Dissertations / Theses on the topic 'Transcription Start Sites'
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Down, T. "Computational localization of promoters and transcription start sites in mammalian genomes." Thesis, University of Cambridge, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.598623.
Full textSchroeder, Diane Irene. "Two stories of human transcription regulation : bidirectional promoters and the multiple transcription start sites of FOXP2 /." May be available electronically:, 2008. http://proquest.umi.com/login?COPT=REJTPTU1MTUmSU5UPTAmVkVSPTI=&clientId=12498.
Full textVan, Jaarsveld Ida CecIlia. "Basal promoter landscape in Eucalyptus grandis : annotation of distal transcription start sites and core promoter usage." Diss., University of Pretoria, 2014. http://hdl.handle.net/2263/79196.
Full textDissertation (MSc)--University of Pretoria, 2014.
Biochemistry
MSc
Unrestricted
Li, Xiaomeng. "Human Promoter Recognition Based on Principal Component Analysis." Thesis, The University of Sydney, 2008. http://hdl.handle.net/2123/3656.
Full textLi, Xiaomeng. "Human Promoter Recognition Based on Principal Component Analysis." University of Sydney, 2008. http://hdl.handle.net/2123/3656.
Full textThis thesis presents an innovative human promoter recognition model HPR-PCA. Principal component analysis (PCA) is applied on context feature selection DNA sequences and the prediction network is built with the artificial neural network (ANN). A thorough literature review of all the relevant topics in the promoter prediction field is also provided. As the main technique of HPR-PCA, the application of PCA on feature selection is firstly developed. In order to find informative and discriminative features for effective classification, PCA is applied on the different n-mer promoter and exon combined frequency matrices, and principal components (PCs) of each matrix are generated to construct the new feature space. ANN built classifiers are used to test the discriminability of each feature space. Finally, the 3 and 5-mer feature matrix is selected as the context feature in this model. Two proposed schemes of HPR-PCA model are discussed and the implementations of sub-modules in each scheme are introduced. The context features selected by PCA are III used to build three promoter and non-promoter classifiers. CpG-island modules are embedded into models in different ways. In the comparison, Scheme I obtains better prediction results on two test sets so it is adopted as the model for HPR-PCA for further evaluation. Three existing promoter prediction systems are used to compare to HPR-PCA on three test sets including the chromosome 22 sequence. The performance of HPR-PCA is outstanding compared to the other four systems.
Zehentner, Barbara Katrin [Verfasser], Siegfried [Akademischer Betreuer] Scherer, Wolfgang [Gutachter] Liebl, Siegfried [Gutachter] Scherer, and Lindsay [Gutachter] Hall. "Experimental characterization of overlapping genes in enterohemorrhagic E. coli: Overexpression phenotypes and high-throughput NGS analysis of transcription start sites / Barbara Katrin Zehentner ; Gutachter: Wolfgang Liebl, Siegfried Scherer, Lindsay Hall ; Betreuer: Siegfried Scherer." München : Universitätsbibliothek der TU München, 2020. http://d-nb.info/1233427962/34.
Full textMoos, Abdul Ragmaan. "A case-control approach to assess variability in distribution of distance between transcription factor binding site and transcription start site." Thesis, Rhodes University, 2017. http://hdl.handle.net/10962/5315.
Full textCARSON, DANIEL J. "DECIPHERING THE ROLE OF TFIIB IN TRANSCRIPTIONAL ACTIVATION AND START SITE DETERMINATION." University of Cincinnati / OhioLINK, 2002. http://rave.ohiolink.edu/etdc/view?acc_num=ucin1022683318.
Full textRaborn, R. Taylor. "Genome-wide analysis of transcription initiation and promoter architecture in eukaryotes." Diss., University of Iowa, 2012. https://ir.uiowa.edu/etd/4728.
Full textMwangi, Sarah Wambui. "In silico investigation of glossina morsitans promoters." University of the Western Cape, 2013. http://hdl.handle.net/11394/3990.
