請用此 Handle URI 來引用此文件: http://hdl.handle.net/11455/60842
標題: 人類基因調控之整合型網站
A Comprehensive Web Server for Human Gene Regulation
作者: 洪偉欣
Hung, Wei-Hsin
關鍵字: predict
目標基因
target genes
SNPs
單核苷酸多態性
出版社: 基因體暨生物資訊學研究所
引用: 1. 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. 2. Bartel, D.P., MicroRNAs: target recognition and regulatory functions. Cell, 2009. 136(2): p. 215-33. 3. Latchman, D.S., Transcription Factors:An Overview. Biochemistry & Cell Biology, 1997. 4. Betel, D., et al., Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol, 2010. 11(8): p. R90. 5. Magalhaes, J.P.d., et al., The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell, 2009. 6. BERCHTOLD, N.C. and C.W. COTMAN, Evolution in the Conceptualization of Dementia and Alzheimer's Disease:Greco-Roman Period to the 1960s. Neurobiology of Aging, 1998. 7. Jankovic, J., Parkinson''s disease: clinical features and diagnosis. J Neurol Neurosurg Psychiatry, 2008. 79(4): p. 368-76. 8. Phukan, J., N.P. Pender, and O. Hardiman, Cognitive impairment in amyotrophic lateral sclerosis. The Lancet Neurology, 2007. 6(11): p. 994-1003. 9. ES Lander, L.L., B Birren, C Nusbaum, MC Zody,... Initial sequencing and analysis of the human genome. NATURE, 2001 10. Snoep, J.L. and H.V. Westerhoff, From isolation to integration, a systems biology approach for building the Silicon Cell. 2005. 13: p. 13-30. 11. Lykke-Andersen, S. and T.H. Jensen, Overlapping pathways dictate termination of RNA polymerase II transcription. Biochimie, 2007. 89(10): p. 1177-82. 12. Chesler EJ, L.L., Wang J, Williams RW, Manly KF., WebQTL: rapid exploratory analysis of gene expression and genetic networks for brain and behavior. Nat Neurosci., 2004. 13. Marbach, D., et al., Generating Realistic in silico Gene Networks for erformance Assessment of Reverse Engineering Methods. J Comput Biol., 2009. 14. Pollack, J.R., et al., Genome-wide analysis of DNA copy number variation in breast cancer using DNA microarrays. Nature America Inc., 1999. 15. Rosenbloom, K.R., et al., ENCODE whole-genome data in the UCSC Genome Browser. Nucleic Acids Res, 2010. 38(Database issue): p. D620-5. 16. Reinhardt, U.E., Does The Aging Of The Population Really Drive The Demand For Health Care? Health Affairs, 2003. 22(6): p. 27-39. 17. Fujita, P.A., et al., The UCSC Genome Browser database: update 2011. Nucleic Acids Res, 2011. 39(Database issue): p. D876-82. 18. Chamberlin, D.D. and R.F. Boyce, SEQUEL: A structured English query language. ACM, 1974. 19. Romanenko, S.A., et al., Chromosomal evolution in Rodentia. Heredity (Edinb), 2012. 108(1): p. 4-16. 20. Ashburner, M., et al., Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet, 2000. 25(1): p. 25-9. 21. Betel, D., et al., Comprehensive modeling of microRNA targets predicts functional non-conserved and non-canonical sites. Genome Biol, 2010. 11(8): p. R90. 22. Kanehisa*, M. and S. Goto, KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucl. Acids Res. , 2000. 23. Varela, M.A. and W. Amos, Heterogeneous distribution of SNPs in the human genome: microsatellites as predictors of nucleotide diversity and divergence. Genomics, 2010. 95(3): p. 151-9. 24. Margis, R. and C.R. Rieder, Identification of blood microRNAs associated to Parkinsonis disease. J Biotechnol, 2011. 152(3): p. 96-101.
摘要: 在過去的研究中,整合了一些廣泛被使用的大型資料庫,建置了一個整合性基因調控資料庫(CRSD http://biochip.nchu.edu.tw/crsd1)。在本研究工作,我們在CRSD的基礎下,建立了第二版的整合性基因調控資料庫(CRSD2 http://syslab.nchu.edu.tw/crsd2)。 CRSD2可用來預測微核醣核酸調控特徵基因群(microRNA regulatory signatures)與轉錄調控特徵基因群(transcription factor regulatory signature)的目標基因(target genes),使用者可應用於微核醣核酸調控及轉錄調控。為了在CRSD2提供廣泛的生物資訊分析,我們整合了六個廣泛被使用的大型資料庫,包含微核醣核酸、啟動子、轉錄因子、生物途徑及基因功能分類。此外,我們也建構了二個全基因組規模的資料庫:微核醣核酸調控特徵基因群及轉錄調控特徵基因群資料庫。除此之外,我們也加入了單核苷酸多態性的註解功能。
Previously, we constructed a composite regulatory signature database (CRSD http://biochip.nchu.edu.tw/crsd1). In this work, based on our previous framework, we established CRSD release 2 (CRSD2, http://syslab.nchu.edu.tw/crsd2). The CRSD2 can predict target genes for microRNAs and transcription factors. Users can use CRSD2 in investigating complex regulatory behaviors involving the microRNA regulatory signatures and TF regulatory signatures. We integrated six large-scale databases to construct two core genome-wide databases. The former are those for microRNAs, promoters, transcription factors, pathways and gene functions, while the latter are microRNA regulatory signatures and transcription factor signatures. In addition, CRSD2 also provides information for single nucleotide polymorphisms.
URI: http://hdl.handle.net/11455/60842
其他識別: U0005-2506201217005600
文章連結: http://www.airitilibrary.com/Publication/alDetailedMesh1?DocID=U0005-2506201217005600
顯示於類別:基因體暨生物資訊學研究所

文件中的檔案:
沒有與此文件相關的檔案。


在 DSpace 系統中的文件,除了特別指名其著作權條款之外,均受到著作權保護,並且保留所有的權利。