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Adjustment of diagnostic instrument Array Reader C-series
Čičatka, Michal ; Hesko, Branislav (referee) ; Mézl, Martin (advisor)
Thesis deals with actualization of application for adjustment of the chemical analyser Array Reader C-series developed by company BioVendor. At the beginning it defines and sorts out chemical analysers; then describes their physical principles. Following chapters sum up knowledge about microarray analysis and describes it’s chemical and physical principles. Furthermore, the thesis deals with quality and it’s management and machine adjustment. In the thesis is also mentioned .NET Framework – software platform that will be used in the practical part of the thesis. At the end of the theoretical part is described Array Reader C-series. Practical part documents current application for adjusting the analyser. Based on personal experiences with the adjusting application was created and thoroughly described concept of a new adjusting application. Main task of this new concept should be simplification and automatization of the adjusting process. After that implementation of the new concept is described including automatation processes. In the end of this thesis both original and new versions are compared with regards to time consumption and user experience. Newer version of the application was evaluted as better than it's previous version in light of time consumption and user experience. Application was expanded for fluorescent analyzer and for both types of analyzers were developed derivated applications for service adjustment. Each of these applications was implemented to the software of BioVendor company and is used on daily basis.
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Microarray Data Interpretation
Ludwig, Petr ; Šilhavá, Jana (referee) ; Smrž, Pavel (advisor)
This Bachelor thesis explains the basics of biochip or microarray data interpretation, starting with short introduction to genetics, especially genetic information significance evaluating. The focus was set mainly on the set of scripts transforming and analyzing the sample data. The data used in this thesis are a result of biochip analysis of the Colon Tumor tissues. The secondary result represents disclosing the main marker for this particular type of cancer, the primary result is evaluation of marker significance in the context of signaling pathways. The resulting pathways are sorted by relevance.
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Molecular Signature as Optima of Multi-Objective Function with Applications to Prediction in Oncogenomics
Aligerová, Zuzana ; Maděránková, Denisa (referee) ; Provazník, Ivo (advisor)
Náplní této práce je teoretický úvod a následné praktické zpracování tématu Molekulární signatura jako optimální multi-objektivní funkce s aplikací v predikci v onkogenomice. Úvodní kapitoly jsou zaměřeny na téma rakovina, zejména pak rakovina prsu a její podtyp triple negativní rakovinu prsu. Následuje literární přehled z oblasti optimalizačních metod, zejména se zaměřením na metaheuristické metody a problematiku strojového učení. Část se odkazuje na onkogenomiku a principy microarray a také na statistiku a s důrazem na výpočet p-hodnoty a bimodálního indexu. Praktická část je pak zaměřena na konkrétní průběh výzkumu a nalezené závěry, vedoucí k dalším krokům výzkumu. Implementace vybraných metod byla provedena v programech Matlab a R, s využitím dalších programovacích jazyků a to konkrétně programů Java a Python.
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Classification Methods for Micriarrays Data
Hudec, Vladimír ; Bartík, Vladimír (referee) ; Burgetová, Ivana (advisor)
This paper discusses about the data obtained from gene chips and methods of their analysis. Analyzes some methods for analyzing these data and focus on the method of "Random Forests". Shows dataset that is used for specific experiments. Methods are realized in R language environment. Than they are tested, and the results are presented and compared. Results with method "Random Forests" are compared with other experiments on same dataset.
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Multidimensional statistics and applications to study genes
Bubelíny, Peter ; Klebanov, Lev (advisor) ; Jurečková, Jana (referee) ; Kalina, Jan (referee)
Title: Multidimensional statistics and applications to study genes Author: Mgr. Peter Bubelíny Department: Department of probability and mathematical statistics Supervisor: prof. Lev Klebanov, DrSc., KPMS MFF UK Abstract: Microarray data of gene expressions consist of thousands of genes and just some tens of observations. Moreover, genes are highly correlated between themselves and contain systematic errors. Hence the magnitude of these data does not afford us to estimate their correlation structure. In many statistical problems with microarray data, we have to test some thousands of hypotheses simultaneously. Due to dependence between genes, p-values of these hypotheses are dependent as well. In this work, we compared conve- nient multiple testing procedures reasonable for dependent hypotheses. The common manner to make microarray data more uncorrelated and partially eliminate systematic errors is normalizing them. We proposed some new normalizations and studied how different normalizations influence hypothe- ses testing. Moreover, we compared tests for finding differentially expressed genes or gene sets and identified some interesting properties of some tests such as bias of two-sample Kolmogorov-Smirnov test and interesting behav- ior of Hotelling's test for dependent components of observations. In the end of...
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Genetic and Proteomic Screening in Patients with Cardiovascular Disease.
