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4101MCID_676f085df306d7202f067694 32908931 Jin-Han Gu[author] Gu, Jin Han[Full Author Name] gu, jin han[Author] trying2...
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2314-614120202020BioMed research internationalBiomed Res IntThe Expression and Potential Role of Tubulin Alpha 1b in Wilms' Tumor.98093479809347980934710.1155/2020/9809347We explored the difference in expression of tubulin alpha 1b (TUBA1B) between Wilms' tumor (WT) and normal tissues (NT) from in-house patients and databases, to determine TUBA1B expression in WT and the predictive pathways of coexpressed genes. In-house RNA-sequencing data were performed with WT and NT from three patients from our institute. Other four RNA-sequencing and microarray data were also downloaded from multiple public databases. The TUBA1B expression between WT and NT was analyzed by Student's t-test and meta-analysis. The correlation between the expression of TUBA1B and other genes in each study was analyzed. Genes with p < 0.05 and r > 0.5 were considered as the coexpressing genes of TUBA1B. Overlapping the coexpressed genes of the five studies, including three in-house patients (3 WT vs. 3 NT), GTEx-TARGET (126 WT vs. 51 NT), GSE2172 (18 WT vs. 3 NT), GSE11024 (27 WT vs. 12 NT), and GSE73209 (32 WT vs. 6 NT), were performed with limma and VennDiagram packages in R software. The website of WEB-based GEne SeT AnaLysis toolkit were used to analyze the gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) functional annotations for the overlapped genes. The results showed that the relative expression of TUBA1B in WT tissues from in-house three patients was 280.0086, 141.7589, and 303.8292 and that in NT was 16.5836, 104.8141, and 12.79 (3 WT vs. 3 NT, p = 0.0285, ROC = 100%, SMD = 2.74). Student's t-test and meta-analysis in all studies revealed that the expression of TUBA1B was upregulated in WT tissues compared to that in NT (p < 0.05, SMD = 2.89, sROC = 0.98). Finally, the research identified the expression of TUBA1B in WT tissues was significantly upregulated than that in NT. The coexpressed genes of TUBA1B were enriched in the pathway of DNA replication, mismatch repair, cell cycle, pathogenic Escherichia coli infection, and spliceosome.Copyright © 2020 Qiong-Qian Xu et al.XuQiong-QianQQDepartment of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.QinLi-TingLTDepartment of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.LiangSong-WuSWDepartment of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.ChenPengPDepartment of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.GuJin-HanJHDepartment of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.HuangZhi-GuangZGDepartment of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.YangXiaXDepartment of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.GaoLiLDepartment of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.WangShi-ShuoSSDepartment of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.LuoYi-GeYGDepartment of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.LiuLin-Le-YiLLDepartment of First Clinical Medical College, Guangxi Medical University, Nanning 530021, China.WangJunJDepartment of First Clinical Medical College, Guangxi Medical University, Nanning 530021, China.LinJin-YanJYDepartment of First Clinical Medical College, Guangxi Medical University, Nanning 530021, China.ChenGangG0000-0003-2402-2987Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.ChenJia-BoJB0000-0003-1757-3481Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning 530021, China.engJournal Article20200825
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2288-65759922020AugAnnals of surgical treatment and researchAnn Surg Treat ResNomogram for predicting overall survival in children with neuroblastoma based on SEER database.118126118-12610.4174/astr.2020.99.2.118This study was performed to establish and validate a nomogram for predicting the overall survival in children with neuroblastoma.The latest clinical data of neuroblastoma in Surveillance, Epidemiology, and End Results (SEER) database was extracted from 2000 to 2016. The cases included were randomly divided into training and validation cohorts. The survival curves were drawn with a Kaplan-Meier estimator to investigate the influences of certain single factors on overall survival. Also, least absolute shrinkage and selection operator regression was applied to further select the prognostic variables for neuroblastoma. Additionally, receiver operating characteristic (ROC) curves and calibration curves were used to evaluate the accuracy of the nomogram.In total, 1,262 patients were collected and 8 independent prognostic factors were achieved, including patients' age, sex, race, tumor grade, radiotherapy, chemotherapy, tumor site, and tumor size. Then