Full textTsetse flies (Glossina spp) are the biological vectors for Trypanosomes, the causative magents of Human African Trypanosomiasis (HAT). HAT is a debilitating disease that continues to present a major public health problem and a key factor limiting rural development in vast regions of tropical Africa. To augment vector control efforts, the International Glossina Genome Initiative (IGGI) was established in 2004 with the ultimate goal of generating a fully annotated whole genome sequence for Glossina morsitans. A working draft genome of Glossina morsitans was availed in 2011. In this thesis, transcriptional regulatory features in Glossina morsitans were analysed using the draft genome. A method for TSS identification in the newly sequenced Glossina morsitans genome was developed using TSS-seq tags sampled from two developmental stages of Glossina morsitans. High throughput next generation sequencing reads obtained from Glossina morsitans larvae and pupae were used to locate transcription start sites (TSS) in the Glossina morsitans genome. TSS-seq tag clusters, defined as a minimum number of reads at the 5’ predicted UTR or first coding exon, were used to define transcription start sites. A total of 3134 tag clusters were identified on the Glossina genome. Approximately 45.4% (1424) of the tag clusters mapped to the first coding exons or their proximal predicted 5’UTR regions and include 31 tag clusters that mapped to transposons. A total of 1101 (35.1%) tag clusters mapped outside the genic region and/or scaffolds without gene predictions and may correspond to previously un-annotated transcripts or noncoding RNA TSS. The core promoter regions were classified as narrow or broad based on the number of TSS positions within a TSS-seq cluster. Majority (95%) of the core promoters analysed in this study were of the broad type while only 5% were of the narrow type. Comparison of canonical core promoter motif occurences between random and bona fide core promoters showed that, generally, the number of motifs in biologically functional genomic windows in the true dataset exceeded those in the random dataset (p <= 0.00164, 0.00135, 0.00185 for the narrow, broad with peak and broad without peak categories respectively). Frequency of motif co-occurrence in core promoter was found to be fundamentally different across various initiation patterns. Narrow core promoters recorded higher frequency of the TATA-box and INR motifs and two-way motif co-occurrence showed that the TATA-box-INR pair is over-represented in the narrow category. Broad core promoters showed higher frequency of the BREd and MTE motifs and two-way motif co-occurrence showed that the MTE-DPE pair is over-represented in broad core promoters. TATA-less promoters account for 77% of the core promoters in this analysis. TATA-less core promoters showed a higher frequency of the MTE and INR motifs in contrast to observations in Drosophila where the DPE motif has been reported to occur frequently in TATA-less promoters. These motif combinations suggest their equal importance to transcription in their corresponding promoter classes in Glossina morsitans.
Xia, Yu. "Molecular cloning and characterization of the human [alpha]-synuclein (SNCA) gene : genomic structure, transcription start site, promoter region and polymorphisms /." Diss., Connect to a 24 p. preview or request complete full text in PDF format. Access restricted to UC campuses, 1998. http://wwwlib.umi.com/cr/ucsd/fullcit?p9835292.
Full textBeder, Thomas [Verfasser], Hans Peter [Gutachter] Saluz, Rainer [Gutachter] König, and Nicole [Gutachter] Borel. "Differential RNA-Seq and transcription start site annotation in Chlamydia / Thomas Beder ; Gutachter: Hans Peter Saluz, Rainer König, Nicol Borel." Jena : Friedrich-Schiller-Universität Jena, 2019. http://d-nb.info/1210026996/34.
Full textGrech, Brian James. "Bioinformatic prediction of conserved promoters across multiple whole genomes of Chlamydia." Thesis, Queensland University of Technology, 2007. https://eprints.qut.edu.au/16521/1/Brian_James_Grech_Thesis.pdf.
Full textGrech, Brian James. "Bioinformatic prediction of conserved promoters across multiple whole genomes of Chlamydia." Queensland University of Technology, 2007. http://eprints.qut.edu.au/16521/.
Full textTaylor, Russell Haywood. "A guanine to adenine mutation -76bp from the transcriptional start site decreases constitutive CYP1A2 expression in a novel mouse strain." Thesis, University of Ottawa (Canada), 2007. http://hdl.handle.net/10393/27924.
Full textAlmeida, João Paulo Pereira de. "O transcritoma antisense primário de Halobacterium salinarum NRC-1." Universidade de São Paulo, 2018. http://www.teses.usp.br/teses/disponiveis/17/17131/tde-15012019-101127/.
