Abramson J, Adler J, Dunger J, Evans R, Green T et al (2024) Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature 630(8016):493–500. https://doi.org/10.1038/s41586-024-07487-w

Article  CAS  PubMed  PubMed Central  Google Scholar 

Capitanio U, Bensalah K, Bex A, Boorjian SA, Bray F, Coleman J, Gore JL, Sun M, Wood C, Russo P (2019) Epidemiology of renal cell carcinoma. Eur Urol 75(1):74–84. https://doi.org/10.1016/j.eururo.2018.08.036

Article  PubMed  Google Scholar 

Cerami E, Gao J, Dogrusoz U, Gross BE, Sumer SO et al (2012) The cBio cancer genomics portal: an open platform for exploring multidimensional cancer genomics data. Cancer Discov 2(5):401–404. https://doi.org/10.1158/2159-8290.CD-12-0095

Article  PubMed  Google Scholar 

Chandrashekar DS, Karthikeyan SK, Korla PK, Patel H, Shovon AR et al (2022) UALCAN: an update to the integrated cancer data analysis platform. Neoplasia 25:18–27. https://doi.org/10.1016/j.neo.2022.01.001

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen SA, Zhang JP, Wang N, Chen J (2023) Identifying TYMP as an immune prognostic marker in clear cell renal cell carcinoma. Technol Cancer Res Treat 22:15330338231194555. https://doi.org/10.1177/15330338231194555

Article  CAS  PubMed  PubMed Central  Google Scholar 

Danková Z, Braný D, Dvorská D, Ňachajová M, Fiolka R, Grendár M, Hatok J, Kubatka P, Holubeková V, Halašová E, Bielik T, Žúbor P (2018) Methylation status of KLF4 and HS3ST2 genes as predictors of endometrial cancer and hyperplastic endometrial lesions. Int J Mol Med 42(6):3318–3328. https://doi.org/10.3892/ijmm.2018.3872

Article  CAS  PubMed  PubMed Central  Google Scholar 

Das PM, Singal R (2004) DNA methylation and cancer. J Clin Oncol 22(22):4632–4642. https://doi.org/10.1200/JCO.2004.07.151

Article  CAS  PubMed  Google Scholar 

Díez-Villanueva A, Mallona I, Peinado MA (2015) Wanderer, an interactive viewer to explore DNA methylation and gene expression data in human cancer. Epigenetics Chromatin 8:22. https://doi.org/10.1186/s13072-015-0014-8

Article  CAS  PubMed  PubMed Central  Google Scholar 

Filosto M, Cotti Piccinelli S, Caria F, Gallo Cassarino S, Baldelli E, Galvagni A, Volonghi I, Scarpelli M, Padovani A (2018) Mitochondrial Neurogastrointestinal Encephalomyopathy (MNGIE-MTDPS1). J Clin Med 7(11):389. https://doi.org/10.3390/jcm7110389

Article  CAS  PubMed  PubMed Central  Google Scholar 

Huang X, Wang L, Chen Y, Zheng X, Wang X (2017) Poor prognosis associated with high levels of thymidine phosphorylase and thrombocytosis in patients with renal cell carcinoma. Urol Int 98(2):162–168. https://doi.org/10.1159/000448483

Article  CAS  PubMed  Google Scholar 

Koch A, Joosten SC, Feng Z, de Ruijter TC, Draht MX et al (2018) Analysis of DNA methylation in cancer: location revisited. Nat Rev Clin Oncol 15(7):459–466. https://doi.org/10.1038/s41571-018-0004-4

Article  CAS  PubMed  Google Scholar 

Li Y, Fan C, Hu Y, Zhang W, Li H, Wang Y, Xu Z (2024) Multi-cohort validation: a comprehensive exploration of prognostic marker in clear cell renal cell carcinoma. Int Immunopharmacol 135:112300. https://doi.org/10.1016/j.intimp.2024.112300

Article  CAS  PubMed  Google Scholar 

Liu M, Pan Q, Xiao R, Yu Y, Lu W, Wang L (2020) A cluster of metabolism-related genes predict prognosis and progression of clear cell renal cell carcinoma. Sci Rep 10(1):12949. https://doi.org/10.1038/s41598-020-67760-6

