ABSTRACT
In this paper, we try to find the differentially expressed lncRNA and differentially expressed miRNA of Liver cancer, especially between the different gender's patients. The differentially expressed genes were screened from TCGA liver data. Based on the extracted differentially expressed lncRNAs and differentially expressed miRNAs, we reveal an 8-lncRNA (TTTY14, UCA1, LINC00162, TTTY10, XIST, ERVH48-1, ZFY-AS1 and TTTY15) to 3-miRNA (hsa-mir-506, hsa-mir-508, hsa-mir-205) regulatory network of 13 pairs inter-regulatory between male and female. The 8 differentially expressed lncRNAs in the lncRNA-miRNA regulatory network were analyzed by the multivariable COX regression model, and LINC00162 and TTTY10 were found as the co-expression differentially expressed lncRNAs. After survival kmplot analysis and receiver operating characteristic analysis of the co-expression differentially expressed lncRNAs, TTTY10 was selected and proved as the potential biomarker of liver cancer for the diagnose and therapy.
- S. F. Altekruse, S. J. Henley, J. E. Cucinelli, and K. A. McGlynn, "Changing hepatocellular carcinoma incidence and liver cancer mortality rates in the United States," Am J Gastroenterol, vol. 109, no. 4, pp. 542--53, Apr, 2014.Google ScholarCross Ref
- A. Tang, O. Hallouch, V. Chernyak, A. Kamaya, and C. B. Sirlin, "Epidemiology of hepatocellular carcinoma: target population for surveillance and diagnosis," Abdom Radiol (NY), vol. 43, no. 1, pp. 13--25, Jan, 2018.Google ScholarCross Ref
- Y. Sun, Y. Wang, M. Li, K. Cheng, X. Zhao, Y. Zheng, Y. Liu, S. Lei, and L. Wang, "Long-term trends of liver cancer mortality by gender in urban and rural areas in China: an age-period-cohort analysis," BMJ Open, vol. 8, no. 2, pp. e020490, Feb 8, 2018.Google ScholarCross Ref
- M. Deng, J. Bragelmann, J. L. Schultze, and S. Perner, "Web-TCGA: an online platform for integrated analysis of molecular cancer data sets," BMC Bioinformatics, vol. 17, pp. 72, Feb 6, 2016.Google ScholarCross Ref
- C. W. Law, M. Alhamdoosh, S. Su, X. Dong, L. Tian, G. K. Smyth, and M. E. Ritchie, "RNA-seq analysis is easy as 1-2-3 with limma, Glimma and edgeR," F1000Res, vol. 5, 2016.Google Scholar
- Y. Z. jianzhi Deng, "Big data analysis of differentially expressed mRNA in acute lymphoblastic leukemia patients with different genders " in 2019 10th International Conference on IT in Medicine and Education (ITME2019), Qingdao, China 2019.Google Scholar
- B. B. Khomtchouk, J. R. Hennessy, and C. Wahlestedt, "MicroScope: ChIP-seq and RNA-seq software analysis suite for gene expression heatmaps," BMC Bioinformatics, vol. 17, no. 1, pp. 390, Sep 22, 2016.Google ScholarCross Ref
- A. Jeggari, D. S. Marks, and E. Larsson, "miRcode: a map of putative microRNA target sites in the long non-coding transcriptome," Bioinformatics, vol. 28, no. 15, pp. 2062--3, Aug 1, 2012.Google Scholar
- M. Y. Jianzhi Deng, Xiaohui Cheng and Yuehan Zhou, "Screening of differentially expressed lncRNAs for predicting Low Grade Glioma between different genders by Computational Biology," in 2019 5th International Conference on Energy, Environment and Materials Science (ICEEMS 2019), Singapore, 2019, pp. 032005.Google Scholar
- A. Mizukami, Y. Matsue, Y. Naruse, S. Kowase, K. Kurosaki, M. Suzuki, A. Matsumura, A. Nogami, K. Aonuma, and Y. Hashimoto, "Kaplan-Meier survival analysis and Cox regression analyses regarding right ventricular septal pacing: Data from Japanese pacemaker cohort," Data Brief, vol. 8, pp. 1303--7, Sep, 2016.Google ScholarCross Ref
- X. C. Jianzhi Deng, Yuehan Zhou, "Gene clustering, enrichment and survival analysis of differentially expressed genes in Low Grade Glioma between different genders by big data analysis," in ICDMML2019, Hong Kong, 2019.Google Scholar
