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完整後設資料紀錄
DC 欄位 | 值 | 語言 |
---|---|---|
dc.contributor.advisor | 劉力瑜 | |
dc.contributor.author | Hau-Jiun Hsu | en |
dc.contributor.author | 許皓鈞 | zh_TW |
dc.date.accessioned | 2021-06-17T03:20:08Z | - |
dc.date.available | 2021-06-29 | |
dc.date.copyright | 2018-06-29 | |
dc.date.issued | 2018 | |
dc.date.submitted | 2018-06-25 | |
dc.identifier.citation | Anders, Simon, and Wolfgang Huber. 'Differential expression analysis for sequence count data.' Genome biology 11 (2010): R106.
Andrews, Simon. 'FastQC: a quality control tool for high throughput sequence data.' (2010). Auffray, Charles, Zhu Chen, and Leroy Hood. 'Systems medicine: the future of medical genomics and healthcare.' Genome medicine 1 (2009): 2. Barabási, Albert-László, and Eric Bonabeau. 'Scale-free networks.' Scientific american 288 (2003): 60-69. Bastian, Mathieu, Sebastien Heymann, and Mathieu Jacomy. 'Gephi: an open source software for exploring and manipulating networks.' Icwsm 8 (2009): 361-362. Benesty, Jacob, et al. 'Pearson correlation coefficient.' Noise reduction in speech processing. Springer Berlin Heidelberg, (2009): 1-4. Benjamini, Yoav, and Yosef Hochberg. 'Controlling the false discovery rate: a practical and powerful approach to multiple testing.' Journal of the royal statistical society. Series B (Methodological) (1995): 289-300. Blondel, Vincent D., et al. 'Fast unfolding of communities in large networks.' Journal of statistical mechanics: theory and experiment 2008 (2008): P10008. Bolger, Anthony M., Marc Lohse, and Bjoern Usadel. 'Trimmomatic: a flexible trimmer for Illumina sequence data.' Bioinformatics 30 (2014): 2114-2120. Cui, Xiangqin, and Gary A. Churchill. 'Statistical tests for differential expression in cDNA microarray experiments.' Genome biology 4 (2003): 210. Draghici, Sorin, et al. 'Reliability and reproducibility issues in DNA microarray measurements.' TRENDS in Genetics 22 (2006): 101-109.2 Fisher, Ronald A. 'On the probable error of a coefficient of correlation deduced from a small sample.' Metron 1 (1921): 3-32. Forster, Samuel C., et al. 'RNA-eXpress annotates novel transcript features in RNA-seq data.' Bioinformatics 29 (2013): 810-812. Gravez, Basile, et al. 'Aldosterone promotes cardiac endothelial cell proliferation in vivo.' Journal of the American Heart Association 4 (2015): e001266. Langfelder, Peter, and Steve Horvath. 'WGCNA: an R package for weighted correlation network analysis.' BMC bioinformatics 9 (2008): 559. Li, Heng, and Richard Durbin. 'Fast and accurate short read alignment with Burrows–Wheeler transform.' Bioinformatics 25 (2009): 1754-1760.2 Love, Michael I., Wolfgang Huber, and Simon Anders. 'Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.' Genome biology 15 (2014): 550. Luo, Feng, et al. 'Constructing gene co-expression networks and predicting functions of unknown genes by random matrix theory.' BMC bioinformatics 8 (2007): 299.2 Mi, Huaiyu, et al. 'PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium.' Nucleic acids research 38 (2009): D204-D210. Newfell, Brenna G., et al. 'Aldosterone regulates vascular gene transcription via oxidative stress–dependent and–independent pathways.' Arteriosclerosis, thrombosis, and vascular biology 31 (2011): 1871-1880. Pržulj, Nataša. 'Biological network comparison using graphlet degree distribution.' Bioinformatics 23 (2007): e177-e183. Valente, Thomas W. Social networks and health: Models, methods, and applications. Vol. 1. New York: Oxford University Press, (2010). Yuan, Yanggang, et al. 