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    Wyświetlanie 1-33 z 33
    Tytuł:
    Development of a new, simple and cost-effective diagnostic tool for genetic screening of hereditary colorectal cancer - the DNA microarray assay
    Autorzy:
    Stojcev, Zoran
    Banasiewicz, Tomasz
    Kaszuba, Michał
    Sikorski, Adam
    Szczepkowski, Marek
    Bobkiewicz, Adam
    Paszkowski, Jacek
    Krokowicz, Łukasz
    Biczysko, Maciej
    Szmeja, Jacek
    Jurkowska, Monika
    Majewski, Przemysław
    Mackiewicz, Andrzej
    Lamperska, Katarzyna
    Drews, Michał
    Wojciechowicz, Jacek
    Powiązania:
    https://bibliotekanauki.pl/articles/1039574.pdf
    Data publikacji:
    2013
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    HNPCC
    DNA microarray
    colon cancer
    Opis:
    Detection of mutations in families with a hereditary predisposition to colon cancer gives an opportunity to precisely define the high-risk group. 36 patients operated on for colon cancer, with familiar prevalence of this malignancy, were investigated using the DNA microarrays method with the potential detection of 170 mutations in MLH1, MSH2, MSH6, CHEK2, and NOD2 genes. In microarrays analysis of DNA in 9 patients (25% of the investigated group), 6 different mutations were found. The effectiveness of genetic screening using the microarray method is comparable to the effectiveness of other, much more expensive and time-consuming methods.
    Źródło:
    Acta Biochimica Polonica; 2013, 60, 2; 195-198
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    DNA microarrays, a novel approach in studies of chromatin structure.
    Autorzy:
    Widłak, Piotr
    Powiązania:
    https://bibliotekanauki.pl/articles/1043314.pdf
    Data publikacji:
    2004
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    chromatin
    genomics
    epigenomics
    DNA microarray
    nucleosomes
    Opis:
    The DNA microarray technology delivers an experimental tool that allows surveying expression of genetic information on a genome-wide scale at the level of single genes - for the new field termed functional genomics. Gene expression profiling - the primary application of DNA microarrays technology - generates monumental amounts of information concerning the functioning of genes, cells and organisms. However, the expression of genetic information is regulated by a number of factors that cannot be directly targeted by standard gene expression profiling. The genetic material of eukaryotic cells is packed into chromatin which provides the compaction and organization of DNA for replication, repair and recombination processes, and is the major epigenetic factor determining the expression of genetic information. Genomic DNA can be methylated and this modification modulates interactions with proteins which change the functional status of genes. Both chromatin structure and transcriptional activity are affected by the processes of replication, recombination and repair. Modified DNA microarray technology could be applied to genome-wide study of epigenetic factors and processes that modulate the expression of genetic information. Attempts to use DNA microarrays in studies of chromatin packing state, chromatin/DNA-binding protein distribution and DNA methylation pattern on a genome-wide scale are briefly reviewed in this paper.
    Źródło:
    Acta Biochimica Polonica; 2004, 51, 1; 1-8
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    The methods of normalization used in the analysis of two-color microarrays
    Metody normalizacji w analizie dwukolorowych mikromacierzy
    Autorzy:
    Siatkowski, I.
    Zyprych, J.
    Handschuh, L.
    Figlerowicz, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/9613.pdf
    Data publikacji:
    2009
    Wydawca:
    Uniwersytet Przyrodniczy w Lublinie. Katedra Zastosowań Matematyki i Informatyki
    Tematy:
    normalization method
    analysis
    microarray analysis
    bioconductor
    Źródło:
    Colloquium Biometricum; 2009, 39
    1896-7701
    Pojawia się w:
    Colloquium Biometricum
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Transcriptional pattern of TGF-beta1 inhibitory effect on mouse C2C12 myoblasts differentiation
    Autorzy:
    Wicik, Z.
    Sadkowski, T.
    Jank, M.
    Motyl, T.
    Powiązania:
    https://bibliotekanauki.pl/articles/30377.pdf
    Data publikacji:
    2010
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    transforming growth factor-beta 1
    myogenesis
    microarray
    DNA microarray
    differentiation
    myoblast
    mouse
    mice
    muscle cell
    myosin heavy chain
    Opis:
    The aim of the present study was to define the effect of TGF-β1 on C2C12 myoblasts myogenesis. TGF-β1 together with its receptor is a negative auto-paracrine regulator of myogenesis, which influences the proliferation, differentiation, and functions of muscle cells. TGF-β1 exerts highly significant inhibitory effect on differentiation of C2C12 mouse myoblasts manifested by the impairment of cell fusion and very low expression of myosin heavy chain. The study of differentiating C2C12 mouse myoblasts treated with TGF-β1 revealed 502 genes (436 down-regulated and 66 up-regulated) with statistically different expression. TGF-β1-regulated genes were identified to be involved in 29 biological processes, 29 molecular functions groups and 59 pathways. The strongest inhibiting effect of TGF-β1 was observed in the cadherin and Wnt pathways. The key-genes that could play the role of TGF-β1 targets during myoblasts differentiation was identified such as: Max, Creb1, Ccna2, Bax, MdfI, Tef, Tubg1, Cxcl5, Rho, Calca and Lgals4.
