Identification of ZMYND19 as a novel biomarker of colorectal cancer: RNA-sequencing and machine learning analysis

Agarwal S, Behring M, Hale K, Al Diffalha S, Wang K, Manne U et al (2019) MTHFD1L, a folate cycle enzyme, is involved in progression of colorectal cancer. Transl Oncol 12(11):1461–1467

Article  PubMed  PubMed Central  Google Scholar 

Akkoca AN, Yanık S, Özdemir ZT, Cihan FG, Sayar S, Cincin TG et al (2014) TNM and Modified Dukes staging along with the demographic characteristics of patients with colorectal carcinoma. Int J Clin Exp Med 7(9):2828

PubMed  PubMed Central  Google Scholar 

Alzahrani SM, Al Doghaither HA, Al-Ghafari ABJM, Oncology C (2021) General insight into cancer: an overview of colorectal cancer. Mol Clin Oncol 15(6):1–8

Article  Google Scholar 

Ayala GE, Dai H, Li R, Ittmann M, Thompson TC, Rowley D et al (2006) Bystin in perineural invasion of prostate cancer. Prostate 66(3):266–272

Article  CAS  PubMed  Google Scholar 

Bi J, Huang Y, Liu Y (2019) Effect of NOP2 knockdown on colon cancer cell proliferation, migration, and invasion. Transl Cancer Res 8(6):2274

Article  CAS  PubMed  PubMed Central  Google Scholar 

Biau G, Scornet EJT (2016) A random forest guided tour. TEST 25(2):197–227

Article  Google Scholar 

Dinga R, Penninx BW, Veltman DJ, Schmaal L, Marquand AF (2019) Beyond accuracy: measures for assessing machine learning models, pitfalls and guidelines

Diray-Arce J, Liu B, Cupp JD, Hunt T, Nielsen BL (2013) The ArabidopsisAt1g30680 gene encodes a homologue to the phage T7 gp4 protein that has both DNA primase and DNA helicase activities. BMC Plant 13(1):1–11

Google Scholar 

Dong D, Zhang W, Xiao W, Wu Q, Cao Y, Gao X et al (2021) A GRN autocrine-dependent FAM135B/AKT/mTOR feedforward loop promotes esophageal squamous cell carcinoma progression. Cancer Res 81(4):910–922

Article  CAS  PubMed  Google Scholar 

Du J, Gong A, Zhao X, Wang G (2022) Pseudouridylate synthase 7 promotes cell proliferation and invasion in colon cancer through activating PI3K/AKT/mTOR signaling pathway. Dig Dis Sci 67(4):1260–1270

Article  CAS  PubMed  Google Scholar 

Duan L, Yang W, Wang X, Zhou W, Zhang Y, Liu J et al (2019) Advances in prognostic markers for colorectal cancer. Expert Rev Mol Diagn 19(4):313–324

Article  CAS  PubMed  Google Scholar 

Eich M-L, Pena MDCR, Chandrashekar DS, Chaux A, Agarwal S, Gordetsky JB et al (2019) Expression and role of methylenetetrahydrofolate dehydrogenase 1 like (MTHFD1L) in bladder cancer. Transl Oncol 12(11):1416–1424

Article  PubMed  PubMed Central  Google Scholar 

Estève D, Roumiguié M, Manceau C, Milhas D, Muller C (2020) Periprostatic adipose tissue: a heavy player in prostate cancer progression. Curr Opin Endocr Metab Res 10:29–35

Article  Google Scholar 

Fergus P, Chalmers C (2022) Performance evaluation metrics. Applied deep learning. Springer, pp 115–138

Chapter  Google Scholar 

Gao S, Sha Z, Zhou J, Wu Y, Song Y, Li C et al (2021) BYSL contributes to tumor growth by cooperating with the mTORC2 complex in gliomas. Cancer Biol Med 18(1):88