we constructed a nomogram by using the data of the training cohort with 886 cases. Subsequently, the nomogram was validated internally and externally with 886 and 376 cases, respectively. The internal validation revealed that the area under the curves (AUC) of ROC curves of 1-, 3-, and 5-year overall survival were 0.69, 0.78, and 0.81, respectively. Accordingly, the external validation also showed that the AUC of 1-, 3-, and 5-year overall survival were all ≥0.69. Both methods of validation demonstrated that the predictive calibration curves were consistent with standard curves.The nomogram possess the potential to be a new tool in predicting the survival rate of neuroblastoma patients.Copyright © 2020, the Korean Surgical Society.LiangSong-WuSW0000-0002-5664-8776Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.ChenGangG0000-0002-4864-1451Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.LuoYi-GeYG0000-0002-2929-4482Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.ChenPengP0000-0001-5893-8120Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.GuJin-HanJH0000-0003-1663-6532Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.XuQiong-QianQQ0000-0003-0924-2658Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.DangYi-WuYW0000-0002-7793-1239Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.QinLi-TingLT0000-0003-0213-2499Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.LuHui-PingHP0000-0001-7765-0763Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.HuangWen-TingWT0000-0002-8635-1500Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.HuangZhi-GuangZG0000-0003-4457-9491Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.GaoLiL0000-0003-4418-0528Department of Pathology, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.ChenJia-BoJB0000-0003-1757-3481Department of Pediatric Surgery, The First Affiliated Hospital of Guangxi Medical University, Nanning, China.engJournal Article20200731
Korea (South)Ann Surg Treat Res1016228952288-6575NeuroblastomaNomogramsPrognosisRisk factorsSEER programConflict of Interest: No potential conflict of interest relevant to this article was reported.201912262020525202065202081860202081860202081861202081ppublish32802817PMC740640010.4174/astr.2020.99.2.118Jubierre L, Jiménez C, Rovira E, Soriano A, Sábado C, Gros L, et al. Targeting of epigenetic regulators in neuroblastoma. Exp Mol Med. 2018;50:51.PMC593802129700278Rickman DS, Schulte JH, Eilers M. The expanding world of N-MYC-driven tumors. Cancer Discov. 2018;8:150–163.29358508Meena JP, Gupta AK. Neuroblastoma in a developing country: miles to go. Indian J Pediatr. 2019;86:403–405.30915646Zareifar S, Shakibazad N, Zekavat OR, Bordbar M, Shahriari M. Successful treatment of refractory metastatic neuroblastoma with panobinostat in combination with chemotherapy agents and iodine-131-meta-iodobenzylguanidine therapy. J Oncol Pharm Pract. 2020;26:481–486.31156056Herd F, Basta NO, McNally RJQ, Tweddle DA. A systematic review of re-induction chemotherapy for children with relapsed high-risk neuroblastoma. Eur J Cancer. 2019;111:50–58.PMC645896330822684Swift CC, Eklund MJ, Kraveka JM, Alazraki AL. Updates in diagnosis, management, and treatment of neuroblastoma. Radiographics. 2018;38:566–580.29528815PDQ Pediatric Treatment Editorial Board. PDQ Cancer Information Summaries. Bethesda (MD): National Cancer Institute (US); 2002. Neuroblastoma Treatment (PDQ®): Health Professional Version.Valter K, Zhivotovsky B, Gogvadze V. Cell death-based treatment of neuroblastoma. Cell Death Dis. 2018;9:113.PMC583387429371588Pastor ER, Mousa SA. Current management of neuroblastoma and future direction. Crit Rev Oncol Hematol. 2019;138:38–43.31092383Han Y, Ye X, Cheng J, Zhang S, Feng W, Han Z, et al. Integrative analysis based on survival associated co-expression gene modules for predicting Neuroblastoma patients' survival time. Biol Direct. 2019;14:4.PMC637520330760313Yao W, Li K, Dong KR, Zheng S, Xiao XM. Long-term prognosis of low-risk neuroblastoma treated by surgery alone: an experience from a single institution of China. World J Pediatr. 2019;15:148–152.30446974Pinto NR, Applebaum MA, Volchenboum SL, Matthay KK, London WB, Ambros PF, et al. Advances in risk classification and treatment strategies for neuroblastoma. J Clin Oncol. 2015;33:3008–3017.PMC456770326304901Morgenstern DA, Bagatell R, Cohn SL, Hogarty MD, Maris JM, Moreno L, et al. The challenge of defining “ultra-high-risk” neuroblastoma. Pediatr Blood Cancer. 2019;66:e27556.30479064Park JR, Bagatell R, Cohn SL, Pearson AD, Villablanca JG, Berthold F, et al. Revisions to the international neuroblastoma response criteria: a consensus statement from the National Cancer Institute clinical trials planning meeting. J Clin Oncol. 2017;35:2580–2587.PMC567695528471719Matthay KK, Maris JM, Schleiermacher G, Nakagawara A, Mackall CL, Diller L, et al. Neuroblastoma. Nat Rev Dis Primers. 