'Mitochondrial dysfunction accounts for aldosterone-induced epithelial-to-mesenchymal transition of renal proximal tubular epithelial cells.' Free Radical Biology and Medicine 53 (2012): 30-43. Zhang, Bin, and Steve Horvath. 'A general framework for weighted gene co-expression network analysis.' Statistical applications in genetics and molecular biology 4 (2005). Zhang, Bin, and Steve Horvath. 'A general framework for weighted gene co-expression network analysis.' Statistical applications in genetics and molecular biology 4 (2005). Zhu, Jun, Bin Zhang, and Eric E. Schadt. 'A systems biology approach to drug discovery.' Advances in genetics 60 (2008): 603-635. | |
dc.identifier.uri | http://tdr.lib.ntu.edu.tw/jspui/handle/123456789/69584 | - |
dc.description.abstract | RNA序列定序所得的基因表現量,標準分析程序是求得差異顯著基因並對顯著基因進行基因分類分析。近年來有越來越多結合網路的分析方式,像是繪製基因的相關性網路,尋找網路中的團塊化基因等等。但這些方法大多都都只能概括性的描述網路特徵,很難進行統計上的檢定,也不太能進行不同處理下網路的差異比較。因此我們以比較兩種不同處理下網路的變化為目標,並且跳脫以往以節點為出發點的分析方式,探討不同情況下顯著基因之間連線上的改變,以達到偵測哪些基因再施打藥劑之後產生了擾動現象。找出在不同形況之下有所擾動的基因後,我們也進行基因分類分析,並且結合了較常運用在社會科學的雙模式網路分析法,視覺化的描述基因分類之間的往來是來自哪些基因。本篇研究建立系統化的網路比較流程,並且結合雙模式網路分析法,說明基因分類之間的關係,期許能替將來相關研究帶來一點貢獻。 | zh_TW |
dc.description.abstract | The gene expression levels estimated from RNA sequencing can be subject to statistical analyses in finding the differentially expressed genes and the gene ontology terms. In recent years, there have been more and more analytical methods that incorporate networks, such as construction of gene association networks, searching for gene modules in networks, and so on. However, most of these methods can only describe the characteristics of the network in a general way. It is difficult to carry out statistical hypotheses tests, and it is not possible to compare the differences between the networks under different conditions. In this study, we aim to compare the networks under two different treatments. Instead of conventional node-based analysis, we propose to explore changes in the connections between significant genes in different situations so as to detect which genes are being disturbed. After identifying genes that are perturbed under different conditions, we also perform GO analysis and adopt the two-mode network method, which is commonly used in the social sciences, to visualize the genes that belong to more than one gene classifications. This study has established a systematic protocol for network comparison. Combined with the two-mode network analysis method, the protocol can assist to explain the relationship between GO terms. The results may contribute to related research in the future. | en |
dc.description.provenance | Made available in DSpace on 2021-06-17T03:20:08Z (GMT). No. of bitstreams: 1 ntu-107-R04621204-1.pdf: 4848935 bytes, checksum: fe7ef034cdfe3bd62f28df1005fa8ece (MD5) Previous issue date: 2018 | en |
dc.description.tableofcontents | 中文摘要 I
ABSTRACT II 目錄 III 圖目錄 IV 表目錄 V 第一章、 緒論 1 第二章、 材料與方法 3 第三章、 結果 7 第四章、 討論 17 第五章、 結論 20 參考文獻 22 附錄 25 | |
dc.language.iso | zh-TW | |
dc.title | 比較老鼠心肌組織施用醛固酮與否之基因調控網路 | zh_TW |
dc.title | Comparison of Gene Regulatory Networks for the use of Aldosterone in Mus Musculus Myocardial Tissue | en |
dc.type | Thesis | |
dc.date.schoolyear | 106-2 | |
dc.description.degree | 碩士 | |
dc.contributor.oralexamcommittee | 溫在弘,林彥宏 | |
dc.subject.keyword | 雙模式網路,基因網路,網路比較,調控網路,醛固酮, | zh_TW |
dc.subject.keyword | two-mode network,gene network,network comparison,regulatory network,aldosterone, | en |
dc.relation.page | 36 | |
dc.identifier.doi | 10.6342/NTU201801103 | |
dc.rights.note | 有償授權 | |
dc.date.accepted | 2018-06-26 | |
dc.contributor.author-college | 生物資源暨農學院 | zh_TW |
dc.contributor.author-dept | 農藝學研究所 | zh_TW |
顯示於系所單位: | 農藝學系 |
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