    Źródło:
    Polish Journal of Veterinary Sciences; 2010, 13, 4
    1505-1773
    Pojawia się w:
    Polish Journal of Veterinary Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    How the RNA isolation method can affect microRNA microarray results
    Autorzy:
    Podolska, Agnieszka
    Kaczkowski, Bogumil
    Litman, Thomas
    Fredholm, Merete
    Cirera, Susanna
    Powiązania:
    https://bibliotekanauki.pl/articles/1039846.pdf
    Data publikacji:
    2011
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    microarray
    microRNA isolation method
    microRNA
    small RNA fraction
    pig
    Opis:
    The quality of RNA is crucial in gene expression experiments. RNA degradation interferes in the measurement of gene expression, and in this context, microRNA quantification can lead to an incorrect estimation. In the present study, two different RNA isolation methods were used to perform microRNA microarray analysis on porcine brain tissue. One method is a phenol-guanidine isothiocyanate-based procedure that permits isolation of total RNA. The second method, miRVana™ microRNA isolation, is column based and recovers the small RNA fraction alone. We found that microarray analyses give different results that depend on the RNA fraction used, in particular because some microRNAs appear very sensitive to the RNA isolation method. We conclude that precautions need to be taken when comparing microarray studies based on RNA isolated with different methods.
    Źródło:
    Acta Biochimica Polonica; 2011, 58, 4; 535-540
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Microarray Inspector: tissue cross contamination detection tool for microarray data
    Autorzy:
    Stępniak, Piotr
    Maycock, Matthew
    Wojdan, Konrad
    Markowska, Monika
    Perun, Serhiy
    Srivastava, Aashish
    Wyrwicz, Lucjan
    Świrski, Konrad
    Powiązania:
    https://bibliotekanauki.pl/articles/1039460.pdf
    Data publikacji:
    2013
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    microarray
    transcription profiling
    contamination analysis
    adipose tissue
    cancer
    data quality
    Opis:
    Microarray technology changed the landscape of contemporary life sciences by providing vast amounts of expression data. Researchers are building up repositories of experiment results with various conditions and samples which serve the scientific community as a precious resource. Ensuring that the sample is of high quality is of utmost importance to this effort. The task is complicated by the fact that in many cases datasets lack information concerning pre-experimental quality assessment. Transcription profiling of tissue samples may be invalidated by an error caused by heterogeneity of the material. The risk of tissue cross contamination is especially high in oncological studies, where it is often difficult to extract the sample. Therefore, there is a need of developing a method detecting tissue contamination in a post-experimental phase. We propose Microarray Inspector: customizable, user-friendly software that enables easy detection of samples containing mixed tissue types. The advantage of the tool is that it uses raw expression data files and analyses each array independently. In addition, the system allows the user to adjust the criteria of the analysis to conform to individual needs and research requirements. The final output of the program contains comfortable to read reports about tissue contamination assessment with detailed information about the test parameters and results. Microarray Inspector provides a list of contaminant biomarkers needed in the analysis of adipose tissue contamination. Using real data (datasets from public repositories) and our tool, we confirmed high specificity of the software in detecting contamination. The results indicated the presence of adipose tissue admixture in a range from approximately 4% to 13% in several tested surgical samples.