2016;2:16078.27830764Cohn SL, Pearson AD, London WB, Monclair T, Ambros PF, Brodeur GM, et al. The International Neuroblastoma Risk Group (INRG) classification system: an INRG Task Force report. J Clin Oncol. 2009;27:289–297.PMC265038819047291Brodeur GM, Pritchard J, Berthold F, Carlsen NL, Castel V, Castelberry RP, et al. Revisions of the international criteria for neuroblastoma diagnosis, staging, and response to treatment. J Clin Oncol. 1993;11:1466–1477.8336186Hu CY, Pan ZY, Yang J, Chu XH, Zhang J, Tao XJ, et al. Nomograms for predicting long-term overall survival and cancer-specific survival in lip squamous cell carcinoma: a population-based study. Cancer Med. 2019;8:4032–4042.PMC663925431112373Liu G, Liu Q, Sun SR. Nomograms for estimating survival in patients with papillary thyroid cancer after surgery. 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1643-3750262020Mar26Medical science monitor : international medical journal of experimental and clinical researchMed Sci MonitRNA-Sequencing, Connectivity Mapping, and Molecular Docking to Investigate Ligand-Protein Binding for Potential Drug Candidates for the Treatment of Wilms Tumor.e920725e92072510.12659/MSM.920725BACKGROUND Wilms tumor, or nephroblastoma, is a malignant pediatric embryonal renal tumor that has a poor prognosis. This study aimed to use bioinformatics data, RNA-sequencing, connectivity mapping, molecular docking, and ligand-protein binding to identify potential targets for drug therapy in Wilms tumor. MATERIAL AND METHODS Wilms tumor and non-tumor samples were obtained from high throughput gene expression databases, and differentially expressed genes (DEGs) were analyzed using the voom method in the limma package. The overlapping DEGs were obtained from the intersecting drug target genes using the Connectivity Map (CMap) database, and systemsDock was used for molecular docking. Gene databases were searched for gene expression profiles for complementary analysis, analysis of clinical significance, and prognosis analysis to refine the study. RESULTS From 177 cases of Wilms tumor, there were 648 upregulated genes and 342 down-regulated genes. Gene Ontology (GO) enrichment analysis showed that the identified DEGs that affected the cell cycle. After obtaining 21 candidate drugs, there were seven overlapping genes with 75 drug target genes and DEGs. Molecular docking results showed that relatively high scores were obtained when retinoic acid and the cyclin-dependent kinase inhibitor, alsterpaullone, were docked to the overlapping genes. There were significant standardized mean differences for three overlapping genes, CDK2, MAP4K4, and CRABP2. However, four upregulated overlapping genes, CDK2, MAP4K4, CRABP2, and SIRT1 had no prognostic significance. CONCLUSIONS RNA-sequencing, connectivity mapping, and molecular docking to investigate ligand-protein binding identified retinoic acid and alsterpaullone as potential drug candidates for the treatment of Wilms tumor.LuoJia-YuanJYDepartment of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).YanShi-BaiSBDepartment of Medical Oncology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).ChenGangGDepartment of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).ChenPengPDepartment of Pediatric Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).LiangSong-WuSWDepartment of Pediatric Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).XuQiong-QianQQDepartment of Pediatric Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).GuJin-HanJHDepartment of Pediatric Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).HuangZhi-GuangZGDepartment of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).QinLi-TingLTDepartment of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).LuHui-PingHPDepartment of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).MoWei-JiaWJDepartment of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).LuoYi-GeYGDepartment of Pediatric Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).ChenJia-BoJBDepartment of Pediatric Surgery, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China (mainland).engJournal Article20200326