Article  CAS  PubMed  PubMed Central  Google Scholar 

Gatalica Z, Torlakovic E (2008) Pathology of the hereditary colorectal carcinoma. Fam Cancer 7(1):15–26

Article  PubMed  Google Scholar 

Gaviraghi M, Vivori C, Tonon G (2019) How cancer exploits ribosomal RNA biogenesis: a journey beyond the boundaries of rRNA transcription. Cells 8(9):1098

Article  CAS  PubMed  PubMed Central  Google Scholar 

Godoy H, Mhawech-Fauceglia P, Beck A, Miliotto A, Miller A, Lele S et al (2013) Developmentally restricted differentiation antigens are targets for immunotherapy in epithelial ovarian carcinoma. Int J Gynecol Pathol 32(6):536

Article  CAS  PubMed  PubMed Central  Google Scholar 

Goswami MT, Chen G, Chakravarthi BV, Pathi SS, Anand SK, Carskadon SL et al (2015) Role and regulation of coordinately expressed de novo purine biosynthetic enzymes PPAT and PAICS in lung cancer. Oncotarget 6(27):23445

Article  PubMed  PubMed Central  Google Scholar 

Guerrieri AN (2020) Evaluation of the role of DKC1 overexpression in breast cancer

Hammad A, Elshaer M, Tang XJMB (2021) Engineering identification of potential biomarkers with colorectal cancer based on bioinformatics analysis and machine learning. Math Biosci Eng 18(6):8997–9015

Article  PubMed  Google Scholar 

He J, Yu J (2019) Long noncoding RNA FAM83A-AS1 facilitates hepatocellular carcinoma progression by binding with NOP58 to enhance the mRNA stability of FAM83A. Bioscience reports. Biosci Rep 39(11)

Hirano M, DiMauro SJN (2001) ANT1, Twinkle, POLG, and TP: new genes open our eyes to ophthalmoplegia. AAN Enterprises, pp 2163–2165

Hossain MJ, Chowdhury UN, Islam MB, Uddin S, Ahmed MB, Quinn JM et al (2021) Machine learning and network-based models to identify genetic risk factors to the progression and survival of colorectal cancer. Comput Biol Med 135:104539

Article  CAS  PubMed  Google Scholar 

Hou P, Shi P, Jiang T, Yin H, Chu S, Shi M et al (2020) DKC1 enhances angiogenesis by promoting HIF-1α transcription and facilitates metastasis in colorectal cancer. Br J Cancer 122(5):668–679

Article  CAS  PubMed  Google Scholar 

Hu M, Fu X, Si Z, Li C, Sun J, Du X et al (2019) Identification of differently expressed genes associated with prognosis and growth in colon adenocarcinoma based on integrated bioinformatics analysis. Front Genet 10:1245

Article  CAS  PubMed  PubMed Central  Google Scholar 

Hu Q, Masuda T, Koike K, Sato K, Tobo T, Kuramitsu S et al (2021) Oxysterol binding protein-like 3 (OSBPL3) is a novel driver gene that promotes tumor growth in part through R-Ras/Akt signaling in gastric cancer. Sci Rep 11(1):1–12

Google Scholar 

Jiao H-l, Weng B-s, Yan S-s, Lin Z-m, Wang S-y, Chen X-p et al (2020) Upregulation of OSBPL3 by HIF1A promotes colorectal cancer progression through activation of RAS signaling pathway. Cell Death Dis 11(7):1–13

Article  Google Scholar 

Kadowaki S, Kakuta M, Takahashi S, Takahashi A, Arai Y, Nishimura Y et al (2015) Prognostic value of KRAS and BRAF mutations in curatively resected colorectal cancer. World J Gastroenterol WJG 21(4):1275

Article  CAS  PubMed  Google Scholar 

Katsoulas A, Rachid Z, McNamee JP, Williams C, Jean-Claude BJ (2008) Combi-targeting concept: an optimized single-molecule dual-targeting model for the treatment of chronic myelogenous leukemia. Mol Cancer Ther 7(5):1033–1043

