Benitez JA, Ma J, D’Antonio M et al (2017) PTEN regulates glioblastoma oncogenesis through chromatin-associated complexes of DAXX and histone H3.3. Nat Commun 8:15223. https://doi.org/10.1038/ncomms15223

Benjamini Y, Hochberg Y (1995) Controlling the false discovery rate: a practical and powerful approach to multiple testing. J Roy Stat Soc: Ser B (Methodol) 57:289–300. https://doi.org/10.1111/j.2517-6161.1995.tb02031.x

Article  Google Scholar 

Bland JM, Altman DG (1998) Survival probabilities (the Kaplan-Meier method). BMJ 317:1572. https://doi.org/10.1136/bmj.317.7172.1572

Article  CAS  PubMed  PubMed Central  Google Scholar 

Brière G, Darbo É, Thébault P, Uricaru R (2021) Consensus clustering applied to multi-omics disease subtyping. BMC Bioinformatics 22:361. https://doi.org/10.1186/s12859-021-04279-1

Article  PubMed  PubMed Central  Google Scholar 

Bruning-Richardson A, Droop A, Tams D et al (2018) Identification of transcriptional targets of GSK3 involved in glioblastoma invasion. Neuro Oncol 20:i26. https://doi.org/10.1093/neuonc/nox238.117

Article  PubMed Central  Google Scholar 

Burrell RA, McGranahan N, Bartek J, Swanton C (2013) The causes and consequences of genetic heterogeneity in cancer evolution. Nature 501:338–345. https://doi.org/10.1038/nature12625

Article  CAS  PubMed  Google Scholar 

Caswell DR, Swanton C (2017) The role of tumour heterogeneity and clonal cooperativity in metastasis, immune evasion and clinical outcome. BMC Med 15:133. https://doi.org/10.1186/s12916-017-0900-y

Article  CAS  PubMed  PubMed Central  Google Scholar 

Chen J (2016) The cell-cycle arrest and apoptotic functions of p53 in Tumor initiation and progression. Cold Spring Harb Perspect Med 6:a026104. https://doi.org/10.1101/cshperspect.a026104

Article  CAS  PubMed  PubMed Central  Google Scholar 

Copenhaver M, Yu C-Y, Hoffman RP (2019) Complement components, C3 and C4, and the metabolic syndrome. Curr Diabetes Rev 15:44–48. https://doi.org/10.2174/1573399814666180417122030

Article  CAS  PubMed  Google Scholar 

Craene BD, Berx G (2013) Regulatory networks defining EMT during cancer initiation and progression. Nat Rev Cancer 13:97–110. https://doi.org/10.1038/nrc3447

Article  CAS  PubMed  Google Scholar 

de Vivar Chevez AR, Finke J, Bukowski R (2014) The role of inflammation in kidney cancer. Adv Exp Med Biol 816:197–234. https://doi.org/10.1007/978-3-0348-0837-8_9

Article  CAS  PubMed  Google Scholar 

Gene Ontology Consortium (2015) Gene ontology consortium: going forward. Nucleic Acids Res 43:D1049–1056. https://doi.org/10.1093/nar/gku1179

Article  CAS  Google Scholar 

Grivennikov SI, Greten FR, Karin M (2010) Immunity, inflammation, and Cancer. Cell 140:883–899. https://doi.org/10.1016/j.cell.2010.01.025

Article  CAS  PubMed  PubMed Central  Google Scholar 

Groelly FJ, Fawkes M, Dagg RA et al (2023) Targeting DNA damage response pathways in cancer. Nat Rev Cancer 23:78–94. https://doi.org/10.1038/s41568-022-00535-5

Article  CAS  PubMed  Google Scholar 

Guengerich FP (2000) Metabolism of chemical carcinogens. Carcinogenesis 21:345–351. https://doi.org/10.1093/carcin/21.3.345

Article  CAS  PubMed  Google Scholar 

Guess MJ, Wilson SB (2002) Introduction to hierarchical clustering. J Clin Neurophysiol 19:144–151. https://doi.org/10.1097/00004691-200203000-00005

