博碩士論文 89522026 詳細資訊




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姓名 曾國炎(Kuo-Yen Tseng)  查詢紙本館藏   畢業系所 資訊工程學系
論文名稱 應用人類基因表現資料於基因表現關聯性之研究
(Correlations of Tissue Gene Expression by Analyzing Digital Expression Profiles of Human Tissues)
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摘要(中) 本研究試圖去分析現有大量來自不同人類組織的基因表現資料,去尋找那些具有規則性表現或是會同時表現於某幾種組織裡面的基因,這些基因可能具有某些生物上或是藥理學上的關聯性。在本文中,我們提出兩種不同的方式去分析那些表現在不同人類組織中的大量基因之間的關聯性,這些會特別地或是規則地表現在某些特定組織裡的關係透露出這些基因可能具有某些調控上的意義或者是屬於同一個反應路徑和訊號傳導流程的其中一環。
摘要(英) The study attempts to analyze a large number of human genome transcription products from diverse tissues and to discover genes that are co-expressed in some different tissues. Those genes may be of potential biological or pharmaceutical relevance. We proposed two approaches to discover the correlations of gene expression by analyzing multiple expression profiles of different human tissues. The correlations of gene expression reveal that genes are specifically or regularly expressed in particular tissues simultaneously. Besides, the correlations of gene expression can be used to identify the relationships of genes which are potential to be co-regulated, involving in the same biochemical pathway or signal transduction process.
關鍵字(中) ★ 統計分析
★ 基因表現關聯性
★ 資料探勘
關鍵字(英) ★ gene expression
★ Chi-square
★ association rule
★ UniGene
★ SAGE
★ data mining
論文目次 Chapter 1 Introduction 1
Chapter 2 Related Work 7
2.1 The Property of Expressed Sequence Tags (ESTs) 7
2.2 The Property of UniGene 7
2.3 The Property of Serial Analysis of Gene Expression (SAGE) 8
2.4 The Property of Cancer Genome Anatomy Project (CGAP) 9
2.5 The Property of HomoloGene 9
2.6 Association Rules 10
2.7 Chi-square Test Statistics 11
Chapter 3 Materials and Methods 12
3.1 Materials 13
3.1.1 Human Gene Expression Profiles from UniGene 13
3.1.2 Human Gene Expression Profiles from SAGE 19
3.1.3 Mouse Gene Expression Profiles from UniGene 21
3.2 Methods 21
3.2.1 Mining Association Rules and Pruning by Chi-square 22
3.2.2 Mining Correlations using Chi-square Test 23
Chapter 4 Experiments and Results 25
4.1 Environments of Implementation 25
4.2 Experimental Results 25
4.2.1 Results after Applying Association Rules 25
4.2.2 Results after Applying Chi-square Test 28
4.3 Results Published on Web 28
Chapter 5 Conclusions 28
References 28
Appendix 28
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[2] Agrawal, R. and Srikant, R. (1994) Fast Algorithms for Mining Association Rules, VLDB-94, 487-499.
[3] Ali, K., Manganaris, S. and Srikant, R. (1997) Partial classification using association rules, KDD-97, 115-118.
[4] Audic, S. and Claverie, J. M. (1997) The significance of digital gene expression profiles, Genome Res., 7:986-995.
[5] Boguski, M. S., Lowe, T. M. and Tolstoshev, C. M. (1993) dbEST -- database for "expressed sequence tags”, Nat. Genet., 4, 332-333.
[6] Brijs, T., Vanhoof, K. and Wets, G. (2000) Reducing redundancy in characteristic rule discovery by using IP-Techniques, In Intelligent Data Analysis Journal, 4 (3).
[7] Caron, H., et al. (2001) The Human Transcriptome Map: Clustering of Highly Expressed Genes in Chromosomal Domains, Science, 291, 1289-1292.
[8] Eickhoff, H., et al. (2000) Tissue gene expression analysis using arrayed normalized cDNA libraries, Genome Res., 10:1230-1240.
[9] Ewing, R.M. and Claverie, J-M. (2000) EST databases as multi-condition gene expression datasets, Pac. Symp. Biocomput., 430-442
[10] Greller, L. D. and Tobin, F. L. (1999) Detecting selective expression of genes and proteins. Genome Res., 9:282-296.
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[16] Srikant, R., Vu, Q., and Agrawal, R. (1997) Mining Association rules with item constraints, KDD-97, 67-73.
[17] Stekel, D. J., Git, Y. and Falciani, F. (2000) The comparison of gene expression from multiple cDNA libraries, Genome Res., 10:2055-2061.
[18] Toivonen, H., Klemettinen, M., Ronkainen, P, Hätönen, K, and Mannila, H. (1995) Pruning and grouping discovered association rules, Mlnet Workshop on Statistics, Machine Learning, and Discovery in Database, 47-52.
[19] Vasmatzis, G., Essand, M., Brinkmann, U., Lee, B. and Pastan, I. (1998) Discovery of three genes specifically expressed in human prostate by expressed sequence tag database analysis, Proc. Natl. Acad. Sci., 95, 300-304.
[20] Velculescu, V. E., et al. (1999) Analysis of human transcriptomes, Nat. Genet., 23, 387-388.
[21] Velculescu, V. E., et al. (1995) Serial analysis of gene expression, Science, 270, 484-487.
[22] Zhuo, D., et al. (2001) Assembly, annotation, and integration of UniGene clusters into the human genome draft, Genome Res., 11, 904-918.
指導教授 董啟功(Chi-Gong Tong) 審核日期 2002-6-27
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