Cohen P. The structure and regulation of protein phosphatases. Annu Rev Biochem. 1989;58:453–508.

Article  CAS  PubMed  Google Scholar 

Stebbing J, Lit LC, Zhang H, Darrington RS, Melaiu O, Rudraraju B, et al. The regulatory roles of phosphatases in cancer. Oncogene. 2014;33:939–53.

Article  CAS  PubMed  Google Scholar 

Tonks NK. Protein tyrosine phosphatases: from genes, to function, to disease. Nat Rev Mol Cell Biol. 2006;7:833–46.

Article  CAS  PubMed  Google Scholar 

Barford D, Das AK, Egloff M-P, THE STRUCTURE AND, MECHANISM OF PROTEIN PHOSPHATASES. Insights into Catalysis and Regulation. Annu Rev Biophys Biomol Struct. 1998;27:133–64.

Article  CAS  PubMed  Google Scholar 

Li X, Wilmanns M, Thornton J, Köhn M. Elucidating human phosphatase-substrate networks. Sci Signal. 2013;6.

Bononi A, Agnoletto C, De Marchi E, Marchi S, Patergnani S, Bonora M, et al. Protein kinases and phosphatases in the control of cell fate. Enzyme Res. 2011;2011:1–26.

Article  Google Scholar 

Turdo A, D’Accardo C, Glaviano A, Porcelli G, Colarossi C, Colarossi L et al. Targeting phosphatases and kinases: how to Checkmate Cancer. Front Cell Dev Biol. 2021;9.

Fontanillo M, Köhn M, Phosphatases. Their Roles in Cancer and Their Chemical Modulators. 2016. p. 209–40.

Li J, Yen C, Liaw D, Podsypanina K, Bose S, Wang SI, et al. PTEN, a putative protein tyrosine phosphatase gene mutated in human brain, breast, and prostate cancer. Science. 1997;275:1943–7.

Article  CAS  PubMed  Google Scholar 

Calin GA, Di Iasio MG, Caprini E, Vorechovsky I, Natali PG, Sozzi G, et al. Low frequency of alterations of the alpha (PPP2R1A) and beta (PPP2R1B) isoforms of the subunit a of the serine-threonine phosphatase 2A in human neoplasms. Oncogene. 2000;19:1191–5.

Article  CAS  PubMed  Google Scholar 

Zhang Q, Claret FX, Phosphatases. The New brakes for Cancer Development? Enzyme Res. 2012;2012:1–11.

Article  Google Scholar 

Steelman LS, Chappell WH, Abrams SL, Kempf CR, Long J, Laidler P, et al. Roles of the Raf/MEK/ERK and PI3K/PTEN/Akt/mTOR pathways in controlling growth and sensitivity to therapy-implications for cancer and aging. Aging. 2011;3:192.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Wang Z. Mutational analysis of the Tyrosine Phosphatome in Colorectal cancers. Sci (80-). 2004;304:1164–6.

Article  ADS  CAS  Google Scholar 

FUNATO K, YAMAZUMI Y, ODA T. Tyrosine phosphatase PTPRD suppresses colon cancer cell migration in coordination with CD44. Exp Ther Med. 2011;2:457–63.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Veeriah S, Brennan C, Meng S, Singh B, Fagin JA, Solit DB, et al. The tyrosine phosphatase PTPRD is a tumor suppressor that is frequently inactivated and mutated in glioblastoma and other human cancers. Proc Natl Acad Sci U S A. 2009;106:9435–40.

Article  ADS  CAS  PubMed  PubMed Central  Google Scholar 

Yao Z, Darowski K, St-Denis N, Wong V, Offensperger F, Villedieu A, et al. A Global Analysis of the receptor tyrosine kinase-protein phosphatase interactome. Mol Cell. 2017;65:347–60.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Scrima M, De Marco C, De Vita F, Fabiani F, Franco R, Pirozzi G, et al. The nonreceptor-type tyrosine phosphatase PTPN13 is a tumor suppressor gene in non–small cell Lung Cancer. Am J Pathol. 2012;180:1202–14.

Article  CAS  PubMed  Google Scholar 

Caunt CJ, Keyse SM. Dual-specificity MAP kinase phosphatases (MKPs). FEBS J. 2013;280:489–504.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Muniyan S, Ingersoll MA, Batra SK, Lin M-F. Cellular prostatic acid phosphatase, a PTEN-functional homologue in prostate epithelia, functions as a prostate-specific tumor suppressor. Biochim Biophys Acta - Rev Cancer. 2014;1846:88–98.

Article  CAS  Google Scholar 

Hedberg Oldfors C, Dios DG, Linder A, Visuttijai K, Samuelson E, Karlsson S, et al. Analysis of an independent tumor suppressor locus telomeric to Tp53 suggested Inpp5k and Myo1c as novel tumor suppressor gene candidates in this region. BMC Genet. 2015;16:80.

Article  PubMed  PubMed Central  Google Scholar 

Esteller M. Epigenetics in Cancer. N Engl J Med. 2008;358:1148–59.

