臺灣博碩士論文加值系統

功能基因體學專注於基因功能上的註解，並對基因網路有廣泛性的了解，而基因網路組成複雜的生物功能

上的任務，很多的研究仍然致力於在解決這樣的問題，也有很多的研究致力於演算法上準確度的提升，但

是，人類基因體解序後仍然有將近四分之一的基因是功能未知的，而且被標註是假設性基因。
而先前研究指出，基因若有類似的功能通常會有類似的轉錄調控機制，也就是說，在他們的啟動子上會有

類似的轉錄因子結合部位，受到演化壓力下，這些具有功能的因子在演化過程中會比附近沒有功能的區域

要來的慢，因此，在電腦輔助的研究中，多物種的研究方向所找到的轉錄因子結合部位會是很有意義的結

果，這個方法也在很多基因中成功的找到新的轉錄因子結合部位，這個方法就是所謂的「演化腳印分析法

」。此論文用此方法，從起動子的取得、預測直到轉錄因子結合部位的搜尋，而後，再用假設性為材料將

癌症相關基因一同加入搜尋，並比較及搜尋這些基因與癌症基因可能的共同調控因子。
我分析人類的假設性基因具有與異種同源的基因的啟動子部分，並且提供一個網路服務給生物學家可以很

容易的用來分析不同物種間的基因關係。最後，這樣的研究順利找到了這些假設性基因與癌症相關基因共

同的高度保留部位，這結果是很有意義的，並且從分類上區分這些高度保留的調控部位。

Functional genomics focuses on assigning genes into functional categories and providing a comprehensive understanding of genetic networks. Genetic networks are complicated to perform complex biological tasks. Lots of works are still working on deciphering it and forcing to higher accuracy of algorithm. But there are still about one-fourth of genes in human genome functionally indistinct and are annotated to hypothetical genes. Genes involve in the same biological process are often regulated by similar transcriptional mechanism and are likely to contain similar transcription factor binding sites (TFBS) in their proximal promoters. Functional elements tend to evolve much slower than non-functional region, as they are subjected to selective pressure. Multi-species approach is come to make sense of TFBS prediction in silico, and was used with success to identify regulatory elements in various genes. The method is so-called “Phylogenetic Footprinting’’. The work flow goes through promoter extraction, prediction, and regulatory elements detection. Thus, both hypothetical genes and cancer-related genes are the inputs for testing.
In this thesis, I analyzed the promoter region of hypothetical genes of Homo sapiens which are homologous to other organism, and provide a web service for biologists to analyze genetic networks between different organisms easily. Finally, the results are interesting because of discovering several conserved elements within some hypothetical genes and cancer-related genes, and supplying the highly conserved regulatory elements from different taxonomic nodes.

Chapter 1 Introduction 3
1.1 Background 3
1.1.1 Structural Characteristics of Eukaryotic Genes 4
1.1.2 General Promoter Structure 6
1.1.3 The Gene Expression and Regulation in Eukaryotes 7
1.1.3.1 Transcription 8
1.1.3.2 Regulation of Transcription 10
1.1.4 Genome Projects and Hypothetical Genes 13
1.1.4.1 Genome Projects 13
1.1.4.2 Hypothetical Genes 14
1.1.5 Promoter and Transcription Factor Prediction 15
1.1.6 Cancer-Related Transcription Factors 16
1.2 Motivation 18
1.3 Contribution 19
1.4 Thesis Organization 19
Chapter 2 Related Work 20
2.1 Sequence Database in NCBI 20
2.1.1 UniGene 21
2.1.2 HomoloGene 22
2.2 FirstEF: Promoter Prediction Program 24
2.2.1 Methods of FirstEF 24
2.2.2 Interface 25
2.3 TRANSFAC: Transcription Factor Database 26
2.4 Transcription Factor Prediction 26
2.4.1 TFSearch 26
2.4.1.1 Method 27
2.4.1.2 Interface 28
2.4.2 Footprinter: Phylogenetic Footprinting Program 28
2.4.2.1 Method of Footprinter 29
2.4.2.2 The Interface in Footprinter 31
2.4.3 ClustalW 32
2.4.3.1 The Method for ClustalW 33
2.4.3.2 The Interface for ClustalW 34
Chapter 3 Methods 35
3.1 Introduction 35
3.2 Methodology 37
3.2.1 Architecture 37
3.2.2 Gene Candidates of Hypothetical Genes 38
3.2.3 Subtraction and Substitution of Multiple Sequences 40
3.2.3.1 Extraction and Prediction of an Eukaryotic Promoter 41
3.2.3.2 FirstEF 41
3.2.4 Prediction of TFBSs by Phylogenetic Footprinting 42
3.3 Motif Assemble and Filter 43
3.4 Experimental Validation 44
3.5 Hypothetical Gene Test 46
3.6 Gene Relation 47
3.6.1 Multiple Sequence Alignment 47
Chapter 4 Results and Discussions 49
4.1 Statistics of Hypothetical Genes 49
4.1.1 Hypothetical Genes with Orthologs 49
4.1.2 Promoter Prediction Results 50
4.2 Results of TFSearch and Phylogenetic Footprinting 51
4.2.1 Comparison of Cis-acting Elements Searching between Multiple Species and Single Species 54
4.2.2 Highly Conserved Elements of Hypothetical Genes 55
4.3 System Validation by Experimentally Defined Regulatory Elements 55
4.4 Relation of Hypothetical Genes and Cancer-Related Genes 59
4.5 Discussion on Loss of Motifs 62
4.5.1 Parameters of Phylogenetic Footprinting 62
4.6 Evolutionary Distance of Orthologs 62
4.7 Length of Conserved Elements and Mutations 63
4.8 Interludes of Divergence Nucleotides in Conserved Regions 65
Chapter 5 Conclusion and Future Work 67
5.1 Conclusion 67
5.2 Future Work 68
References 69

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