Full textAntisense RNAs (asRNAs) constitute the most numerous class of non-coding RNAs (ncRNAs) detected by transcriptome highthroughput methods in prokaryotes. Despite this abundance, little is known about regulatory mechanisms and evolutionary aspects of these molecules, mainly in archaea, where the mechanism of double-strand RNA (dsRNA) degradation remains poorly understood. In this study, using dRNA-seq data, we identified 1626 antisense transcription start sites (aTSSs) in the genome of Halobacterium salinarum NRC-1, an important model organism for gene expression regulation studies in Archaea. By integrating gene expression data from 18 RNA-seq paired-end libraries, we were able to annotate 846 asRNAs from mapped aTSSs. We found asRNAs in ~21% of annotated genes including genes related to important characteristics of this organism, such as: gas vesicle proteins, bacteriorhodopsin, translation machinery and transposases. We also found asRNAs in type II toxin-antitoxin systems and using public dRNA-seq data, we show evidences that this phenomenon might be conserved in archaea and bacteria. The interaction of a ncRNA with its target may depend on intermediary proteins action. In archaea, the LSm protein is a RNA chaperone homologous to bacterial Hfq, involved in post-transcriptional regulation. We used RIP-seq data from RNAs immunoprecipitated with LSm and identified 91 asRNAs interacting with this protein, for 81 of these the mRNA of the sense gene is also interacting. We searched for aTSSs present in the same region of orthologous genes in the Haloferax volcanii. We found 160 aTSSs that originated asRNAs in H. salinarum NRC-1 that might be conserved in this two archaea. The expression of annotated asRNAs was analyzed over a growth curve and in a knockout strain for RNase R gene. We found 144 asRNA differentially expressed over the growth curve, for 56 of these the sense gene was also differentially expressed, characterizing possible cis regulators asRNAs. In the knockout strain we found five differentially expressed asRNAs and only one asRNA/gene pair, this result does not allow us to infer a dsRNA degradation in vivo activity for this RNase in H. salinarum NRC- 1. This work contributes to the discovery of the antisense transcriptome in H. salinarum NRC- 1 a relevant step to uncover the post-transcriptional gene regulatory network in this archaeon.
Lloyd, Amanda Lian. "Cloning, characterisation and sequencing of promoters of Helicobacter pylori 4187E." University of Western Australia. Microbiology Discipline Group, 2005. http://theses.library.uwa.edu.au/adt-WU2005.0112.
Full textMillán, Ariño Lluís 1984. "Genomic distribution and functional specificity of human histone H1 subtypes." Doctoral thesis, Universitat Pompeu Fabra, 2013. http://hdl.handle.net/10803/292370.
Full textFins a set variants de la histona H1 s han identificat en mamífers, les quals mostres una prevalença diferent entre tipus cel lulars i durant el procés de diferenciació. Tot i que la histona H1 juga un paper clau en l estructuració de la cromatina, no s acaba d entendre encara com participa exactament en els diferent processos cel lulars. A més a més, encara no està clar si les diferents variants tenen funcions específiques ni si es distribueixen igual al llarg del genoma. Mitjançant anticossos específics per algunes variants d H1 i de línies cel lulars de càncer de mama que expressen H1s recombinant fusionades a un pèptid HA, s ha estudiat la distribució genòmica de H1.2 a H1.5, H1.0 i H1X, combinant ChIP-qPCR, ChIP-chip i ChIP-seq. Totes les H1s es troben a promotors gènics i empobrides a l inici de transcripció dels gens actius, i també a les regions reguladores. El grau de disminució d H1 al promotor depèn de l estat transcripcional del gen i presenta diferències entre variants. Els anàlisis mostren que la histona H1 no es distribueix uniformement al genoma i que hi ha diferències entre variants, essent H1.2 la variant que presenta un patró més específic i una correlació més forta amb repressió gènica a cèl lules de càncer de mama. Aquests resultats suggereixen que variants d H1 diferents es troben presents als diversos tipus de cromatina, i aquest fet podria dependre de la línia cel lular, l estat de diferenciació, o de si les cèl lules s han originat durant un procés neoplàsic. En una segona part de la tesi, es mostra que una línia cel lular anteriorment descrita que inhibeix H1.4 presenta un efecte inespecífic contra lamina B2. Així, s ha desenvolupat una altra línia que inhibeix H1.4 específicament, la qual s assembla a un mutant anteriorment caracteritzat que inhibeix H1.2. Finalment, la inhibició combinada de H1.4/lamina B2 i H1.2/H1.4 provoca efectes fenotípics semblants a cèl lules de càncer de mama T47D.