    Źródło:
    Acta Biochimica Polonica; 2013, 60, 4; 647-655
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Pathogenesis of middle ear acquired cholesteatoma in the light of the research using high throughput, “omics”, technologies of molecular biology
    Autorzy:
    Makuszewska, Maria
    Bartoszewicz, Robert
    Niemczyk, Kazimierz
    Powiązania:
    https://bibliotekanauki.pl/articles/1399639.pdf
    Data publikacji:
    2019
    Wydawca:
    Index Copernicus International
    Tematy:
    aquired cholesteatoma
    gene expression
    microarray
    molecular biology
    pathogenesis
    proteomic analysis
    Opis:
    Cholesteatoma is described as cystic lesion consisting of keratinizing squamous cell epithelium, filed with keratin debris, surrounded by inflammatory fibrous tissue, gradually expanding in the middle ear and causing destruction of neighboring bones. This paper presents brief review of existing hypotheses explaining its etiology in the light of the researches using high throughput, “omics”, technologies of molecular biology. Classic theories of pathogenesis of acquired cholesteatoma as: immigration, squamous metaplasia, basal cell hyperplasia or invagination theory have not been able to explain fully all pathological processes observed in cholesteatoma tissue. This also concerns the newer concepts that cholesteatoma is a result of mucosal traction generated by interaction of migrating opposing surfaces, a natural attempt by the body to cure the underlying inflammation in the cavity or chronic wound healing process triggered by micro defects in the basement membrane of the epithelium in the retraction pocket. Introduction of high-throughput, “omics”, technologies of molecular biology to the studies under cholesteatoma pathogenesis allowed identification of cholesteatoma-related gene expression signatures using full-genome microarrays as well as proteomic analysis of cholesteatoma. Those studies confirmed known pathological processes observed in cholesteatoma tissue such as: high proliferative activity, decreased signal transduction, active immunological response, alterations in the extracellular matrix, increased expression of proinflammatory cytokines, neovascularization and may others. This technique allows precise and complete insight into molecular mechanisms in those processes. However, it is still unknown what is the cause that trigger epithelial hyperplasia, inhibited migration and inflammatory response in the preexisting retraction pocket.
    Źródło:
    Polski Przegląd Otorynolaryngologiczny; 2019, 8, 3; 14-19
    2084-5308
    2300-7338
    Pojawia się w:
    Polski Przegląd Otorynolaryngologiczny
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Characterization of Biofilms From Selected Synthetic Materials Used in Water Distribution System
    Autorzy:
    Biedroń, I.
    Traczewska, T.
    Konieczny, T.
    Płaza, G.
    Powiązania:
    https://bibliotekanauki.pl/articles/952367.pdf
    Data publikacji:
    2017
    Wydawca:
    Polskie Towarzystwo Inżynierii Ekologicznej
    Tematy:
    biofilm
    metabolic profile
    drinking water
    bacteria consortia
    phenotypic microarray
    PM
    Opis:
    Materials like polyvinyl chloride (PVC), polypropylene (PP), ultra high molecular weight polyethylene (UHMW-PE) are used for the construction of drinking water supply systems. It was found that regardless of the type of material the distribution network is built of, microorganisms formed biofilms on every available surface. The pipes material plays a key role in terms of biofilm formation. Important factors are the surface roughness, adhesives, plasticizers, stabilizers, which can be a source of nutrients for bacteria. The metabolic activity of microorganisms on polymer materials, induces migration of compounds from the material into water. The aim of this study was to present the differences in the structure and the metabolic profile of biofilm formed on the technical materials.
    Źródło:
    Journal of Ecological Engineering; 2017, 18, 1; 284-293
    2299-8993
    Pojawia się w:
    Journal of Ecological Engineering
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Application of epoxy functional silanes in the preparation of DNA microarrays
    Autorzy:
    Frydrych-Tomczak, E.
    Uszczynska, B.
    Ratajczak, T.
    Markiewicz, W.T.
    Figlerowicz, M.
    Nowicki, M.
    Maciejewski, H.
    Chmielewski, M.K.
    Powiązania:
    https://bibliotekanauki.pl/articles/80900.pdf
    Data publikacji:
    2014
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    DNA microarray
    gene expression
    organofunctional silane
    oligonucleotide
    atomic force microscopy
    goniometer
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2014, 95, 1
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Analysis of genes involved in response to doxorubicin and a GD2 ganglioside-specific 14G2a monoclonal antibody in IMR-32 human neuroblastoma cells
    Autorzy:
    Horwacik, Irena
    Durbas, Małgorzata
    Boratyn, Elżbieta
    Sawicka, Anna
    Węgrzyn, Paulina
    Krzanik, Sylwia
    Górka, Anna
    Drożniak, Joanna
    Augustyniak, Ewa
    Kowalczyk, Aleksandra
    Rokita, Hanna
    Powiązania:
    https://bibliotekanauki.pl/articles/1038977.pdf
    Data publikacji:
    2015
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    doxorubicin
    GD2 ganglioside
    microarray
    14G2a
    neuroblastoma
    mimitin
    Opis:
    Neuroblastoma is the most common extra-cranial solid tumor of childhood and it is characterized by the presence of a glycosphingolipid, GD2 ganglioside. Monoclonal antibodies targeting the antigen are currently tested in clinical trials. Additionally, several research groups reported results revealing that ganglioside-specific antibodies can affect cellular signaling and cause direct cytotoxicity against tumor cells. To shed more light on gene expression signatures of tumor cells, we used microarrays to analyze changes of transcriptome in IMR-32 human neuroblastoma cell cultures treated with doxorubicin (DOX) or a mouse monoclonal antibody binding to GD2 ganglioside 14G2a (mAb) for 24 h. The obtained results highlight that disparate cellular pathways are regulated by doxorubicin and 14G2a. Next, we used RT-PCR to verify mRNA levels of selected DOX-responsive genes such as RPS27L, PPM1D, SESN1, CDKN1A, TNFSF10B, and 14G2a-responsive genes such as SVIL, JUN, RASSF6, TLX2, ID1. Then, we applied western blot and analyzed levels of RPS27L, PPM1D, sestrin 1 proteins after DOX-treatment. Additionally, we aimed to measure effects of doxorubicin and topotecan (TPT) and 14G2a on expression of a novel human NDUFAF2 gene encoding for mimitin protein (MYC-induced mitochondrial protein) and correlate it with expression of the MYCN gene. We showed that expression of both genes was concomitantly decreased in the 14G2a-treated IMR-32 cells after 24 h and 48 h. Our results extend knowledge on gene expression profiles after application of DOX and 14G2a in our model and reveal promising candidates for further research aimed at finding novel anti-neuroblastoma targets.