United StatesMed Sci Monit96090631234-10100Antineoplastic Agents0LigandsIMAntineoplastic Agentspharmacologytherapeutic useDrug Evaluation, PreclinicalGene Expression Regulation, NeoplasticGene OntologyHumansKaplan-Meier EstimateLigandsMolecular Docking SimulationPrognosisProtein BindingROC CurveSequence Analysis, RNAWilms Tumordrug therapygeneticsConflict of interest. None.20203286020203286020201219602020326epublish32214060PMC711944710.12659/MSM.920725920725Fu W, Zhuo Z, Hua RX, et al. Association of KRAS and NRAS gene polymorphisms with Wilms tumor risk: a four-center case-control study. Aging (Albany NY) 2019;11:1551–63.PMC642809530860980Bu Q, He H, Fan D, et al. Association between loss of heterozygosity of chromosome 16q and survival in Wilms’ tumor: A meta-analysis. Pathol Res Pract. 2018;214:1772–77.30143352Cao X, Liu DH, Zhou Y, et al. Histone deacetylase 5 promotes Wilms’ tumor cell proliferation through the upregulation of c-Met. 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1097-465223542020AprJournal of cellular physiologyJ Cell PhysiolA novel risk signature that combines 10 long noncoding RNAs to predict neuroblastoma prognosis.382338343823-383410.1002/jcp.29277Neuroblastoma (NBL) is the most frequently encountered extracranial solid neoplasm and impacts significantly on the survival of patients, especially in cases of advanced tumor stage or relapse. A long noncoding RNA (lncRNA) signature to predict the survival of patients with NBL is proposed in this paper. Differentially expressed lncRNA (DElncRNA) was selected using the Limma plus Voom package in R based on the RNA-sequencing data downloaded from the Therapeutically Applicable Research To Generate Effective Treatments database and Genotype-Tissue Expression database. Univariate cox regression analysis, least absolute shrinkage and selection operator regression analysis, and multivariate cox regression analysis were conducted to identify candidate DElncRNAs for the risk signature. Consequently, 10 DElncRNAs were designated as candidate DElncRNAs for the risk signature. Time-dependent receiver operating characteristic curves and Kapan-Meier survival curves confirmed the efficacy of the risk signature in predicting the survival of patients with NBL (area under the curve = 0.941; p ≤ .001). One of the DElncRNA constituent subparts (LINC01010) was significantly associated with the survival outcome of patients with NBL in GSE62564 (p = .004). Thus, a risk signature comprising 10 DElncRNAs was identified as effective for individual risk stratification and the survival prediction outcomes of patients with NBL.© 2019 Wiley Periodicals, Inc.GaoLiLDepartment of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.LinPengPDepartment of Ultrasound, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.ChenPengPDepartment of Pediatric Surgery, First calculated using the following formula Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.GaoRui-ZhiRZDepartment of Ultrasound, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.YangHongHDepartment of Ultrasound, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.HeYunYDepartment of Ultrasound, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.ChenJia-BoJBDepartment of Pediatric Surgery, First calculated using the following formula Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.LuoYi-GeYGDepartment of Pediatric Surgery, First calculated using the following formula Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.XuQiong-QianQQDepartment of Pediatric Surgery, First calculated using the following formula Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.LiangSong-WuSWDepartment of Pediatric Surgery, First calculated using the following formula Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.GuJin-HanJHDepartment of Pediatric Surgery, First calculated using the following formula Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.HuangZhi-GuangZGDepartment of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.DangYi-WuYWDepartment of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.ChenGangG0000-0002-4864-1451Department of Pathology, First Affiliated Hospital of Guangxi Medical University, Nanning, Guangxi, China.engJournal ArticleResearch Support, Non-U.S. Gov't20191014
United StatesJ Cell Physiol00502220021-95410Biomarkers, Tumor0RNA, Long NoncodingIMBiomarkers, TumorgeneticsFemaleGene Expression Regulation, NeoplasticgeneticsHumansInfantKaplan-Meier EstimateMaleNeoplasm Recurrence, LocalgeneticspathologyNeuroblastomageneticspathologyPrognosisRNA, Long NoncodingclassificationgeneticsRisk FactorsSequence Analysis, RNATranscriptomeTherapeutically Applicable Research to Generate Effective Treatmentslong noncoding RNAneuroblastomaprognosisrisk signature201952820199272019101660202123602019101660ppublish3161248810.1002/jcp.29277REFERENCESBarone, G., Anderson, J., Pearson, A. D. J., Petrie, K., & Chesler, L. (2013). New strategies in neuroblastoma: Therapeutic targeting of MYCN and ALK. Clinical Cancer Research, 19(21), 5814-5821. https://doi.org/10.1158/1078-0432.ccr-13-0680Benjamini, Y., & Hochberg, Y. (1995). Controlling for the false discovery rate: A practical and power approach to multiple testing. 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Publications by Jin-Han Gu | LitMetric
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The Expression and Potential Role of Tubulin Alpha 1b in Wilms' Tumor.
Qiong-Qian Xu Li-Ting Qin Song-Wu Liang Peng Chen Jin-Han Gu Zhi-Guang Huang

