請用此 Handle URI 來引用此文件: http://hdl.handle.net/11455/60841
標題: OrchidWeb:蘭花基因轉錄體之整合性網站
OrchidWeb: A Comprehensive Web Server for De Novo Orchid Transcriptome
作者: 陳怡穎
Chen, Yi-Ying
關鍵字: Orchid
出版社: 基因體暨生物資訊學研究所
引用: 1. Leitch, I.J., et al., Genome size diversity in orchids: consequences and evolution. Ann Bot, 2009. 104(3): p. 469-81. 2. 劉翠玲, 蘭花生物科技重現蝴蝶蘭光輝年代. 農業生技產業季刊, 2009. 第17期: p. 58-62. 3. Moriya, Y., et al., KAAS: an automatic genome annotation and pathway reconstruction server. Nucleic Acids Res, 2007. 35(Web Server issue): p. W182-5. 4. Conesa, A., et al., Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics, 2005. 21(18): p. 3674-3676. 5. Hsu, C.C., et al., An overview of the Phalaenopsis orchid genome through BAC end sequence analysis. BMC Plant Biol, 2011. 11: p. 3. 6. Holtorf, H., M.-C. Guitton, and R. Reski, Plant functional genomics. Naturwissenschaften, 2002. 89(6): p. 235-249. 7. Tsai, W.-C., et al., Expression analysis of the ESTs derived from the flower buds of Phalaenopsis equestris. Plant Science, 2006. 170(3): p. 426-432. 8. Qaim, M., The Economics of Genetically Modified Crops. Annual Review of Resource Economics, 2009. 1(1): p. 665-694. 9. Johannes Spaethe, M.S.a.H.F.P., Why sexually deceptive orchids have colored flowers. Communicative & Integrative Biology, 2010. 3:2: p. 139-141. 10. Joshua Z. Levin, J.C.F., Xuemei Chen and Elliot M. Meyerowitz, A Genetic Screen for Modifiers of UFO Meristem Activity Identifies Three Novel FUSED FLORAL ORGANS Genes Required for Early Flower Development in Arabidopsis. Genetics Society of America, 1998. 11. Bin Guo, S.H., Tian Zhang, Jon K. Pittman, Donghong Chen , Feng Ming1,, Cloning and Characterization of a PI-like MADS-Box Gene in Phalaenopsis Orchid. Biochemistry and Molecular Biology, 2007. 40: p. 845-852. 12. Chang Run Li, X.B.Z.a.C.S.H., Cloning of a sucrose-phosphate synthase gene highly expressed in fowers from the tropical epiphytic orchid Oncidium Goldiana. Experimental Botany, 2003. 54(3990): p. 2189-2191. 13. Conesa, A. and S. Gotz, Blast2GO: A comprehensive suite for functional analysis in plant genomics. Int J Plant Genomics, 2008. 2008: p. 619832. 14. Gotz, S., et al., High-throughput functional annotation and data mining with the Blast2GO suite. Nucleic Acids Res, 2008. 36(10): p. 3420-35. 15. Zhao, P., et al., Protocorm-like body (PLB) formation and plant regeneration from the callus culture of Dendrobium candidum Wall ex Lindl. In Vitro Cellular & Developmental Biology - Plant, 2008. 44(3): p. 178-185. 16. Zerbino, D.R. and E. Birney, Velvet: algorithms for de novo short read assembly using de Bruijn graphs. Genome Res, 2008. 18(5): p. 821-9. 17. Marcel H. Schulz, D.R.Z., Martin Vingron, Ewan Birney, Oases Robust de novo RNA-seq assembly across the dynamic range of expression levels. Bioinformatics, 2012. 28(8). 18. Kim, E., A. Goren, and G. Ast, Alternative splicing: current perspectives. BioEssays, 2008. 30(1): p. 38-47. 19. Edgar, R.C., Search and clustering orders of magnitude faster than BLAST. Bioinformatics, 2010. 26(19). 20. Trapnell, C., et al., Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol, 2010. 28(5): p. 511-5. 21. Roberts, A., et al., Improving RNA-Seq expression estimates by correcting for fragment bias. Genome Biol, 2011. 12(3): p. R22. 22. Roberts A, P.H., Trapnell C, Pachter L. , Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics, 2011. 27(17): p. 2325-9. 23. Liu, C.C., et al., CRSD: a comprehensive web server for composite regulatory signature discovery. Nucleic Acids Res, 2006. 34(Web Server issue): p. W571-7. 24. Poisson, L.M., J.M. Taylor, and D. Ghosh, Integrative set enrichment testing for multiple omics platforms. BMC Bioinformatics, 2011. 12: p. 459. 25. Trapnell, C., L. Pachter, and S.L. Salzberg, TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 2009. 25(9): p. 1105-11. 26. Subramanian, A., Gene set enrichment analysis: A knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences, 2005. 102(43): p. 15545-15550.  
摘要: 蘭花是開花植物中最大、最具多樣性的科,約有超過800個屬和25,000個種。況且蘭花是台灣重要的高經濟價值花卉,目前產量最高的花卉為蝴蝶蘭。由於蝴蝶蘭深受全球人民喜愛,在栽種技術以及育種上有相當的基礎,目前在功能性基因體學上有許多研究。 而本篇論文是以RNA定序技術產生的片段序列來重組蘭花基因轉錄體,並且將這些資料經過組合、註解以及表現量分析,從這之中可以得到更多有價值的資料。接著使用相關演算法、程式來分析此物種,透過資料庫所提供的資訊有效地節省生物實驗者的時間與經費。最後我們得到樣本BUDB-0.2有68,245,430 paired-end reads資料,而樣本BUD+0.2 則有68,241,474 paired-end reads。另一方面也讓生物實驗者能有更多的參考依據,或者是作為實驗結果的一個初步驗證工具。而實驗中則以蝴蝶蘭的野生型與突變型兩種資料,來進行轉錄因子的分析,並且使用Java、JSP和MySQL環境建構成一個整合性網站資料庫,提供相關註解查詢分析以及Blast等結果。
Orchids belong to one of the largest, most diverse flowering plant families. There are over 800 genera of Orchids in the world and more than 25,000 species as well. Orchids are the high value crops in Taiwan. Nowadays the best production is the Phalaenopsis. Phalaenopsis is a beautiful flower in the world, and many people love it. Until now it has a lot of studies for planting technology and plant breeding. The orchid research includes functional genomics, Expressed sequence tag (ESTs), Complementary DNA (cDNA) researches with the databases that helps molecular breeding about gene identification and screening. In this thesis, we used RNA-seq data of the Phalaenopsis wild type (BUD+0.2) and mutant type (BUD-0.2) to study the transcriptome and expression of Phalaenopsis. The BUD-0.2 Orchid sample has 68,245,430 paired-end reads, and the BUD+0.2 Orchid sample has 68,241,474 paired-end reads. Additionally, the OrchidWeb may serve as a basis for the study of experimental results of a preliminary validation tool. The webserver should enable experimental biologist to get more information and biological implication. The OrchidWeb is written in Java, JSP and MySQL. We established a comprehensive web server database, and provided Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway annotation, Blast page. The OrchidWeb database is freely available at http://syslab.nchu.edu.tw/orchid/.
URI: http://hdl.handle.net/11455/60841
其他識別: U0005-2206201223444900
文章連結: http://www.airitilibrary.com/Publication/alDetailedMesh1?DocID=U0005-2206201223444900


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