Boháčová, Jana
The aim of this study is to analyse a genetic and proteomic aspects that could play an important role in development of chosen cardiovascular disease. Matrix metalloproteinases are enzymes that contribute strongly to the degradation of extracellular matrix components. In this study the serological levels of MMP-2 and MMP-9 were investigated using immunological testing in patients with aortic valve disease and in patients with myocardial infarction. Significantly higher levels of MMP-2 and MMP-9 were determined in both above mentioned groups of patients. Association of serum levels of MMP-2 and MMP-9 and development of concomitant aortic dilatation was not confirmed in patients with aortic valve disease. Changes in serum levels within 24 hours and after 6 months post myocardial infarction were characterized. About 10 % of patients operated for aortic valve disease suffer simultaneously from ascending aortic dilatation. The current study did not reveal any significant genetic variation in TGFBR2 gene and in chosen exons of FBN1 gene in these patients. Further genetic research is needed to identify the cause of the pathology in aortic wall. Gene expression of selected genes was measured by microarray screening in patients with myocardial infarction. These genes were related to MMPs and did not show...
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DNA markery pro diagnostiku bakteriálních infekcí
Vilímová, Veronika
Master’s thesis DNA markers for bacterial infection diagnosis engages in matters of pathogenic bacteria that cause urinary tract infections and in matters of diagnostic methods for this bacteria with focus on the usage of DNA probes. The aim of this thesis was to find, design and test suitable DNA probes by using quantitative Real-Time PCR. Probes were designed based on specific bacterial sequences of 16S rRNA gene fragment. Afterwards, testing and optimisation of Real-Time PCR was conducted. Successful optimisation was managed for two probes out of twelve – one for S. aureus, second for P. aeruginosa. These results represent the basis for the follow-up experimental work to ensure improvement and reproducibility of the experiments.
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Adjustment of diagnostic instrument Array Reader C-series
Čičatka, Michal ; Hesko, Branislav (referee) ; Mézl, Martin (advisor)
Thesis deals with actualization of application for adjustment of the chemical analyser Array Reader C-series developed by company BioVendor. At the beginning it defines and sorts out chemical analysers; then describes their physical principles. Following chapters sum up knowledge about microarray analysis and describes it’s chemical and physical principles. Furthermore, the thesis deals with quality and it’s management and machine adjustment. In the thesis is also mentioned .NET Framework – software platform that will be used in the practical part of the thesis. At the end of the theoretical part is described Array Reader C-series. Practical part documents current application for adjusting the analyser. Based on personal experiences with the adjusting application was created and thoroughly described concept of a new adjusting application. Main task of this new concept should be simplification and automatization of the adjusting process. After that implementation of the new concept is described including automatation processes. In the end of this thesis both original and new versions are compared with regards to time consumption and user experience. Newer version of the application was evaluted as better than it's previous version in light of time consumption and user experience. Application was expanded for fluorescent analyzer and for both types of analyzers were developed derivated applications for service adjustment. Each of these applications was implemented to the software of BioVendor company and is used on daily basis.
|
|
|
Genetic and Proteomic Screening in Patients with Cardiovascular Disease.
Boháčová, Jana
The aim of this study is to analyse a genetic and proteomic aspects that could play an important role in development of chosen cardiovascular disease. Matrix metalloproteinases are enzymes that contribute strongly to the degradation of extracellular matrix components. In this study the serological levels of MMP-2 and MMP-9 were investigated using immunological testing in patients with aortic valve disease and in patients with myocardial infarction. Significantly higher levels of MMP-2 and MMP-9 were determined in both above mentioned groups of patients. Association of serum levels of MMP-2 and MMP-9 and development of concomitant aortic dilatation was not confirmed in patients with aortic valve disease. Changes in serum levels within 24 hours and after 6 months post myocardial infarction were characterized. About 10 % of patients operated for aortic valve disease suffer simultaneously from ascending aortic dilatation. The current study did not reveal any significant genetic variation in TGFBR2 gene and in chosen exons of FBN1 gene in these patients. Further genetic research is needed to identify the cause of the pathology in aortic wall. Gene expression of selected genes was measured by microarray screening in patients with myocardial infarction. These genes were related to MMPs and did not show...
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Multidimensional statistics and applications to study genes
Bubelíny, Peter ; Klebanov, Lev (advisor) ; Jurečková, Jana (referee) ; Kalina, Jan (referee)
Title: Multidimensional statistics and applications to study genes Author: Mgr. Peter Bubelíny Department: Department of probability and mathematical statistics Supervisor: prof. Lev Klebanov, DrSc., KPMS MFF UK Abstract: Microarray data of gene expressions consist of thousands of genes and just some tens of observations. Moreover, genes are highly correlated between themselves and contain systematic errors. Hence the magnitude of these data does not afford us to estimate their correlation structure. In many statistical problems with microarray data, we have to test some thousands of hypotheses simultaneously. Due to dependence between genes, p-values of these hypotheses are dependent as well. In this work, we compared conve- nient multiple testing procedures reasonable for dependent hypotheses. The common manner to make microarray data more uncorrelated and partially eliminate systematic errors is normalizing them. We proposed some new normalizations and studied how different normalizations influence hypothe- ses testing. Moreover, we compared tests for finding differentially expressed genes or gene sets and identified some interesting properties of some tests such as bias of two-sample Kolmogorov-Smirnov test and interesting behav- ior of Hotelling's test for dependent components of observations. In the end of...
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