    Źródło:
    Acta Biochimica Polonica; 2015, 62, 3; 423-433
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Chemical regulation of photorespiratory hydrogen peroxide-induced cell death in catalase deficient (cat2) Arabidopsis plants
    Autorzy:
    Kerchev, P.
    Denecker, J.
    Muhlenbock, P.
    Van Breusegem, F.
    Powiązania:
    https://bibliotekanauki.pl/articles/80515.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    conference
    photorespiration
    hydrogen peroxide
    cell death
    catalase
    Arabidopsis
    molecular structure
    microarray
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 2
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Impact of DNA microarray data transformation on gene expression analysis - comparison of two normalization methods
    Autorzy:
    Schmidt, Marcin
    Handschuh, Luiza
    Zyprych, Joanna
    Szabelska, Alicja
    Olejnik-Schmidt, Agnieszka
    Siatkowski, Idzi
    Figlerowicz, Marek
    Powiązania:
    https://bibliotekanauki.pl/articles/1039855.pdf
    Data publikacji:
    2011
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    microarray
    data normalization
    enterocyte
    transcriptome analysis
    probiotic
    adhesion
    gene expression profiling
    Opis:
    Two-color DNA microarrays are commonly used for the analysis of global gene expression. They provide information on relative abundance of thousands of mRNAs. However, the generated data need to be normalized to minimize systematic variations so that biologically significant differences can be more easily identified. A large number of normalization procedures have been proposed and many softwares for microarray data analysis are available. Here, we have applied two normalization methods (median and loess) from two packages of microarray data analysis softwares. They were examined using a sample data set. We found that the number of genes identified as differentially expressed varied significantly depending on the method applied. The obtained results, i.e. lists of differentially expressed genes, were consistent only when we used median normalization methods. Loess normalization implemented in the two software packages provided less coherent and for some probes even contradictory results. In general, our results provide an additional piece of evidence that the normalization method can profoundly influence final results of DNA microarray-based analysis. The impact of the normalization method depends greatly on the algorithm employed. Consequently, the normalization procedure must be carefully considered and optimized for each individual data set.
    Źródło:
    Acta Biochimica Polonica; 2011, 58, 4; 573-580
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Redox state of plastoquionone pool regulates expression of Arabidopsis thaliana genes in response to elevated irradiance*
    Autorzy:
    Adamiec, Małgorzata
    Drath, Maria
    Jackowski, Grzegorz
    Powiązania:
    https://bibliotekanauki.pl/articles/1040834.pdf
    Data publikacji:
    2008
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    hierarchical clustering
    plastoquinone
    elevated irradiance
    gene expression
    transcription factors
    DNA microarray
    Opis:
    DNA microarray technology was applied to gain insight into the role of the redox state of PQ pool as a retrograde factor mediating differential expression of Arabidopsis nuclear genes during the acclimation to changing irradiance. DNA microarray chips containing probes corresponding to 24 000 Arabidopsis nuclear genes were screened with cRNA samples prepared from leaves of plants exposed for 5 h to low irradiance (control) vs. medium, high and excessive irradiances (MI, HI and EI, respectively). Six hundred and sixty three genes were differentially expressed as a result of an exposure to at least one elevated irradiance. Among 663 differentially expressed genes a total of 50 were reverted by DCMU - 24 ones modulated at medium irradiance, 32 ones modulated at high irradiance and a single one modulated at excessive irradiance. We postulate that their expression is regulated by redox state of plastoquinone (PQ) pool. Thus the PQ-mediated redox regulation of expression of Arabidopsis nuclear genes is probably limited to the irradiance window representing non-stressing conditions. We found that the promoter regions of the PQ-regulated genes contained conserved elements, suggesting transcriptional control by a shared set of trans-acting factors which participate in signal transduction from the redox state of the PQ pool.
