政大機構典藏-National Chengchi University Institutional Repository(NCCUR):Item 140.119/136968

政大機構典藏-National Chengchi University Institutional Repository(NCCUR):Item 140.119/136968

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题名:	以資料分析和機器學習用於HiChIP解析T細胞衰竭機制 Using HiChIP investigate T Cell exhaustion by data analysis and machine learning
作者:	楊明翰 Yang, Ming-Han
贡献者:	張家銘 Chang, Jia-Ming 楊明翰 Yang, Ming-Han
关键词:	染色體構象捕獲 T細胞衰竭 T cell exhaustion Hi-C HiChIP T cell exhaustion Hi-C HiChIP
日期:	2021
上传时间:	2021-09-02 16:56:30 (UTC+8)
參考文獻:	Socinski, M., Jotte, R., Cappuzzo, F., Orlandi, F., Stroyakovskiy, D., & Nogami, N. et al. (2018). Atezolizumab for First-Line Treatment of Metastatic Nonsquamous NSCLC. New England Journal Of Medicine, 378(24), 2288-2301. doi: 10.1056/nejmoa1716948 Achinger-Kawecka, J., Stirzaker, C., Chia, K., Portman, N., Campbell, E., & Du, Q. et al. (2021). Epigenetic therapy suppresses endocrine-resistant breast tumour growth by re-wiring ER-mediated 3D chromatin interactions. doi: 10.1101/2021.06.21.449340 Tsai, H., Wu, Y., Lin, S., Chen, I., Lee, J., & Cheng, K. et al. (2019). Abstract A221: Epigenetic therapy restores polyfunctionality of malignant pleural effusion T-cells in patients with non-small cell lung cancer without downregulation of PD-1. Regulating T-Cells And Their Response To Cancer. doi: 10.1158/2326-6074.cricimteatiaacr18-a221 Wu, Y., Tao, B., Zhang, T., Fan, Y., & Mao, R. (2019). Pan-Cancer Analysis Reveals Disrupted Circadian Clock Associates With T Cell Exhaustion. Frontiers In Immunology, 10. doi: 10.3389/fimmu.2019.02451 Kim, Y., Marhon, S., Zhang, Y., Steger, D., Won, K., & Lazar, M. (2018). Rev-erbα dynamically modulates chromatin looping to control circadian gene transcription. Science, 359(6381), 1274-1277. doi: 10.1126/science.aao6891 Liang, C., Huang, S., Zhao, Y., Chen, S., & Li, Y. (2021). TOX as a potential target for immunotherapy in lymphocytic malignancies. Biomarker Research, 9(1). doi: 10.1186/s40364-021-00275-y Lieberman-Aiden, E., van Berkum, N., Williams, L., Imakaev, M., Ragoczy, T., & Telling, A. et al. (2009). Comprehensive Mapping of Long-Range Interactions Reveals Folding Principles of the Human Genome. Science, 326(5950), 289-293. doi: 10.1126/science.1181369 Robertson, G., Hirst, M., Bainbridge, M., Bilenky, M., Zhao, Y., & Zeng, T. et al. (2007). Genome-wide profiles of STAT1 DNA association using chromatin immunoprecipitation and massively parallel sequencing. Nature Methods, 4(8), 651-657. doi: 10.1038/nmeth1068 Mumbach, M., Rubin, A., Flynn, R., Dai, C., Khavari, P., Greenleaf, W., & Chang, H. (2016). HiChIP: efficient and sensitive analysis of protein-directed genome architecture. Nature Methods, 13(11), 919-922. doi: 10.1038/nmeth.3999 Jane B. Reece， Noel Meyers， Lisa A. Urry， Michael L. Cain， Steven A. Wasserman， Peter V. Minorsky ,Campbell Biology Australian and New Zealand Edition, 11th Edition, 367 , Figure 18.8 Haller, F., Bieg, M., Will, R., Körner, C., Weichenhan, D., & Bott, A. et al. (2019). Enhancer hijacking activates oncogenic transcription factor NR4A3 in acinic cell carcinomas of the salivary glands. Nature Communications, 10(1). doi: 10.1038/s41467-018-08069-x Northcott, P., Lee, C., Zichner, T., Stütz, A., Erkek, S., & Kawauchi, D. et al. (2014). Enhancer hijacking activates GFI1 family