Lai, Cheng-Kuo, and 賴政國. "Comparative studies of microRNA transcription start sites between human and chimpanzee." Thesis, 2015. http://ndltd.ncl.edu.tw/handle/86666970495841783343.
Full text國立中興大學
基因體暨生物資訊學研究所
103
Identifying the transcription start sites (TSSs) of microRNA (miRNA) genes is essential for understanding the regulation of miRNA transcription which is extremely important for determining the specific roles that miRNAs play in regulatory pathways. Because humans and chimpanzees share most of genes, comparative studies of the two species are the ways often used to comprehend humans more. In the past, most studies are focused on the divergence of proteins, genes and miRNAs. However, the divergence of the regulation of miRNA transcription between humans and chimpanzees seems still not to be addressed yet. In this study, 86 global-run-on-sequencing (GRO-Seq) validated TSSs of 125 human miRNAs were collected to search their homologous regions in the chimpanzee genome. An un-annotated homologous miRNA region was considered to be a putative chimpanzee miRNA if the sequence of the region can be folded into a hairpin structure. In addition, a homologous TSS location was then confirmed as a putative chimpanzee miRNA TSS if it was able to be identified by a semi-supervised statistical model trained on Pol II ChIP-sequencing data of chimpanzee and several sequence-associated features. From the result, most of the human TSS-miRNA pairs are still kept in chimpanzees. We identified 33 un-annotated chimpanzee miRNAs and 48 putative chimpanzee miRNA TSSs of 69 chimpanzee miRNAs. Interestingly, a number of human TSS-miRNA pairs were missing; we found that 18 miRNAs were lost in chimpanzee during evolution and another missing miRNA, mir-659, might be human specific. We studied the regulatory pathway of mir-659 and found that mir-659 could be involved in neurodevelopmental. These divergence of the regulation of miRNA transcription might be, at least in part, the molecular footprint of speciation events in the human and chimpanzee lineages.
Sung, Tsai-Jung, and 宋采蓉. "Identification of Chlorocebus sabaeus microRNAs and prediction of the microRNA transcription start sites." Thesis, 2019. http://ndltd.ncl.edu.tw/cgi-bin/gs32/gsweb.cgi/login?o=dnclcdr&s=id=%22107NCHU5105029%22.&searchmode=basic.
Full text國立中興大學
基因體暨生物資訊學研究所
107
The Vero cell is a renal epithelial cell line (kidney epithelial cells from a female African green monkey, Chlorocebus sabaeus), and has the cellular characteristics of interferon manufacturing defects. That causes a faster rate of virus spread, compared to the normal cells. Vero cells have been used as a host for mammalian viruses, and play an important role in vaccine manufacturing industry. Many studies have pointed out that the interaction between viruses and hosts may be related to non-coding RNA (ncRNAs, such as microRNAs, miRNAs). For example, siRNA-100, one small interfering RNA (siRNA) of Poliovirus (PV) can indirectly increase the concentration of miR-7 in the host, thereby inhibit the replication rate of poliovirus. Knowledge of the regulation of Vero cell miRNAs and their upstream and downstream will help to identify the factors related to the speed and quality of viral replication in Vero cells, and to achieve the purposes of reducing the cost and uncertainty of the experiment, improving the effectiveness of the vaccine and stabilizing the production quality and yield. However, there is no complete database related to Vero cells miRNA at present. Therefore, we try to identify the corresponding homologous miRNAs of the green monkey based on the Macaca mulatta and Homo sapiens precursor miRNAs. A total of 742 green monkey miRNAs were obtained from the Next Generation Sequencing (NGS) data of the green monkey. At the same time, in order to understand the upstream promoter regulation of miRNAs. The transcription start sites of 236 miRNAs were predicted by using the support vector machine (SVM) combined with the published next generation transcript sequencing data and sequence characteristics (including CpG content and DNA structural properties). This study identified 742 miRNAs, and 49 of these miRNAs have been shown to be involved in the regulation of viral replication in African green monkey cells. At the same time, the transcription start site was also predicted. It is expected that there will be a further understanding of the regulation network of African green monkeys and virus replication. And make vaccine production more stable yield and quality.