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liu Z, Wang P, Chen H, Wold EA, Tian B, Brasier AR, Zhou J (2017) Drug discovery targeting bromodomain-containing protein 4. J Med Chem 60(11):4533–4558. https://doi.org/10.1021/acs.jmedchem.6b01761

Article  CAS  PubMed  PubMed Central  Google Scholar 

Modhukur V, Iljasenko T, Metsalu T, Lokk K, Laisk-Podar T, Vilo J (2018) MethSurv: a web tool to perform multivariable survival analysis using DNA methylation data. Epigenomics 10(3):277–288. https://doi.org/10.2217/epi-2017-0118

Article  CAS  PubMed  Google Scholar 

Mullen NJ, Singh PK (2023) Nucleotide metabolism: a pan-cancer metabolic dependency. Nat Rev Cancer 23(5):275–294. https://doi.org/10.1038/s41568-023-00557-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rambhia A, Patel RD, Okhawere KE, Korn TG, Badani KK (2021) Immunotherapy for metastatic renal cell carcinoma: a brief history, current trends, and future directions. Urol Oncol 39(10):664–677. https://doi.org/10.1016/j.urolonc.2021.06.013

Article  CAS  PubMed  Google Scholar 

Ren LX, Qi JC, Zhao AN, Shi B, Zhang H, Wang DD, Yang Z (2021) Myc-associated zinc-finger protein promotes clear cell renal cell carcinoma progression through transcriptional activation of the MAP2K2-dependent ERK pathway. Cancer Cell Int 21(1):323. https://doi.org/10.1186/s12935-021-02020-9

Article  CAS  PubMed  PubMed Central  Google Scholar 

Ricketts CJ, De Cubas AA, Fan H, Smith CC, Lang M et al (2018) The cancer genome atlas comprehensive molecular characterization of renal cell carcinoma. Cell Rep 23(1):313-326e5. https://doi.org/10.1016/j.celrep.2018.03.075

Article  CAS  PubMed  PubMed Central  Google Scholar 

Rimoldi M, Wang N, Zhang J, Villar D, Odom DT, Taipale J, Flicek P, Roller M (2024) DNA methylation patterns of transcription factor binding regions characterize their functional and evolutionary contexts. Genome Biol 25(1):146. https://doi.org/10.1186/s13059-024-03218-6

Article  CAS  PubMed  PubMed Central  Google Scholar 

Siegel RL, Miller KD, Fuchs HE, Jemal A (2022) Cancer statistics, 2022. CA Cancer J Clin 72(1):7–33. https://doi.org/10.3322/caac.21708

Article  PubMed  Google Scholar 

Siegel RL, Miller KD, Jemal A (2020) Cancer statistics, 2020. CA Cancer J Clin 70(1):7–30. https://doi.org/10.3322/caac.21590

Article  PubMed  Google Scholar 

Sin-Chan P, Mumal I, Suwal T, Ho B, Fan X et al (2019) A C19MC-LIN28A-MYCN oncogenic circuit driven by hijacked super-enhancers is a distinct therapeutic vulnerability in ETMRs: a Lethal Brain Tumor. Cancer Cell 36(1):51-67e7. https://doi.org/10.1016/j.ccell.2019.06.002

Article  CAS  PubMed  Google Scholar 

Sung H, Ferlay J, Siegel RL, Laversanne M, Soerjomataram I, Jemal A, Bray F (2021) Global Cancer statistics 2020: GLOBOCAN estimates of incidence and Mortality Worldwide for 36 cancers in 185 countries. CA Cancer J Clin 71(3):209–249. https://doi.org/10.3322/caac.21660

Article  CAS  PubMed  Google Scholar 

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S et al (2019) STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 47(D1):D607–D613. https://doi.org/10.1093/nar/gky1131

Article  CAS  PubMed  Google Scholar 

Taanman JW, Daras M, Albrecht J, Davie CA, Mallam EA et al (2009) Characterization of a novel TYMP splice site mutation associated with mitochondrial neurogastrointestinal encephalomyopathy (MNGIE). Neuromuscul Disord 19(2):151–154. https://doi.org/10.1016/j.nmd.2008.11.002

Article  PubMed  Google Scholar 

Tomczak K, Czerwińska P, Wiznerowicz M (2015) The cancer genome atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol (Pozn) 19(1A):A68–A77. https://doi.org/10.5114/wo.2014.47136

Article