    Źródło:
    Acta Biochimica Polonica; 2008, 55, 1; 161-174
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Elevated CO2 mitigates the impact of a combination of heat wave and drought in Arabidopsis thaliana
    Autorzy:
    Zinta, G.
    AbdElgawad, H.
    Domagalska, M.
    Vergauwen, L.
    Nijs, I.
    Beemster, G.
    Asard, H.
    Janssens, I.
    Powiązania:
    https://bibliotekanauki.pl/articles/80475.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    conference
    carbon dioxide
    heat wave
    drought stress
    Arabidopsis thaliana
    photosynthesis
    microarray analysis
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 2
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Virulence and antibiotic resistance of Escherichia coli isolated from rooks
    Autorzy:
    Kmet, V.
    Drugdova, Z.
    Kmetova, M.
    Stanko, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/51141.pdf
    Data publikacji:
    2013
    Wydawca:
    Instytut Medycyny Wsi
    Tematy:
    virulence
    antibiotic resistance
    Escherichia coli
    isolation
    rook
    polymerase chain reaction
    DNA microarray
    Opis:
    With regard to antibiotic resistance studies in various model animals in the urban environment, the presented study focused on the rook, many behavioural and ecological aspects of which are important from an epidemiological point of view. A total of 130 Escherichia coli strains isolated from rook faeces during a two-year period (2011–2012) were investigated for antibiotic resistance and virulence. Resistance to ampicillin (60%) and streptomycin (40%) were the most frequent, followed by resistance to fluoroquinolones (ciprofloxacin-22% and enrofloxacin-24%), tetracycline (18%), cotrimoxazol (17%) and florfenicol (14%). Ceftiofur resistance occured in 10.7 % of strains and cefquinom resistance in 1.5 % of strains. Twenty-five E.coli strains with a higher level of MICs of cephalosporins (over 2mg/L of ceftazidime and ceftriaxon) and fluoroquinolones were selected for detection of betalactamase genes (CTX-M, CMY), plasmid-mediated quinolone resistance qnrS, integrase 1, and for APEC (avian pathogenic E.coli) virulence factors (iutA, cvaC, iss, tsh, ibeA, papC, kpsII). Genes of CTX-M1, CMY-2, integrase 1, papC, cvaC, iutA were detected in one strain of E.coli, and qnrS, integrase 1, iss, cvaC, tsh were detected in another E.coli. DNA microarray revealed the absence of verotoxin and enterotoxin genes and pathogenicity islands. The results show that rooks can serve as a reservoir of antibiotic-resistant E. coli with avian pathogenic virulence factors for the human population, and potentially transmit such E.coli over long distances.
    Źródło:
    Annals of Agricultural and Environmental Medicine; 2013, 20, 2
    1232-1966
    Pojawia się w:
    Annals of Agricultural and Environmental Medicine
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Smooth muscle contamination analysis in clinical oncology gene expression research
    Autorzy:
    Markowska, Monika
    Stępniak, Piotr
    Wojdan, Konrad
    Świrski, Konrad
    Powiązania:
    https://bibliotekanauki.pl/articles/1039298.pdf
    Data publikacji:
    2014
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    microarray
    transcription profiling
    smooth muscle contamination
    tissue specific genes
    cancer
    data quality
    Opis:
    Gene expression profiling is one of the most explored methods for studying cancers and microarray data repositories have become a rich and important resource. The most common human cancers develop in organs that are walled by smooth muscles. The only method of sample extraction free of unintentional contamination with surrounding tissue is microdissection. Nevertheless, such an approach is implemented infrequently. In the light of the above, there is a possibility of smooth muscle contamination in a large portion of publicly available data. In this study, 2292 publicly available microarrays were analysed to develop a simple screening method for detecting smooth muscle contamination. Microarray Inspector software was used to perform the tests since it has the unique ability to use many selected genes and probesets in a single group as a tissue definition. Furthermore, the test was dataset-independent. Two strategies of tissue definition were explored and compared. The first one depended on Tissue Specific Genes Database (TiSGeD) and BioGPS web resources, which themselves were based on meta-analysis of thousands of microarrays. The second method was based on a differential gene expression analysis of a few hundred preselected arrays. The comparison of the two methods proved the latter to be superior. Among the tested samples of undefined contamination, nearly half were identified to possibly contain significant smooth muscle traces. The obtained results equip researches with a simple method of examining microarray data for smooth muscle contamination. The presented work serves as an example of how to create definitions when searching for other possible contaminations.
    Źródło:
    Acta Biochimica Polonica; 2014, 61, 2; 333-340
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Transcriptome signature of the lactation process, identified by meta-analysis of microarray and RNA-Seq data
    Autorzy:
    Farhadian, M.
