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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

Nassar ZD, Aref AT, Miladinovic D, Mah CY, Raj GV, Hoy AJ et al (2018) Peri-prostatic adipose tissue: the metabolic microenvironment of prostate cancer. BJU Int 121:9–21

Nazari E, Aghemiri M, Avan A, Mehrabian A, Tabesh HJGR (2021) Machine learning approaches for classification of colorectal cancer with and without feature selection method on microarray data. Gen Rep 25:101419

Nazari E, Chang H-CH, Deldar K, Pour R, Avan A, Tara M et al (2020) A comprehensive overview of decision fusion technique in healthcare: a systematic scoping review. Iran Red Crescent Med J 22(10)

Nazari E, Biviji R, Roshandel D, Pour R, Shahriari MH, Mehrabian A et al (2022) Decision fusion in healthcare and medicine: a narrative review. Mhealth 8.

Nikali K, Suomalainen A, Saharinen J, Kuokkanen M, Spelbrink JN, Lönnqvist T et al (2005) Infantile onset spinocerebellar ataxia is caused by recessive mutations in mitochondrial proteins twinkle and twinky. Hum Mol Genet 14(20):2981–2990

O’Brien R, Tran SL, Maritz MF, Liu B, Kong CF, Purgato S et al (2016) MYC-driven neuroblastomas are addicted to a telomerase-independent function of dyskerin. Cancer Res 76(12):3604–3617

Ołdak M, Oziębło D, Pollak A, Stępniak I, Lazniewski M, Lechowicz U et al (2017) Novel neuro-audiological findings and further evidence for TWNK involvement in perrault syndrome. J Transl Med 15(1):1–13

Ramos M, Esteva M, Cabeza E, Llobera J, Ruiz A (2008) Lack of association between diagnostic and therapeutic delay and stage of colorectal cancer. Eur J Cancer 44(4):510–521

Siegel RL, Miller KD, Fuchs HE, Jemal A (2021) Cancer statistics, 2021. CA Cancer J Clin 71(1):7–33

Sieron P, Hader C, Hatina J, Engers R, Wlazlinski A, Müller M et al (2009) DKC1 overexpression associated with prostate cancer progression. Br J Cancer 101(8):1410–1416

Song D, Guo M, Xu S, Song X, Bai B, Li Z et al (2021) HSP90-dependent PUS7 overexpression facilitates the metastasis of colorectal cancer cells by regulating LASP1 abundance. J Exp Clin Cancer Res 40(1):1–24

Spelbrink JN, Li F-Y, Tiranti V, Nikali K, Yuan Q-P, Tariq M et al (2001) Human mitochondrial DNA deletions associated with mutations in the gene encoding Twinkle, a phage T7 gene 4-like protein localized in mitochondria. Nat Genet 28(3):223–231

Sperandei S (2014) Understanding logistic regression analysis. Biochem Med 24(1):12–18

Su Y, Zhang M, Zhang L, Chen S, Zhang D, Zhang XJA (2019) Construction of an miRNA–mRNA regulatory network in colorectal cancer with bioinformatics methods. Anti Cancer Drugs 30(6):588–595

Szklarczyk D, Gable AL, Lyon D, Junge A, Wyder S, Huerta-Cepas J 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

Tomczak K, Czerwińska P, Wiznerowicz M (2015) The Cancer Genome Atlas (TCGA): an immeasurable source of knowledge. Contemp Oncol 19(1A):A68

Varoquaux G, Colliot O (2022) Evaluating machine learning models and their diagnostic value

Wang H, Xiao W, Zhou Q, Chen Y, Yang S, Sheng J et al (2009) Bystin-like protein is upregulated in hepatocellular carcinoma and required for nucleologenesis in cancer cell proliferation. Cell Res 19(10):1150–1164

Wang F, Yuan JH, Wang SB, Yang F, Yuan SX, Ye C et al (2014) Oncofetal long noncoding RNA PVT1 promotes proliferation and stem cell-like property of hepatocellular carcinoma cells by stabilizing NOP2. Hepatology 60(4):1278–1290

Wang T-H, Lee C-Y, Lee T-Y, Huang H-D, Hsu JB-K, Chang T-H (2021) Biomarker identification through multiomics data analysis of prostate cancer prognostication using a deep learning model and similarity network fusion. Cancers 13(11):2528

Wang J, Huang R, Huang Y, Chen Y, Chen F (2021a) Overexpression of NOP58 as a prognostic marker in hepatocellular carcinoma: a TCGA data-based analysis. Adv Ther 38(6):3342–3361

Wang G, Qu F, Liu S, Zhou J, Wang Y (2021b) Nucleolar protein NOP2 could serve as a potential prognostic predictor for clear cell renal cell carcinoma. Bioengineered 12(1):4841–4855

Wei C, Wang B, Chen Z-H, Xiao H, Tang L, Guan J-F et al (2022) Validating RRP12 expression and its prognostic significance in HCC basebd on data mining and bioinformatics methods. Front Oncol 12:812009

Wu H, Qin W, Lu S, Wang X, Zhang J, Sun T et al (2020) Long noncoding RNA ZFAS1 promoting small nucleolar RNA-mediated 2′-O-methylation via NOP58 recruitment in colorectal cancer. Mol Cancer 19(1):1–22

Yang Y-S, Yuan Y, Hu W-P, Shang Q-X, Chen L-Q (2018) The role of mitochondrial folate enzyme MTHFD1L in esophageal squamous cell carcinoma. Scand J Gastroenterol 53(5):533–540

Zhang S, Li X, Zong M, Zhu X, Cheng DJ (2017) Technology learning k for Knn classification. ACM Trans Intell Syst Technol 8(3):1–19

Zhang M, Meng L, Zhang Z, Wu J, Chen X, He J (2022) The respective relations of expression of OSBPL3 with Ki-67 expression and KRAS mutation in CRC for diagnosis and prognosis

Zhou C, Ye M, Ni S, Li Q, Ye D, Li J et al (2018) DNA methylation biomarkers for head and neck squamous cell carcinoma. Epigenetics 13(4):398–409