Yang, Shang-Teng, and 楊翔騰. "Identification of microRNA Transcription Start Sites of Vertebrates Using Transcriptome Data and Sequence Features." Thesis, 2016. http://ndltd.ncl.edu.tw/handle/69723278750184061681.
Full text國立中興大學
基因體暨生物資訊學研究所
104
To identify microRNA (miRNA) transcription start sites (TSSs) is still difficult. Some studies utilized machine learning methods as well as the TSS-related data, such as CAGE (cap analysis gene expression) data, histone modification site data and TSS-seq data, and some sequence features to predict miRNA TSSs. However, at present, the TSS-related data are available only for human or mouse. In this study, we would like to develop a method that can be applied to more species; we predict miRNA TSSs using the technique of SVM (support vector machine) trained on RNA-seq data and some sequence features like CpG content and sequence conservation. Our results are comparable to that of the other studies on human and mouse. In addition, we applied our method to some other species, such as opossum, chicken, xenopus, zebrafish and Arabidopsis, and found that the accuracy of the proposed method is decreasing from opossum to Arabidopsis; the accuracy of the proposed method is about 70% for opossum and zebrafish but less than 70% for Arabidopsis. We then studied the sequences around TSSs and found that the animal promoter regions become CG-rich during evolution. Our method is able to predict miRNA TSSs in vertebrates and has higher prediction accuracy in placental mammals.
Hsiao, Yu-Ming, and 蕭鈺銘. "Sequence-based prediction of microRNA transcription start sites from transcriptome data using DNA structural properties." Thesis, 2018. http://ndltd.ncl.edu.tw/handle/57u4de.
Full text國立中興大學
基因體暨生物資訊學研究所
106
microRNAs (miRNAs) are important small non-coding RNAs, mainly regulating gene expression in cells. Understanding upstream promoter regions of miRNAs is also an important issue. Current developed methods to identify miRNA transcription start sites (TSSs) all require specifically designed experiments or integrated multiple data. Therefore, we want to construct a more generic method. We use standard RNA sequencing (RNA-seq) data and sequence features (including conservation score, CpG content, and structural properties), and utilize the Support Vector Machine (SVM) maching learning algorithm to predict miRNA TSSs. Based on the method we have established before, this time we incorporate the structural properties into models, which improve the performance of the models. Comparison of our prediction results with experimentally validated TSS data shows that our method can identify miRNA TSSs. Moreover, this prediction system is not limited to human or mouse. It can be applied to more species because of its generic characteristics in sequence features. We hope these predicted TSSs can compensate for the lack of experimentally validated TSS data or provide TSS candidate sites for further experimental verification, to comprehensively understand the role of miRNAs in regulatory network.
Liu, Hsiang-Hua, and 劉湘華. "Integration of experimental data of human microRNA transcription start sites and comparative studies of microRNA promoter regions between human and chimpanzee." Thesis, 2017. http://ndltd.ncl.edu.tw/handle/54492480172777603249.
Full text國立中興大學
基因體暨生物資訊學研究所
105
MicroRNAs (miRNAs) are small non-coding RNAs of ~20-24 nucleotides (nt) that participate the regulation of expression of protein coding genes in multicellular eukaryotes. Although there have been many studies on the mechanism of miRNA target gene regulation and the methods of target gene prediction, little is known regarding the regulation of miRNA genes themselves. Even though both miRNA genes and protein coding genes are transcribed by RNA polymerase II, it is still very difficult to identify miRNA transcription start sites (TSSs) or promoter regions with a common sequencing method because the distances between miRNAs and their TSSs vary a lot and the primary miRNA transcripts will be sliced and degraded by enzyme quickly after they are transcribed. In this study, we integrated three sets of experimentally validated human miRNA TSS data and found that most TSSs from different sets for a specific miRNA were located within regions of approximately 100 nt in length. We then utilized the alignment tool to search 199 precursor miRNAs and their corresponding promoters obtained from the human integration data against the chimpanzee genome. There were 192 (97%) miRNAs and the corresponding promoters that could be found in the chimpanzee genome. In order to examine the miRNA and promoter candidates found in the chimpanzee genome, we further checked some sequence and structure properties of the candidates as well as their expression. Finally, we found that 7 human TSS-miRNA pairs were missing and 1 human miRNA might lose function in chimpanzee. We further tried to date the missing events in evolution by using some primate out group data and found that mir-4717 and mir-5091 may play important roles in human. In this study, we propose a homology search approach to identify miRNAs and their promoter regions in closely related species by using precursor miRNA sequences and experimentally validated miRNA TSSs.