Biomed Res Int

May 2021

We explored the difference in expression of tubulin alpha 1b (TUBA1B) between Wilms' tumor (WT) and normal tissues (NT) from in-house patients and databases, to determine TUBA1B expression in WT and the predictive pathways of coexpressed genes. In-house RNA-sequencing data were performed with WT and NT from three patients from our institute. Other four RNA-sequencing and microarray data were also downloaded from multiple public databases.

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Nomogram for predicting overall survival in children with neuroblastoma based on SEER database.
Song-Wu Liang Gang Chen Yi-Ge Luo Peng Chen Jin-Han Gu Zhi-Guang Huang

Ann Surg Treat Res

August 2020

Purpose: This study was performed to establish and validate a nomogram for predicting the overall survival in children with neuroblastoma.

Methods: The latest clinical data of neuroblastoma in Surveillance, Epidemiology, and End Results (SEER) database was extracted from 2000 to 2016. The cases included were randomly divided into training and validation cohorts.

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RNA-Sequencing, Connectivity Mapping, and Molecular Docking to Investigate Ligand-Protein Binding for Potential Drug Candidates for the Treatment of Wilms Tumor.
Jia-Yuan Luo Shi-Bai Yan Gang Chen Peng Chen Song-Wu Liang Jin-Han Gu Zhi-Guang Huang

Med Sci Monit

March 2020

BACKGROUND Wilms tumor, or nephroblastoma, is a malignant pediatric embryonal renal tumor that has a poor prognosis. This study aimed to use bioinformatics data, RNA-sequencing, connectivity mapping, molecular docking, and ligand-protein binding to identify potential targets for drug therapy in Wilms tumor. MATERIAL AND METHODS Wilms tumor and non-tumor samples were obtained from high throughput gene expression databases, and differentially expressed genes (DEGs) were analyzed using the voom method in the limma package.

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A novel risk signature that combines 10 long noncoding RNAs to predict neuroblastoma prognosis.
Li Gao Peng Lin Peng Chen Rui-Zhi Gao Hong Yang Jin-Han Gu Zhi-Guang Huang

J Cell Physiol

April 2020

Neuroblastoma (NBL) is the most frequently encountered extracranial solid neoplasm and impacts significantly on the survival of patients, especially in cases of advanced tumor stage or relapse. A long noncoding RNA (lncRNA) signature to predict the survival of patients with NBL is proposed in this paper. Differentially expressed lncRNA (DElncRNA) was selected using the Limma plus Voom package in R based on the RNA-sequencing data downloaded from the Therapeutically Applicable Research To Generate Effective Treatments database and Genotype-Tissue Expression database.

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