    Rafat, S.A.
    Hasanpur, K.
    Ebrahimie, E.
    Powiązania:
    https://bibliotekanauki.pl/articles/80629.pdf
    Data publikacji:
    2018
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    transcriptome
    lactation
    milk production
    microarray
    expression analysis
    cDNA synthesis
    RNA sequence
    gene expression
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2018, 99, 2
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Complex analysis of genes involved in the inflammatory response: interleukin-1-induced differential transcriptome of cultured human hepatoma HepG2 cells.
    Autorzy:
    Koj, Aleksander
    Jura, Jolanta
    Powiązania:
    https://bibliotekanauki.pl/articles/1043427.pdf
    Data publikacji:
    2003
    Wydawca:
    Polskie Towarzystwo Biochemiczne
    Tematy:
    proteome
    transcriptome
    microarray
    hepatoma cells
    gene expression
    inflammatory reaction
    acute phase response
    differential display
    Opis:
    The systemic inflammatory reaction (acute phase response) is induced by many noxious stimuli but in all cases the inflammatory cytokines, such as interleukin-1-beta (IL-1β) and interleukin-6 (IL-6), are involved. Liver cell response to inflammation manifested by a characteristic change in the profile of synthesized plasma proteins (acute phase proteins) has been extensively studied. Here we describe a model system of cultured human hepatoma HepG2 cells stimulated with IL-1β to evaluate the transcriptome induced by this cytokine during 24 h of treatment. By using differential display analysis we found IL-1β-induced upregulation of several genes coding for cellular trafficking/motor proteins, proteins participating in the translation machinery or involved in posttranscription/posttranslation modifications, proteases, proteins involved in cellular metabolism, activity modulators, proteins of the cell cycle machinery and also some new proteins so far functionally not classified.
    Źródło:
    Acta Biochimica Polonica; 2003, 50, 3; 573-582
    0001-527X
    Pojawia się w:
    Acta Biochimica Polonica
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Application of the Adaptive Center-Weighted Vector Median Framework for the Enhancement of cdna Microarray Images
    Autorzy:
    Lukac, R.
    Smołka, B.
    Powiązania:
    https://bibliotekanauki.pl/articles/908149.pdf
    Data publikacji:
    2003
    Wydawca:
    Uniwersytet Zielonogórski. Oficyna Wydawnicza
    Tematy:
    informatyka
    DNA microarray images
    multichannel image processing
    order-statistic theory
    vector filters
    impulsive noise
    Opis:
    In this paper a novel method of noise reduction in color images is presented. The new technique is capable of attenuating both impulsive and Gaussian noise, while preserving and even enhancing the sharpness of the image edges. Extensive simulations reveal that the new method outperforms significantly the standard techniques widely used in multivariate signal processing. In this work we apply the new noise reduction method for the enhancement of the images of the so called gene chips. We demonstrate that the new technique is capable of reducing the impulsive noise present in microarray images and that it facilitates efficient spot location and the estimation of the gene expression levels due to the smoothing effect and preservation of the spot edges. This paper contains a comparison of the new technique of impulsive noise reduction with the standard procedures used for the processing of vector valued images, as well as examples of the efficiency of the new algorithm when applied to typical microarray images.
    Źródło:
    International Journal of Applied Mathematics and Computer Science; 2003, 13, 3; 369-383
    1641-876X
    2083-8492
    Pojawia się w:
    International Journal of Applied Mathematics and Computer Science
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Identification of novel genes potentially involved in rice (Oryza sativa L.) drought tolerance
    Autorzy:
    Zinati, Z.
    Powiązania:
    https://bibliotekanauki.pl/articles/80145.pdf
    Data publikacji:
    2017
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    microarray analysis
    Oryza sativa
    rice
    drought tolerance
    drought stress
    transcription factor
    gene encoding
    quantitative trait locus
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2017, 98, 3
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    DNA microarrays - future in oncology research and therapy
    Autorzy:
    Krol, M.
    Pawlowski, K.M.
    Otrebska, D.
    Motyl, T.
    Powiązania:
    https://bibliotekanauki.pl/articles/3349.pdf
    Data publikacji:
    2008
    Wydawca:
    Instytut Medycyny Wsi
    Tematy:
    DNA microarray
    future
    oncology
    research
    therapy
    genomics
    gene expression
    canine mammary cancer
    tumour
    human disease
    cancer
    Źródło:
    Journal of Pre-Clinical and Clinical Research; 2008, 02, 2
    1898-2395
    Pojawia się w:
    Journal of Pre-Clinical and Clinical Research
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Analysis of expression profiles of barley, medicago and soybean galactinol synthase through microarray data integration
    Autorzy:
    Paukszto, L.
