published_or_final_version / Pathology / Doctoral / Doctor of Philosophy

published_or_final_version / abstract / Pathology / Master / Master of Philosophy

Transcription factors are macromolecules that are involved in transcriptional regulation by interacting with specific DNA regions, and they can cause activation or silencing of their target genes. Gene regulation by transcriptional control explains different biological processes such as development, function, and disease. Even though transcriptional control has been of great interest for molecular biology, much still remains unknown. This study was designed to generate the most current list of human transcription factor genes. Unique entries of transcription factor genes were collected and entered into Microsoft Office 2007 Access Database along with information about each gene. Microsoft Office 2007 Access tools were used to analyze and group collected entries according to different properties such as activator or repressor record, or presence of certain protein domains. Furthermore, protein sequence alignments of members of different groups were performed, and phylogenetic trees were used to analyze relationship between different members of each group. This work contributes to the existing knowledge of transcriptional regulation in humans. / by Ala Savitskaya. / Thesis (M.S.)--Florida Atlantic University, 2010. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2010. Mode of access: World Wide Web.

Microarray expression data which contains the expression levels of a large number of simultaneously observed genes have been used in many scientific research and clinical studies. Due to its high dimensionalities, selecting a small number of genes has shown to be beneficial for many tasks such as building prediction models from the microarray expression data or gene regulatory network discovery. Traditional gene selection methods, however, fail to take the class distribution into the selection process. In biomedical science, it is very common to have microarray expression data which is severely biased with one class of examples (e.g., diseased samples) significantly less than other classes (e.g., normal samples). These sample sets with biased distributions require special attention from researchers for identification of genes responsible for a particular disease. In this thesis, we propose three filtering techniques, Higher Weight ReliefF, ReliefF with Differential Minority Repeat and ReliefF with Balanced Minority Repeat to identify genes responsible for fatal diseases from biased microarray expression data. Our solutions are evaluated on five well-known microarray datasets, Colon, Central Nervous System, DLBCL Tumor, Lymphoma and ECML Pancreas. Experimental comparisons with the traditional ReliefF filtering method demonstrate the effectiveness of the proposed methods in selecting informative genes from microarray expression data with biased sample distributions. / by Abu Hena Mustafa Kamal. / Thesis (M.S.C.S.)--Florida Atlantic University, 2009. / Includes bibliography. / Electronic reproduction. Boca Raton, Fla., 2009. Mode of access: World Wide Web.

by Zhang Yanbo. / "December 2003." / Thesis (Ph.D.)--Chinese University of Hong Kong, 2003. / Includes bibliographical references (p. 163-185). / Electronic reproduction. Hong Kong : Chinese University of Hong Kong, [2012] System requirements: Adobe Acrobat Reader. Available via World Wide Web. / Mode of access: World Wide Web. / Abstracts in English and Chinese.