- D. Sahu, C. L. Hsu, C. C. Lin, T. W. Yang, W. M. Hsu, S. Y. Ho, H. F. Juan, and H. C. Huang, "Co-expression analysis identifies long noncoding RNA SNHG1 as a novel predictor for event-free survival in neuroblastoma," Oncotarget, vol. 7, no. 36, pp. 58022--58037, Sep 6, 2016.Google ScholarCross Ref
- R. El Bezawy, S. Tinelli, M. Tortoreto, V. Doldi, V. Zuco, M. Folini, C. Stucchi, T. Rancati, R. Valdagni, P. Gandellini, and N. Zaffaroni, "miR-205 enhances radiation sensitivity of prostate cancer cells by impairing DNA damage repair through PKCepsilon and ZEB1 inhibition," J Exp Clin Cancer Res, vol. 38, no. 1, pp. 51, Feb 4, 2019.Google Scholar
- F. Asghari, N. Haghnavaz, D. Shanehbandi, V. Khaze, B. Baradaran, and T. Kazemi, "Differential altered expression of let-7a and miR-205 tumor-suppressor miRNAs in different subtypes of breast cancer under treatment with Taxol," Adv Clin Exp Med, vol. 27, no. 7, pp. 941--945, Jul, 2018.Google ScholarCross Ref
- W. Cao, Y. Zhao, L. Wang, and X. Huang, "Circ0001429 regulates progression of bladder cancer through binding miR-205-5p and promoting VEGFA expression," Cancer Biomark, vol. 25, no. 1, pp. 101--113, 2019.Google ScholarCross Ref
- H. Zhu, J. Yu, H. Zhu, Y. Guo, and S. Feng, "Identification of key lncRNAs in colorectal cancer progression based on associated protein-protein interaction analysis," World J Surg Oncol, vol. 15, no. 1, pp. 153, Aug 10, 2017.Google ScholarCross Ref
- F. Chen, Z. Li, C. Deng, and H. Yan, "Integrated analysis identifying new lncRNA markers revealed in ceRNA network for tumor recurrence in papillary thyroid carcinoma and build of nomogram," J Cell Biochem, vol. 120, no. 12, pp. 19673--19683, Dec, 2019.Google ScholarCross Ref
- M. A. Bhat, J. B. Sharma, K. K. Roy, J. Sengupta, and D. Ghosh, "Genomic evidence of Y chromosome microchimerism in the endometrium during endometriosis and in cases of infertility," Reprod Biol Endocrinol, vol. 17, no. 1, pp. 22, Feb 13, 2019.Google ScholarCross Ref
Index Terms
- Gene Big Data Analysis of Differentially Expressed lncRNA and MiRNA in Liver Cancer with Different Gender
Recommendations
Gene clustering, enrichment and survival analysis of differentially expressed genes in Low Grade Glioma between different genders by big data analysis
ICDMML 2019: Proceedings of the 2019 International Conference on Data Mining and Machine LearningIn this study, we aim to reveal the relationship between differentially expressed mRNAs and genders in low grade glioma (LGG) patients. Based on the downloaded RNA-seq files of LGG patients from The Cancer Genome Atlas database (TCGA), 89 differentially ...
Biological Big Data Analysis of Competing Endogenous RNA Network and mRNA Biomarker in Liver Cancer
ICCAI '20: Proceedings of the 2020 6th International Conference on Computing and Artificial IntelligenceIn our research, we try to find out the Competing Endogenous RNA Network (ceRNA) and the biomarker of Liver cancer (LC). 490 differentially expressed mRNAs, 248 differentially expressed lncRNAs and 66 differentially expressed miRNAs were screened from ...
Analysis MicroRNA-Gene Co-Modules in Glioblastoma Multiforme Based on Integrative Two Types of Genomic Data
ICBEB 2018: Proceedings of the 2nd International Conference on Biomedical Engineering and BioinformaticsGlioblastoma multiforme (GBM) is the most common primary central nervous system tumor. Although treatment continues to make progress in the past, the pathogenesis is still unknown to a large extent. MicroRNA (miRNA) is known to regulate cooperatively ...
Comments