    Myszczynski, K.
    Gojlo, E.
    Jastrzebski, J.P.
    Pupel, P.
    Podlinski, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/79948.pdf
    Data publikacji:
    2013
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    conference
    expression analysis
    barley
    Medicago truncatula
    soybean
    Hordeum vulgare
    Glycine max
    galactinol synthase
    microarray
    biosynthesis
    gene expression
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2013, 94, 3
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Analysis of entity-attribute-value model applications in freely available database management systems for dna microarray data processing
    Autorzy:
    Waller, T.
    Zapart, D.
    Tkacz, M.
    Wróbel, Z.
    Powiązania:
    https://bibliotekanauki.pl/articles/332994.pdf
    Data publikacji:
    2012
    Wydawca:
    Uniwersytet Śląski. Wydział Informatyki i Nauki o Materiałach. Instytut Informatyki. Zakład Systemów Komputerowych
    Tematy:
    system zarządzania relacyjną bazą danych
    mikromacierz DNA
    entity-attribute-value model
    relational database management system
    DNA microarray
    Opis:
    Large volumes of data are generated during DNA microarrays experiments. Database management systems (DBMS) are increasingly applied to these data, providing optimum processing and management from multiple microarray experiments. In this study, freely accessible DBMS software versions were compared (Microsoft SQL Server 2008 Express Edition, Oracle Database 10g Express Edition, DB2 Express-C 9.7.2, MySQL 5.1, and PostgreSQL 9.0). We examined them in the context of possible Entity-Attribute-Value (EAV) application as an optimal organization method for microarray data. It was confirmed in the comparative analysis of component data processing methods, consistent with the EAV model, that efficient methods for microarray data analysis are available in Microsoft SQL Server 2008 Express Edition and PostgreSQL 9.0 systems. Also, DNA microarray data processing was confirmed to be more efficient with Microsoft SQL Server 2008 Express Edition as compared with PostgreSQL 9.0. The EAV method was also shown to be suitable for use with open-source versions of DBMS software as an optimum storage model for DNA microarray data. In terms of data processing methods and performance, the Microsoft SQL Server 2008 Express Edition proved to be the best among compared database systems.
    Źródło:
    Journal of Medical Informatics & Technologies; 2012, 20; 59-63
    1642-6037
    Pojawia się w:
    Journal of Medical Informatics & Technologies
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    An Extension of TSP-family Algorithms for Microarray Classification
    Rozszerzenie metod z rodziny TSP w klasyfikacji mikromacierzy DNA
    Autorzy:
    Czajkowski, M.
    Krętowski, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/341039.pdf
    Data publikacji:
    2009
    Wydawca:
    Politechnika Białostocka. Oficyna Wydawnicza Politechniki Białostockiej
    Tematy:
    klasyfikacja par genów zależnych
    analiza mikromacierzy
    reguły decyzyjne
    ekspresja genów
    pairwise classification
    decision rules
    microarray
    gene expression
    Opis:
    Classification of microarray data and generation of simple and efficient decision rules may be successfully performed with Top Scoring Pair algorithms. TSP-family methods are based on pairwise comparisons of gene expression values. This paper presents a new method, referred as Linked TSP that extends previous approaches kˇTSP and Weight kˇTSP algorithms by linking top pairwise mRNA comparisons of gene expressions in different classes. Opposite to existing TSP-family classifiers, the proposed approach creates decision rules involving single genes that most frequently appeared in top scoring pairs. Motivation of this paper is to improve classification accuracy results and to extract simple, readily interpretable rules providing biological insight as to how classification is performed. Experimental validation was performed on several human microarray datasets and obtained results are promising.
    Klasyfikacja danych mikromacierzowych a także późniejsza interpretacja reguł decyzyjnych może być skutecznie przeprowadzona za pomocą metod z rodziny Top Scoring Pair, polegających na analizie par genow o przeciwstawych poziomach ekspresji w róźnych klasach. W poniższym artykule zaprezentowano nową metodę: Linked TSP, ktora rozszerza działanie klasyfikatorów k-TSP i Weight k-TSP. W przeciwieństwie do algorytmow z rodziny TSP proponowane rozwiązanie tworzy reguły decyzyjne zbudowane z pojedynczych genów, co znacznie ułatwia ich późniejszą interpretację medyczną. W algorytmie wykorzystywane są pary genow uzyskane z algorytmow TSP z których następnie, wybierane są pojedyncze, najczęściej powtarzające się geny. Testy algorytmu Linked TSP przeprowadzone zostająy na rzeczywistych zbiorach danych pacjentow a uzyskane wyniki są obiecujące.