Neste trabalho realizamos um programa de seqüenciamento em larga escala de cDNAs obtidos de bibliotecas construídas a partir de mRNA de células de B. emersonii submetidas ao choque térmico e ao estresse por cádmio. Obtivemos 6350 seqüências expressas (ESTs) de alta qualidade, que representam 2326 seqüências únicas putativas (unigenes) do fungo. Destes unigenes putativos, 1282 genes foram classificados em pelo menos uma das categorias do Consórcio Gene Ontology (GO). A análise do transcriptoma parcial de B. emersonii determinado até o momento permitiu a identificação de 78 unigenes codificando chaperones moleculares de todas as famílias conhecidas. Para avaliarmos a expressão global dos genes em resposta a estresses ambientais, como o choque térmico e o cádmio, realizamos ensaios de microarranjos de DNA nestas condições de estresse. Observamos que em resposta ao choque térmico, B. emersonii induz a expressão de genes que codificam proteínas relacionadas com o enovelamento de proteínas e com a proteólise, o que seria esperado em condições de temperaturas elevadas, assim como genes que codificam proteínas com propriedades antioxidantes, além de proteínas envolvidas no metabolismo de nucleotídeos e no metabolismo de carboidratos. Em resposta ao estresse por cádmio, verificou-se a indução de genes que codificam principalmente proteínas com propriedades antioxidantes, proteínas envolvidas no metabolismo de aminoácidos, proteínas relacionadas com o transporte celular e proteínas envolvidas no enovelamento de proteínas e proteólise. Uma das conseqüências do estresse por cádmio é o aumento do estresse oxidativo e proteínas antioxidantes têm um papel fundamental na resposta a este tipo de estresse. Dentre os genes observados durante o seqüenciamento das ESTs de B. emersonii, observamos dez genes codificando proteínas distintas da família Hsp70. Nove genes hsp70 são expressos em pelo menos um dos estágios do desenvolvimento do fungo e sete apresentam uma indução significativa após o choque térmico. Estes dados sugerem que estes genes desempenham um papel importante durante o desenvolvimento e em resposta ao estresse térmico em B. emersonii. Outro dado interessante obtido neste trabalho foi o enriquecimento de ESTs que continham íntrons em sua seqüência nas bibliotecas de estresse. Portanto, o choque térmico e o estresse por cádmio em B. emersonii diminuem a eficiência de processamento dos íntrons permitindo sua caracterização. O cDNA da proteína Hsp17 foi o que apresentou o maior número de ESTs seqüenciadas nas bibliotecas de estresse. Experimentos de Northern blot indicaram que o gene hsp17 possui um nível de expressão muito baixo durante o ciclo de vida de B. emersonii, no entanto, como esperado sua expressão aumenta drasticamente quando as células de esporulação ou germinação são submetidas a choque térmico. Os níveis da proteína Hsp17 acompanham os níveis do seu mRNA, indicando que o controle da expressão do gene hsp17 deve ocorrer em nível de transcrição. / In this work we realized a large scale, sequencing program of cDNAs libraries obtained from mRNA of B. emersonii cells submitted to heat shock and cadmium stress. A total of 6350 high quality expressed sequence tags (ESTs) were obtained, representing 2326 unique putative genes (unigenes) of this fungus. From these putative unigenes, 1282 genes were classified at least in one of the three Gene Ontology Consortium (GO) categories. The analysis of the partial transcriptome of B. emersonii, determined until now, allowed the identification of 78 unigenes encoding molecular chaperones of all known protein families. To evaluate the global expression of the genes in response to environmental stresses, such as heat shock and cadmium, DNA microarray assays were performed. We observed that in response to heat shock B. emersonii induces the expreession of genes encoding proteins related to protein folding and proteolysis, as expected under high temperature conditions, as well as genes encoding proteins with antioxidant properties and proteins involved in nucleotide and carbohydrate metabolism. In response to cadmium stress, we mainly verified the induction of genes for proteins with antioxidant properties, proteins involved in amino acid metabolism, proteins related to cellular transport and proteins related to protein folding and proteolysis. One of the consequences of the exposure to cadmium is the increase of oxidative stress, and antioxidant proteins have a fundamental role in the response to this kind of injury. Amongst the genes observed during the B. emersonii EST sequencing program, ten genes encoding distinct proteins from the Hsp70 family were observed. Nine of them are expressed at least in one stage of the fungus development and seven genes presented a significant induction during heat shock treatment. These data suggest that the hsp70 genes perform an important role during development and in response to heat stress in B. emersonii. Another interesting result from this work was the enrichment of ESTs containing introns in the stress libraries. Thus, heat shock and cadmium stress decrease the efficiency of intron processing in B. emersonii, allowing for intron characterization. The cDNA for the Hsp17 protein presented the highest number of ESTs sequenced from the stress libraries. Northern blot experiments indicated that the hsp17 gene is expressed at very low levels throughout the life cycle of B. emersonii, however, as expected its expression increases drastically when sporulation or germination cells are submitted to heat shock. Hsp17 protein levels accompany its mRNA levels, indicating that the control of expression of the hsp17 gene occurs at a transcriptional level.

La compréhension des mécanismes qui contrôlent l'expression des gènes est un enjeu majeur pour la recherche médicale. Elle nécessite un ensemble d'approches pangénomiques telles que les puces à ADN et plus récemment le séquençage à très haut débit qui génèrent une masse toujours plus grande de données numériques à traiter. Au cours de ma thèse, j'ai développé plusieurs outils informatiques innovants pour faciliter leur exploitation. Ainsi, j'ai créé une librairie R (AgiND) qui vérifie la qualité des données de puces à ADN Agilent et permet de les normaliser. Le nombre croissant d'expériences stockées dans Gene Expression Omnibus a motivé la mise en place du projet TBrowser. Une méthode originale DBF-MCL a été créée pour extraire des signatures transcriptionnelles annotées par l'intégration de diverses sources d'information. Stockées dans une base de données, elles sont accessibles à travers une interface Java, un service web SOAP et une librairie R/Bioconductor (RTools4TB). Enfin, un pipeline d'analyse dédié au ChIP-seq a été implémenté. Tous ces outils ont servi pour l'étude de diverses maladies dans le cadre de collaborations. / Understanding the mechanisms that control gene expression is a major challenge for medical research. This requires using a large set of pangenomic approaches such as those using DNA microarrays and high-throughput sequencing that generate an ever growing mass of digital data. During my thesis, I have developed several computer-based tools to facilitate their processing and analysis. I have created a R library (AgiND) that controls the quality of Agilent DNA microarray data and allows their statistical normalization. The growing number of experiences stored in Gene Expression Omnibus has motivated the development of the TBrowser project. An original method, DBF-MCL, was created to extract annotated transcriptional signatures by integrating various sources of information. Stored in a database, these signatures are accessible using a Java interface, a SOAP web service and a R/Bioconductor library (RTools4TB). Finally, a pipeline dedicated to the ChIP-seq analyses has been implemented. All these tools were used to study various diseases in collaborations.

Source: Masters Abstracts International, Volume: 47-06, page: 3373. Adviser: Wenyaw Chan. Includes bibliographical references.

published_or_final_version / Pathology / Doctoral / Doctor of Philosophy

The number of high-dimensional datasets recording multiple aspects of a single phenomenon is ever increasing in many areas of science. This is accompanied by a fundamental need for mathematical frameworks that can compare data tabulated as multiple large-scale matrices of di erent numbers of rows. The only such framework to date, the generalized singular value decomposition (GSVD), is limited to two matrices. This thesis addresses this limitation and de fines a higher-order GSVD (HO GSVD) of N > 2 datasets, that provides a mathematical framework that can compare multiple high-dimensional datasets tabulated as large-scale matrices of different numbers of rows. / text