Gene Big Data Analysis of Differentially Expressed lncRNA and MiRNA in Liver Cancer with Different Gender
Pages 24 - 28
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.
References
[1]
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.
[2]
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.
[3]
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.
[4]
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.
[5]
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.
[6]
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.
[7]
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.
[8]
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.
[9]
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.
[10]
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.
[11]
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.
[12]
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.
[13]
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.
[14]
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.
[15]
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.
[16]
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.
[17]
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.
[18]
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.
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- Gene Big Data Analysis of Differentially Expressed lncRNA and MiRNA in Liver Cancer with Different Gender
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Published In
May 2020
146 pages
ISBN:9781450377225
DOI:10.1145/3404512
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Published: 05 July 2020
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- National Natural Science Foundation of China
- Guangxi Natural Science Foundation of China
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BDE 2020
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