Article  CAS  PubMed  Google Scholar 

Kelley RK, Venook AP (2011) Prognostic and predictive markers in stage II colon cancer: is there a role for gene expression profiling? Clin Colorectal Cancer 10(2):73–80

Article  CAS  PubMed  PubMed Central  Google Scholar 

Kim GP, Colangelo LH, Wieand HS, Paik S, Kirsch IR, Wolmark N et al (2007) Prognostic and predictive roles of high-degree microsatellite instability in colon cancer: a National Cancer Institute-National Surgical Adjuvant Breast and Bowel Project Collaborative Study. J Clin Oncol 25(7):767–772

Article  CAS  PubMed  Google Scholar 

Kim JH, Kim SY, Baek JY, Cha YJ, Ahn JB, Kim HS et al (2020) A phase II study of avelumab monotherapy in patients with mismatch repair-deficient/microsatellite instability-high or POLE-mutated metastatic or unresectable colorectal cancer. Cancer Res Treat 52(4):1135–1144

CAS  PubMed  PubMed Central  Google Scholar 

Kristensen VN, Lingjærde OC, Russnes HG, Vollan HKM, Frigessi A, Børresen-Dale A-L (2014) Principles and methods of integrative genomic analyses in cancer. Nat Rev Cancer 14(5):299–313

Article  CAS  PubMed  Google Scholar 

Lee JK, Chan AT (2011) Molecular prognostic and predictive markers in colorectal cancer: current status. Curr Colorectal Cancer Rep 7(2):136–144

Article  CAS  PubMed  PubMed Central  Google Scholar 

Lee D, Xu IM-J, Chiu DK-C, Lai RK-H, Tse AP-W, Li LL et al (2017) Folate cycle enzyme MTHFD1L confers metabolic advantages in hepatocellular carcinoma. J Clin Investig 127(5):1856–1872

Article  PubMed  PubMed Central  Google Scholar 

Li H, Chen L, Han Y, Zhang F, Wang Y, Han Y et al (2021) The identification of RNA modification gene PUS7 as a potential biomarker of ovarian cancer. Biology 10(11):1130

Article  CAS  PubMed  PubMed Central  Google Scholar 

Liang J, Wen J, Huang Z, Chen X-p, Zhang B-x, Chu L (2019) Small nucleolar RNAs: insight into their function in cancer. Front Oncol 9:587

Article  PubMed  PubMed Central  Google Scholar 

Liao H, Gaur A, McConie H, Shekar A, Wang K, Chang JT et al (2021) hNOP2/NSUN1 regulates ribosome biogenesis through stabilization of snoRNP complexes and cytosine-5 methylation of 28S rRNA. bioRxiv

Liu K, Chen H-L, Wang S, Gu M-M, Chen X-M, Zhang S-L et al (2016) High expression of RIOK2 and NOB1 predict human non-small cell lung cancer outcomes. Sci Rep 6(1):1–8

Google Scholar 

Liu H, Li J, Zhao H, Liu X, Ye X (2021) DNAJC2 is reversely regulated by miR-627-3p, promoting the proliferation of colorectal cancer. Mol Med Rep 24(2):1–10

Article  Google Scholar 

Liu B, Zhang J, Huang C, Liu H (2012) Dyskerin overexpression in human hepatocellular carcinoma is associated with advanced clinical stage and poor patient prognosis

Maurya NS, Kushwaha S, Chawade A, Mani A (2021) Transcriptome profiling by combined machine learning and statistical R analysis identifies TMEM236 as a potential novel diagnostic biomarker for colorectal cancer. Sci Rep 11(1):1–11

Article  Google Scholar 

Micu BV, Andercou O, Vesa SC, Micu CM, Pop TR, Constantea N (2017) The prognostic role of microsatellite instability in colorectal cancer patients. Ann Ital Chir 6:425–432

PubMed 

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