: 368

nalysis (PTM-SEA) of quantitative MS data. We used a well-characterized data set of epidermal growth factor (EGF)-perturbed cancer cells to evaluate our approach and demonstrated better representation of signaling events compared with gene-centric methods. We then applied PTM-SEA to analyze the phosphoproteomes of cancer cells treated with cell-cycle inhibitors and detected mechanism-of-action specific signatures of cell cycle kinases. We also applied our methods to analyze the phosphoproteomes of PI3K-inhibited human breast cancer cells and detected signatures of compounds inhibiting PI3K as well as targets downstream of PI3K (AKT, MAPK/ERK) covering a substantial fraction of the PI3K pathway. PTMsigDB and PTM-SEA can be freely accessed at https://github.com/broadinstitute/ssGSEA2.0.