Article  PubMed  Google Scholar 

Hänzelmann S, Castelo R, Guinney J (2013) GSVA: gene set variation analysis for microarray and RNA-seq data. BMC Bioinformatics 14:7. https://doi.org/10.1186/1471-2105-14-7

Article  PubMed  PubMed Central  Google Scholar 

He Y, Jiang Z, Chen C, Wang X (2018) Classification of triple-negative breast cancers based on immunogenomic profiling. J Exp Clin Cancer Res 37:327. https://doi.org/10.1186/s13046-018-1002-1

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hetman M, Cavanaugh JE, Kimelman D, Xia Z (2000) Role of glycogen synthase Kinase-3β in neuronal apoptosis Induced by trophic ithdrawal. J Neurosci 20:2567–2574. https://doi.org/10.1523/JNEUROSCI.20-07-02567.2000

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hosein AN, Brekken RA, Maitra A (2020) Pancreatic cancer stroma: an update on therapeutic targeting strategies. Nat Rev Gastroenterol Hepatol 17:487–505. https://doi.org/10.1038/s41575-020-0300-1

Article  PubMed  PubMed Central  Google Scholar 

Hur E-M, Zhou F-Q (2010) GSK3 signalling in neural development. Nat Rev Neurosci 11:539–551. https://doi.org/10.1038/nrn2870

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kotliarova S, Pastorino S, Kovell LC et al (2008) Glycogen synthase kinase 3 inhibition induces glioma cell death through c-MYC, NF-κB and glucose regulation. Cancer Res 68:6643–6651. https://doi.org/10.1158/0008-5472.CAN-08-0850

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lei J, Luo J, Liu Q, Wang X (2023) Identifying cancer subtypes based on embryonic and hematopoietic stem cell signatures in pan-cancer. Cell Oncol. https://doi.org/10.1007/s13402-023-00886-7

Li L, Wang X (2021) Identification of gastric cancer subtypes based on pathway clustering. npj Precis Onc 5:46. https://doi.org/10.1038/s41698-021-00186-z

Article  CAS  Google Scholar 

Li M, Zhang Z, Li L, Wang X (2020) An algorithm to quantify intratumor heterogeneity based on alterations of gene expression profiles. Commun Biol 3:505. https://doi.org/10.1038/s42003-020-01230-7

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lu Q, Wang S, Pan Y et al (2022) The immune-based prognostic score for the immunogenomic LandscapeAanalysis and application of chemotherapy in breast cancer. Curr Bioinf 17:624–631. https://doi.org/10.2174/1574893617666220524123825

Article  CAS  Google Scholar 

Marinus MG (2012) DNA mismatch repair. EcoSal Plus 5. https://doi.org/10.1128/ecosalplus.7.2.5

Merico D, Isserlin R, Stueker O et al (2010) Enrichment map: a network-based method for gene-set enrichment visualization and interpretation. PLoS ONE 5:e13984. https://doi.org/10.1371/journal.pone.0013984

Article  CAS  PubMed  PubMed Central  Google Scholar 

Mermel CH, Schumacher SE, Hill B et al (2011) GISTIC2.0 facilitates sensitive and confident localization of the targets of focal somatic copy-number alteration in human cancers. Genome Biol 12:R41. https://doi.org/10.1186/gb-2011-12-4-r41

Monti S, Tamayo P, Mesirov J, Golub T (2003) Consensus clustering: a resampling-based method for class discovery and visualization of gene expression microarray data. Mach Learn 52:91–118. https://doi.org/10.1023/A:1023949509487

Article  Google Scholar 

Morris JDH, Eddleston ALWF, Crook T (1995) Viral infection and cancer. Lancet 346:754–758. https://doi.org/10.1016/S0140-6736(95)91510-9

Article  CAS  PubMed  Google Scholar 

Negrini S, Gorgoulis VG, Halazonetis TD (2010) Genomic instability — an evolving hallmark of cancer. Nat Rev Mol Cell Biol 11:220–228. https://doi.org/10.1038/nrm2858

Article  CAS  PubMed