藉由比較基因表現資料研究次世代定序與晶片技術分析差異

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姓名

賴俊傑(Chun-chieh Lai) 查詢紙本館藏

畢業系所

系統生物與生物資訊研究所

論文名稱

藉由比較基因表現資料研究次世代定序與晶片技術分析差異
(The gene expression characteristic differences between next-generation sequencing and microarray)

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摘要(中)

人類基因體計畫完成之後，DNA序列的分析的規模出現了重大的變化。高通量技術以具有成本效益的方式提供了非常詳細和大規模的數據。其中，尤其次世代定序技術與微陣列晶片兩大平台被廣泛的使用在分析基因表現上。所以我們發展了一個工作流程來結合次世代定序技術與微陣列晶片的資料在基因表現的層級上來研究轉錄體的複雜性。相對使用單一平台的資料，這個工作流程產生更可靠的資料並提供更多方面的資訊來描述全基因體基因表現的特性。最後，我們初步討論了在這兩平台產生分析差異的原因。

摘要(英)

There has been a dramatic changed in the scale of sequence analyses, especially the time after human genome project. High-throughput technologies provide highly detailed and large scale data that can be generated by cost-effective manner. In particular, next-generation sequencing and microarray technologies are two major platforms that immensely used for study gene expression. We developed a workflow to integrate next-generation sequencing and microarray data, to survey the complexity of transcriptomes in gene expression level. This workflow generates more reliable information than using single platform data, and provides more aspects of information to characterize gene expression of whole genome. Finally, we had a preliminary discussion on the cause of the characteristic differences between next-generation sequencing and microarray.

關鍵字(中)

★ 次世代定序
★ 微陣列晶片
★ 基因表現

關鍵字(英)

★ microarray
★ next-generation sequencing
★ gene expression

論文目次

Chinese abstract ...................................................................................................................... i
English abstract ..................................................................................................................... ii
Figure content ....................................................................................................................... v
Table content ...................................................................................................................... vi
Chapter 1 Introduction ................................................................................................. 1
1-1 Next-Generation Sequencing ........................................................................... 1
1-1-1 SOLiD System ..................................................................................... 2
1-1-2 Solexa System ..................................................................................... 4
1-2 Microarray ....................................................................................................... 5
1-3 Motivation ....................................................................................................... 7
Chapter 2 Material and Methods .................................................................................. 8
2-1 Data Source...................................................................................................... 8
2-2 Workflow ......................................................................................................... 9
2-3 Methods ......................................................................................................... 10
2-3-1 CLC Genomic Workbench ................................................................ 10
2-3-2 Affymetrix Expression Console ........................................................ 13
2-3-3 Principle Component Analysis (PCA) ............................................... 16
2-4 Gene Ontology (GO) Enrichment.................................................................. 17
Chapter 3 Results ....................................................................................................... 18
3-1 Microarray data analyses ............................................................................... 18
3-1-1 Principle Component Analysis .......................................................... 18
3-1-2 Affymetrix Expression Console analysis .......................................... 20
3-2 Sequencing data analyses .............................................................................. 22
3-2-1 CLC Genomic Workbench analysis ................................................... 22
3-3 Integration of Sequencing and Microarray .................................................... 24
3-3-1 Comparison of gene expression between two platforms ................... 25
3-4 Genes in microarray sensitive region ............................................................ 30
3-5 Genes in sequencing sensitive region ............................................................ 33
Chapter 4 Discussion .................................................................................................. 34
References ..................................................................................................................... 36

參考文獻

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指導教授

吳立青(Li-ching Wu)

審核日期

2010-7-19

推文