Tompkins, Leslie Meredith. "Identification of novel transcription start sites and distinct proximal promoter regions for pregnane X receptor (PXR) isoforms PXR 1 and PXR 2." 2007. http://www.lib.ncsu.edu/theses/available/etd-08152007-133052/unrestricted/etd.pdf.
Full textWang, Ting-Yuan, and 王定遠. "Identification of MicroRNA Transcriptional Start Sites in Human Genome." Thesis, 2008. http://ndltd.ncl.edu.tw/handle/26407504225695503774.
Full text國立交通大學
生物資訊研究所
96
The miRNAs are ~21nt single-strand short nucleotide that can induce RNAi mechanism through complete or partial complementarities. Most of the miRNAs are transcribed by RNA polymerase II [1]. The pri-miRNA transcribed by RNA polymerase II contained 5’cap and 3’poly-A tail [2]. For those intergenic miRNA, non-gene-overlap miRNA, they have their own promoter. It is important to understand those promoters of intergenic miRNA gene to facilitated understanding the regulation of intergenic miRNA. Because of the nature of the enzymatic reaction the probability of retrieving the sequence of extreme 5’ end region was very low with traditional PCR technology. Here, we use 5’RACE [3, 4] to ensure that the 5’end region of pri-miRNAs was obtained. In addition, we incorporate miRNA expression profile [5] to filter out those lower-expressed miRNA. With a series of computational promoter prediction, we could choose the putative TSS that has many support evidences. In order to identify whether putative TSS is true or false, the putative TSS specific primer was designed. Finally, the RT-PCT results were used to confirm the putative promoter regions.
Hsu, Yu-Pin, and 許郁彬. "Identification of human microRNA transcriptional start sites from transcriptome." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/e7794f.
Full text國立中興大學
基因體暨生物資訊學研究所
101
Identifying gene transcription start sites (TSSs) is the basis for determining gene upstream regulatory region. With the progress of the next generation sequencing (NGS) technologies, many kinds of NGS data have been utilized to identify TSSs. For example, RNA PolⅡChIP-seq (Chromatin immunoprecipitation sequencing) is used to recognize RNA PolⅡbinding sites and therefore is a direct way to identify TSSs. In addition, some other kinds of data like nucleosome-seq, DNase-seq (DNase I hypersensitive sites sequencing) and FAIRE-seq (Formaldehyde-Assisted Isolation of Regulatory Elements sequencing), which are associated with histone modification sites, hyper-sensitive sites and regulatory activity, respectively, are alone or combined to determine TSSs. Several statistical or machine learning methods have been developed for finding and characterizing TSSs. These datasets and methods can be also used to locate miRNA TSSs because it is believed that most miRNA genes, like protein coding genes, require RNA Pol II for expression. In this thesis, we utilized RNA-seq data, i.e. transcriptome sequencing data, to locate miRNA TSSs. We observed that there are signals of RNA-seq sequences near the TSS of well-annotated protein coding genes so we proposed that the miRNA TSSs may also have similar pattern. We then located splice junction region and tried to complete primary transcripts of miRNAs (i.e. pri-miRNAs) and then miRNA TSSs were identified. This approach can not only locate miRNA TSSs but also give information to characterize TSSs of other gene types. Information obtained from transcriptome sequencing data could be a new feature for predicting gene TSSs and analyzing gene regulation. KEY WORDS MicroRNA, Transcription Start Site, TSS, Transcription Factor Binding Site, TFBS, upstream regulation
"Promoter Identification in Daphnia Populations Revealed by Transcription Start Site Profiling." Master's thesis, 2020. http://hdl.handle.net/2286/R.I.62809.
Full textDissertation/Thesis
Masters Thesis Molecular and Cellular Biology 2020
Fang, Hao-Yu, and 方浩宇. "Using high-throughput sequencing data to identify the transcriptional start sites of mouse microRNAs." Thesis, 2013. http://ndltd.ncl.edu.tw/handle/32453885381096374336.
