{"doi":"10.1016/j.mcpro.2023.100596","title":"PhosphoDisco: A Toolkit for Co-regulated Phosphorylation Module Discovery in Phosphoproteomic Data","abstract":"Kinases are key players in cancer-relevant pathways and are the targets of many successful precision cancer therapies (1Bhullar K.S. Lagarón N.O. McGowan E.M. Parmar I. Jha A. Hubbard B.P. Rupasinghe H.P.V. Kinase-targeted cancer therapies: progress, challenges and future directions.Mol Cancer. 2018; 17: 48Crossref PubMed Scopus (613) Google Scholar, 2Malone E.R. Oliva M. Sabatini P.J.B. Stockley T.L. Siu L.L. Molecular profiling for precision cancer therapies.Genome Med. 2020; 12: 8Crossref PubMed Scopus (287) Google Scholar). Phosphoproteomics is a powerful approach to study kinase activity and has been used increasingly for the characterization of tumor samples leading to the identification of novel chemotherapeutic targets and biomarkers (3Clark, D. J., Dhanasekaran, S. M., Petralia, F., Pan, J., Song, X., Hu, Y., da Veiga Leprevost, F., Reva, B., Lih, T.-S. M., Chang, H.-Y., Ma, W., Huang, C., Ricketts, C. J., Chen, L., Krek, A., Li, Y., Rykunov, D., Li, Q. K., Chen, L. S., Ozbek, U., Vasaikar, S., Wu, Y., Yoo, S., Chowdhury, S., Wyczalkowski, M. A., Ji, J., Schnaubelt, M., Kong, A., Sethuraman, S., Avtonomov, D. M., Ao, M., Colaprico, A., Cao, S., Cho, K.-C., Kalayci, S., Ma, S., Liu, W., Ruggles, K., Calinawan, A., Gümüş, Z. H., Geiszler, D., Kawaler, E., Teo, G. C., Wen, B., Zhang, Y., Keegan, S., Li, K., Chen, F., Edwards, N., Pierorazio, P. M., Chen, X. S., Pavlovich, C. P., Hakimi, A. A., Brominski, G., Hsieh, J. J., Antczak, A., Omelchenko, T., Lubinski, J., Wiznerowicz, M., Linehan, W. M., Kinsinger, C. R., Thiagarajan, M., Boja, E. S., Mesri, M., Hiltke, T., Robles, A. I., Rodriguez, H., Qian, J., Fenyö, D., Zhang, B., Ding, L., Schadt, E., Chinnaiyan, A. M., Zhang, Z., Omenn, G. S., Cieslik, M., Chan, D. W., Nesvizhskii, A. I., Wang, P., Zhang, H., and Clinical Proteomic Tumor Analysis Consortium (2019) Integrated Proteogenomic Characterization of Clear Cell Renal Cell Carcinoma. Cell 179, 964-983.e31Google Scholar, 4Dou, Y., Kawaler, E. A., Cui Zhou, D., Gritsenko, M. A., Huang, C., Blumenberg, L., Karpova, A., Petyuk, V. A., Savage, S. R., Satpathy, S., Liu, W., Wu, Y., Tsai, C.-F., Wen, B., Li, Z., Cao, S., Moon, J., Shi, Z., Cornwell, M., Wyczalkowski, M. A., Chu, R. K., Vasaikar, S., Zhou, H., Gao, Q., Moore, R. J., Li, K., Sethuraman, S., Monroe, M. E., Zhao, R., Heiman, D., Krug, K., Clauser, K., Kothadia, R., Maruvka, Y., Pico, A. R., Oliphant, A. E., Hoskins, E. L., Pugh, S. L., Beecroft, S. J. I., Adams, D. W., Jarman, J. C., Kong, A., Chang, H.-Y., Reva, B., Liao, Y., Rykunov, D., Colaprico, A., Chen, X. S., Czekański, A., Jędryka, M., Matkowski, R., Wiznerowicz, M., Hiltke, T., Boja, E., Kinsinger, C. R., Mesri, M., Robles, A. I., Rodriguez, H., Mutch, D., Fuh, K., Ellis, M. J., DeLair, D., Thiagarajan, M., Mani, D. R., Getz, G., Noble, M., Nesvizhskii, A. I., Wang, P., Anderson, M. L., Levine, D. A., Smith, R. D., Payne, S. H., Ruggles, K. V., Rodland, K. D., Ding, L., Zhang, B., Liu, T., Fenyö, D., and Clinical Proteomic Tumor Analysis Consortium (2020) Proteogenomic Characterization of Endometrial Carcinoma. Cell 180, 729-748.e26Google Scholar, 5Drake J.M. Paull E.O. Graham N.A. Lee J.K. Smith B.A. Titz B. Stoyanova T. Faltermeier C.M. Uzunangelov V. Carlin D.E. Fleming D.T. Wong C.K. Newton Y. Sudha S. Vashisht A.A. Huang J. Wohlschlegel J.A. Graeber T.G. Witte O.N. Stuart J.M. Phosphoproteome Integration Reveals Patient-Specific Networks in Prostate Cancer.Cell. 2016; 166: 1041-1054Abstract Full Text Full Text PDF PubMed Scopus (144) Google Scholar, 6Huang K.-L. Li S. Mertins P. Cao S. Gunawardena H.P. Ruggles K.V. Mani D.R. Clauser K.R. Tanioka M. Usary J. Kavuri S.M. Xie L. Yoon C. Qiao J.W. Wrobel J. Wyczalkowski M.A. Erdmann-Gilmore P. Snider J.E. Hoog J. Singh P. Niu B. Guo Z. Sun S.Q. Sanati S. Kawaler E. Wang X. Scott A. Ye K. McLellan M.D. Wendl M.C. Malovannaya A. Held J.M. Gillette M.A. Fenyö D. Kinsinger C.R. Mesri M. Rodriguez H. Davies S.R. Perou C.M. Ma C. Reid Townsend R. Chen X. 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