Article  CAS  PubMed  Google Scholar 

Ortiz-Barahona V, Joshi RS, Esteller M. Use of DNA methylation profiling in translational oncology. Semin Cancer Biol. 2020. https://doi.org/10.1016/j.semcancer.2020.12.011.

Article  PubMed  Google Scholar 

Luo S, Chen J, Mo X. The association of PTEN hypermethylation and breast cancer: a meta-analysis. Onco Targets Ther. 2016;9:5643–50.

Article  PubMed  PubMed Central  Google Scholar 

Vanaja DK, Ballman KV, Morlan BW, Cheville JC, Neumann RM, Lieber MM, et al. PDLIM4 repression by hypermethylation as a potential biomarker for prostate cancer. Clin Cancer Res. 2006;12:1128–36.

Article  CAS  PubMed  Google Scholar 

Ying J, Li H, Cui Y, Wong AHY, Langford C, Tao Q. Epigenetic disruption of two proapoptotic genes MAPK10/JNK3 and PTPN13/FAP-1 in multiple lymphomas and carcinomas through hypermethylation of a common bidirectional promoter. Leukemia. 2006;20:1173–5.

Article  CAS  PubMed  Google Scholar 

Li D, Guo J, Wang S, Zhu L, Shen Z. Identification of novel methylated targets in colorectal cancer by microarray analysis and construction of co–expression network. Oncol Lett. 2017;14:2643–8.

Article  PubMed  PubMed Central  Google Scholar 

Takane K, Midorikawa Y, Yagi K, Sakai A, Aburatani H, Takayama T, et al. Aberrant promoter methylation of PPP1R3C and EFHD1 in plasma of colorectal cancer patients. Cancer Med. 2014;3:1235–45.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Barazeghi E, Hellman P, Westin G, Stålberg P. PTPRM, a candidate tumor suppressor gene in small intestinal neuroendocrine tumors. Endocr Connect. 2019;8:1126–35.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Tögel L, Nightingale R, Wu R, Chüeh AC, Al-Obaidi S, Luk I, et al. DUSP5 is methylated in CIMP-high colorectal cancer but is not a major regulator of intestinal cell proliferation and tumorigenesis. Sci Rep. 2018;8:1767.

Article  ADS  PubMed  PubMed Central  Google Scholar 

Schmid CA, Robinson MD, Scheifinger NA, Müller S, Cogliatti S, Tzankov A, et al. DUSP4 deficiency caused by promoter hypermethylation drives JNK signaling and tumor cell survival in diffuse large B cell lymphoma. J Exp Med. 2015;212:775–92.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Iorio F, Knijnenburg TA, Vis DJ, Bignell GR, Menden MP, Schubert M, et al. A Landscape of Pharmacogenomic interactions in Cancer. Cell. 2016;166:740–54.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Team RC, R Core Team. (2021). R: A language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria. URL https://www.R-project.org/.

Aryee MJ, Jaffe AE, Corrada-Bravo H, Ladd-Acosta C, Feinberg AP, Hansen KD, et al. Minfi: a flexible and comprehensive Bioconductor package for the analysis of Infinium DNA methylation microarrays. Bioinformatics. 2014;30:1363–9.

Article  CAS  PubMed  PubMed Central  Google Scholar 

Fortin J-P, Triche TJ, Hansen KD. Preprocessing, normalization and integration of the Illumina HumanMethylationEPIC array with minfi. Bioinformatics. 2016. btw691.

Joshi R, Castro De Moura M, Piñeyro D, Alvarez-Errico D, Arribas C, Esteller M. The DNA methylation landscape of human cancer organoids available at the American type culture collection. Epigenetics. 2020;15:1167–77.

Article  PubMed  PubMed Central  Google Scholar 

Suzuki R, Shimodaira H. Pvclust: an R package for assessing the uncertainty in hierarchical clustering. Bioinformatics. 2006;22:1540–2.

Article  CAS  PubMed  Google Scholar 

Müllner D. Fastcluster: fast hierarchical, agglomerative clustering routines for R and Python. J Stat Softw. 2013;53.

van der Maaten LJP, Hinton GE. Visualizing high-dimensional data using t-SNE. J Mach Learn Res. 2008;9:2579–605.

Google Scholar 

LVD M. Accelerating t-SNE using tree-based algorithms. J Mach Learn Res. 2014;15:3221–45.

MathSciNet  Google Scholar 

Colaprico A, Silva TC, Olsen C, Garofano L, Cava C, Garolini D, et al. TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data. Nucleic Acids Res. 2016;44:e71–1.

Article  PubMed  Google Scholar 

Silva TC, Colaprico A, Olsen C, D’Angelo F, Bontempi G, Ceccarelli M, et al. TCGA Workflow: analyze cancer genomics and epigenomics data using Bioconductor packages. F1000Research. 2016;5:1542.

Article  PubMed  PubMed Central  Google Scholar 

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