oncogenes in medulloblastoma. Nature, 511(7510), 428-434. doi: 10.1038/nature13379 Zimmerman, M., Liu, Y., He, S., Durbin, A., Abraham, B., & Easton, J. et al. (2017). MYC Drives a Subset of High-Risk Pediatric Neuroblastomas and Is Activated through Mechanisms Including Enhancer Hijacking and Focal Enhancer Amplification. Cancer Discovery, 8(3), 320-335. doi: 10.1158/2159-8290.cd-17-0993 Bhattacharyya, S., Chandra, V., Vijayanand, P., & Ay, F. (2019). Identification of significant chromatin contacts from HiChIP data by FitHiChIP. Nature Communications, 10(1). doi: 10.1038/s41467-019-11950-y Lareau, C., & Aryee, M. (2017). hichipper: A preprocessing pipeline for assessing library quality and DNA loops from HiChIP data. doi: 10.1101/192302 Anders, S., & Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biology, 11(10). doi: 10.1186/gb-2010-11-10-r106 Zhi, D. (2019). Gene2vec: distributed representation of genes based on co-expression. BMC Genomics, 20(S1). doi: 10.1186/s12864-018-5370-x Zufferey, M., Tavernari, D., Oricchio, E., & Ciriello, G. (2018). Comparison of computational methods for the identification of topologically associating domains. Genome Biology, 19(1). doi: 10.1186/s13059-018-1596-9 Lazaris, C., Kelly, S., Ntziachristos, P., Aifantis, I., & Tsirigos, A. (2017). HiC-bench: comprehensive and reproducible Hi-C data analysis designed for parameter exploration and benchmarking. BMC Genomics, 18(1). doi: 10.1186/s12864-016-3387-6 Sanders, J., Freeman, T., Xu, Y., Golloshi, R., Stallard, M., & Hill, A. et al. (2020). Radiation-induced DNA damage and repair effects on 3D genome organization. Nature Communications, 11(1). doi: 10.1038/s41467-020-20047-w Dylan Skola (2018).python-genome-browser. Github,from https://github.com/phageghost/python-genome-browser Knight, P., & Ruiz, D. (2012). A fast algorithm for matrix balancing. IMA Journal Of Numerical Analysis, 33(3), 1029-1047. doi: 10.1093/imanum/drs019 Mumbach, M., Satpathy, A., Boyle, E., Dai, C., Gowen, B., & Cho, S. et al. (2017). Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nature Genetics, 49(11), 1602-1612. doi: 10.1038/ng.3963 Quinlan, A., & Hall, I. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841-842. doi: 10.1093/bioinformatics/btq033 Chen, Z., Ji, Z., Ngiow, S., Manne, S., Cai, Z., & Huang, A. et al. (2019). TCF-1-Centered Transcriptional Network Drives an Effector versus Exhausted CD8 T Cell-Fate Decision. Immunity, 51(5), 840-855.e5. doi: 10.1016/j.immuni.2019.09.013 Im, S., Hashimoto, M., Gerner, M., Lee, J., Kissick, H., & Burger, M. et al. (2016). Defining CD8+ T cells that provide the proliferative burst after PD-1 therapy. Nature, 537(7620), 417-421. doi: 10.1038/nature19330 Sanders, J., Freeman, T., Xu, Y., Golloshi, R., Stallard, M., & Hill, A. et al. (2020). Radiation-induced DNA damage and repair effects on 3D genome organization. Nature Communications, 11(1). doi: 10.1038/s41467-020-20047-w Blank, C., Haining, W., Held, W., Hogan, P., Kallies, A., & Lugli, E. et al. (2019). Defining ‘T cell exhaustion’. Nature Reviews Immunology, 19(11), 665-674. doi: 10.1038/s41577-019-0221-9
描述:	碩士國立政治大學資訊科學系 108753203
資料來源:	http://thesis.lib.nccu.edu.tw/record/#G0108753203
数据类型:	thesis
DOI:	10.6814/NCCU202101394
显示于类别:	[資訊科學系] 學位論文

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