1. NCCU Academic Hub
  2. 資訊學院
  3. 資訊科學系
  4. 學位論文
Please use this identifier to cite or link to this item: https://ah.lib.nccu.edu.tw/handle/140.119/136968
DC FieldValueLanguage
dc.contributor.advisor張家銘zh_TW
dc.contributor.advisorChang, Jia-Mingen_US
dc.contributor.author楊明翰zh_TW
dc.contributor.authorYang, Ming-Hanen_US
dc.creator楊明翰zh_TW
dc.creatorYang, Ming-Hanen_US
dc.date2021en_US
dc.date.accessioned2021-09-02T08:56:30Z-
dc.date.available2021-09-02T08:56:30Z-
dc.date.issued2021-09-02T08:56:30Z-
dc.identifierG0108753203en_US
dc.identifier.urihttp://nccur.lib.nccu.edu.tw/handle/140.119/136968-
dc.description碩士zh_TW
dc.description國立政治大學zh_TW
dc.description資訊科學系zh_TW
dc.description108753203zh_TW
dc.description.tableofcontentsIntroduction 12\nImmunotherapy and T cell exhaustion 12\nCandidate Mechanism of T cell exhaustion 13\nNext-Generation Sequencing Technology 15\nHi-C method 15\nChIP-seq method 17\nHiChIP method 17\nDifferent scales of 3D chromosome 19\nEnhancer Hijacking and T cell exhaustion 19\nMethods 21\nData Analysis Workflow Design 21\nMain Procedure (P) Illustration 23\nHi-C Pro (P1) 23\nhichipper (P2) 24\nHiChIP Loop Scanner (P3) and HiChIP Loop Counter (P4) 25\nDESeq2 (P5) 29\nDESeq2 Normalization Re-implementation (P6) 29\nHiChIP Loop Intensity Regulation Imputation Model with Machine Learning 30\nArtificial Neural Network 30\nHiChIP Loop Intensity Neural Network 31\nHiChIP Loop Intensity Gene Set Enrichment (GSEA) Analysis 32\nInsulation Score Analysis and TAD Calling 32\nA / B Compartment Analysis 34\nQuality Control (Q) 35\nLibrary QC (Q1,Q2) 35\nMapping Coverage QC (Q3) 35\nHi-C Contact Map Correlation QC (Internal Consistency QC) (Q4) 35\nhichipper QC (Q5) 35\nData Visualization 35\nConvert bed file to longrange 35\nExperimental Results 36\nSummary of Data 36\nPilot Run Results (lab00) 37\nExperimental Results (lab01 & lab02) 39\nExperimental Data QC - HiC Contact Map Corr (Q-4) 39\nChromatin Loop analysis of T Cell exhaustion 41\nHiChIP Loop Heatmap Visualization Comparison V-4 41\nExperimental Data QC - DESeq2 Scatter QC (Q-6) 43\nExperimental Data QC - DESeq2 PCA QC (Q-7) 44\nDESeq2 Result (V-5) 45\nChromatin Topologically Associating Domain (TAD) analysis of T Cell exhaustion 47\nHiChP Contact Map Enhancement 47\nHiChP Insulation Score analysis 48\nComparison of Chromosome Organization from Small to Middle Scale of T Cell exhaustion 49\nStudy of T cell exhaustion Subtype with HiChIP Loop Intensity Regulation Trend 52\nHiChIP Loop Intensity Neural Network 54\nGene2Vec PCA analysis 54\nNeural Network Training Result 55\nHiChIP Loop Intensity Neural Network prediction in real data 56\nGSEA result 57\nDiscussion and Conclusion 60\nHiChIP Loop Associate With Transcription factors of Genes 60\nRNA Seq & HiChIP Loop Intensity Correlation 66\nHiChIP Full Comparison Plot 68\nConclusion 70\nReferences 71zh_TW
dc.format.extent11018202 bytes-
dc.format.mimetypeapplication/pdf-
dc.source.urihttp://thesis.lib.nccu.edu.tw/record/#G0108753203en_US
dc.subject染色體構象捕獲zh_TW
dc.subjectT細胞衰竭zh_TW
dc.subjectT cell exhaustionzh_TW
dc.subjectHi-Czh_TW
dc.subjectHiChIPzh_TW
dc.subjectT cell exhaustionen_US
dc.subjectHi-Cen_US
dc.subjectHiChIPen_US
dc.title以資料分析和機器學習用於HiChIP解析T細胞衰竭機制zh_TW
dc.titleUsing HiChIP investigate T Cell exhaustion by data analysis and machine learningen_US
dc.typethesisen_US
dc.relation.referenceSocinski, 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\n\nAchinger-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\n\nTsai, 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\n\nWu, 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\n\nKim, 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\n\nLiang, 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\n\nLieberman-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\n\nRobertson, 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\n\n\nMumbach, 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\n\nJane 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\n\nHaller, 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\n\nNorthcott, 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\n\nZimmerman, 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\n\nBhattacharyya, 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\n\nLareau, C., & Aryee, M. (2017). hichipper: A preprocessing pipeline for assessing library quality and DNA loops from HiChIP data. doi: 10.1101/192302\n\nAnders, S., & Huber, W. (2010). Differential expression analysis for sequence count data. Genome Biology, 11(10). doi: 10.1186/gb-2010-11-10-r106\n\nZhi, D. (2019). Gene2vec: distributed representation of genes based on co-expression. BMC Genomics, 20(S1). doi: 10.1186/s12864-018-5370-x\n\n\nZufferey, 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\n\nLazaris, 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\n\nSanders, 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\n\nDylan Skola (2018).python-genome-browser. Github,from https://github.com/phageghost/python-genome-browser\n\nKnight, P., & Ruiz, D. (2012). A fast algorithm for matrix balancing. IMA Journal Of Numerical Analysis, 33(3), 1029-1047. doi: 10.1093/imanum/drs019\n\nMumbach, 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\n\nQuinlan, A., & Hall, I. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics, 26(6), 841-842. doi: 10.1093/bioinformatics/btq033\n\nChen, 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.\nImmunity, 51(5), 840-855.e5. doi: 10.1016/j.immuni.2019.09.013\n\nIm, 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\n\nSanders, 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\n\nBlank, 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/s41577-019-0221-9zh_TW
dc.identifier.doi10.6814/NCCU202101394en_US
item.fulltextWith Fulltext-
item.grantfulltextembargo_20260817-
item.openairetypethesis-
item.cerifentitytypePublications-
item.openairecristypehttp://purl.org/coar/resource_type/c_46ec-
Appears in Collections:學位論文
Files in This Item:
File SizeFormat
320301.pdf10.76 MBAdobe PDF2View/Open
Show simple item record

Google ScholarTM

Check

Altmetric

Altmetric


Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.