Full text國立中興大學
基因體暨生物資訊學研究所
101
MicroRNAs (miRNAs) are non-coding small RNAs that inhibit protein coding gene expression by hybridizing with messenger RNAs (mRNAs). MiRNAs are involved in a lot of diverse biological processes and various diseases. To identify miRNA transcription start sites (TSSs) is important for studying the upstream regulatory networks of miRNAs. Up to now the studies regarding miRNA TSS identification are all focus on human miRNAs. We are interested in other species and our aim in this study is to identify mouse miRNA TSSs and the result would contribute to understanding the evolution of upstream regulatory networks of miRNAs. In this study, we integrated two types of high-throughput sequencing data, i.e. transcription start sites sequencing (TSSseq) and Cap Analysis of Gene Expression (CAGE), as the evidence of miRNA TSSs. A machine-learning-based Support Vector Machine (SVM) was developed to identify mouse miRNA TSSs. In addition, we also incorporated the ESTs (expression sequence tag) and sequence conservation information to provide evidence for mouse miRNA TSSs.
Dieterich, Christoph, Steffen Grossmann, Andrea Tanzer, Stefan Röpcke, Peter F. Arndt, Peter F. Stadler, and Martin Vingron. "Comparative promoter region analysis powered by CORG." 2005. https://ul.qucosa.de/id/qucosa%3A32449.
Full textHsu, Chen-Wei, and 許承偉. "Modeling Transcription Start Site and Promoter Elements with Dependency Graphs and Their Expanded Bayesian Networks." Thesis, 2004. http://ndltd.ncl.edu.tw/handle/85582533837369657887.
Full text國立清華大學
電機工程學系
92
We have a large amount of raw genomic DNA sequence data now with the completion of the Human Genome Project (HGP). There are hundreds of programs developed to analyze these DNA sequences. Promoter is a region usually located at the 5' flanking end of a gene and encompasses the transcription start site. The promoter plays an important role in gene regulation and the detection of the promoter region could help to improve the accuracy of gene-finding. There are also several in silico approaches to predict promoter region or transcription start site, but the performance of these programs are usually unsatisfactory since the number of false positives is too high. In this thesis, we first develop a dependency graph as the basic model for the transcription start site by chi-square test and then expand this graph with a Bayesian network by allowing nucleotides in each position to appear more than once to catch their inter-dependency but avoid overfitting. In consideration of more than one signals within the promoter region, we also construct dependency graph and it's expanded Bayesian network to model TATA box. The prediction of TATA box will be integrated into the prediction of transcription start site in this thesis. The results show that our method has the best performance comparing with four most famous programs available on the Internet.
Qiu, Yu. "Microarray-based Escherichia coli functional genomic studies : cold shock and iron starvation responses, and transcription start site identification /." 2006. http://www.library.wisc.edu/databases/connect/dissertations.html.
Full textHandel, Katherine. "Identification of the promoter and transcription start site of the katE gene, encoding hydroperoxidase HPII, in Escherichia coli." 1995. http://hdl.handle.net/1993/17642.
Full textCarpio, Farro Ronald Erick [Verfasser]. "Studies on transcriptional regulation in the human retina : mapping of transcriptional start sites of retinal expressed genes and functional characterization of the CNGA3 promoter / vorgelegt von Ronald Erick Carpio Farro." 2009. http://d-nb.info/1007612452/34.
Full textSuh, Won-Chul. "The interaction of E. Coli RNA polymerase with lambda phage PR promoter evidence for two open complexes and a requirement for Mg²⁺ to open the transcription start site /." 1993. http://catalog.hathitrust.org/api/volumes/oclc/30697555.html.
Full textMajovski, Robert C. "Structure-function analysis of the Saccharomyces cerevisiae RNA polymerase II active center a functional role for the switch 2 region in transcription start site utilization and abortive initiation /." 2007. http://proquest.umi.com/pqdweb?did=1402170981&sid=15&Fmt=2&clientId=39334&RQT=309&VName=PQD.
Full textTitle from PDF title page (viewed on Mar. 06, 2008) Available through UMI ProQuest Digital Dissertations. Thesis adviser: Ponticelli, Alfred S. Includes bibliographical references.
Wiegand, Sandra. "RNA-Seq and proteomics based analysis of regulatory RNA features and gene expression in Bacillus licheniformis." Doctoral thesis, 2013. http://hdl.handle.net/11858/00-1735-0000-0022-5E88-E.
Full text