    Źródło:
    Zeszyty Naukowe Politechniki Białostockiej. Informatyka; 2009, 4; 31-45
    1644-0331
    Pojawia się w:
    Zeszyty Naukowe Politechniki Białostockiej. Informatyka
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Maximum Separation Partial Least Squares (MSPLS): a new method for classification in microarray experiment
    Autorzy:
    Błaszczyk, P.
    Stąpor, K.
    Powiązania:
    https://bibliotekanauki.pl/articles/333834.pdf
    Data publikacji:
    2007
    Wydawca:
    Uniwersytet Śląski. Wydział Informatyki i Nauki o Materiałach. Instytut Informatyki. Zakład Systemów Komputerowych
    Tematy:
    klasyfikacja
    metoda cząstkowych najmniejszych kwadratów
    eksperyment mikromacierzowy
    partial least squares
    classifications
    maximal separation criterion
    microarray experiment
    supervisor learning
    Opis:
    The purpose of the paper is to propose a new method for classification. Our MSPLS method was deduced from the classic Partial Least Squares (PLS) algorithm. In this method we applied the Maximum Separation Criterion. On the basis of the approach we are able to find such weight vectors that the dispersion between the classes is maximal and the dispersion within the classes is minimal. In order to compare the performance of classifier we used the following types of dataset - biological and simulated. Error rates and confidence intervals were estimated by the jackknife method.
    Źródło:
    Journal of Medical Informatics & Technologies; 2007, 11; 187-195
    1642-6037
    Pojawia się w:
    Journal of Medical Informatics & Technologies
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Application of the adaptive noise removal technique to the enhancement of cDNA microarray images
    Autorzy:
    Smolka, B.
    Bieda, R.
    Powiązania:
    https://bibliotekanauki.pl/articles/333786.pdf
    Data publikacji:
    2005
    Wydawca:
    Uniwersytet Śląski. Wydział Informatyki i Nauki o Materiałach. Instytut Informatyki. Zakład Systemów Komputerowych
    Tematy:
    wzmocnienie obrazu kolorowego
    impulsywne usuwanie szumów
    mikromacierze
    odtworzenie obrazu
    colour image enhancement
    impulsive noise removal
    microarray
    image restoration
    Opis:
    In this paper a novel class of filters designed for the removal of impulsive noise in colour images is presented. The proposed filter family is based on the kernel function which controls the noise suppression properties of the new filtering scheme. The comparison of the new filtering method with the standard techniques used for impulsive noise removal indicates its superior noise removal capabilities and excellent structure preserving properties. The proposed filtering scheme has been successfully applied to the denoising of the cDNA microarray images. Experimental results proved that the new filter is capable of removing efficiently the impulses present in multichannel images, while preserving their textural features.
    Źródło:
    Journal of Medical Informatics & Technologies; 2005, 9; 131-142
    1642-6037
    Pojawia się w:
    Journal of Medical Informatics & Technologies
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Transcriptome sequencing: next generation approach to RNA functional analysis
    Autorzy:
    Zmienko, A.
    Jackowiak, P.
    Figlerowicz, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/81137.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    RNA molecule
    functional analysis
    RNA sequence
    transcriptome
    isoform
    DNA microarray
    qualitative change
    quantitative change
    gene expression
    hybridization
    oligonucleotide probe
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 4
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Gene expression pattern in canine mammary osteosarcoma
    Autorzy:
    Pawlowski, K.
    Majewska, A.
    Szyszko, K.
    Dolka, I.
    Motyl, T.
    Krol, M.
    Powiązania:
    https://bibliotekanauki.pl/articles/32248.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    bone tumour
    canine mammary osteosarcoma
    gene expression
    mammary osteosarcoma
    microarray
    osteosarcoma
    transcriptome
    tumour
    sarcoma
    proliferation
    aggressive tumour
    gene list
    Opis:
    Canine mammary sarcomas are usually very aggressive and easily metastasize. Unfortunately the biology of this type of tumor is not well known because they are a very rare type of tumors. The aim of this study was to find differences in gene expression patterns in canine mammary osteosarcomas (malignant) versus osteomas (benign) using DNA microarrays. Our microarray experiment showed that 11 genes were up-regulated in osteosarcoma in comparison to osteoma whereas 36 genes were down-regulated. Among the up-regulated genes were: PDK1, EXT1, and EIF4H which are involved in AKT/PI3K and GLI/Hedgehog pathways. These genes play an important role in cell biology (cancer cell proliferation) and may be essential in osteosarcoma formation and development. Analyzing the down-regulated genes, the most interesting seemed to be HSPB8 and SEPP1. HSPB8 is a small heat shock protein that plays an important role in cell cycle regulation, apoptosis, and breast carcinogenesis. Also SEPP1 may play a role in carcinogenesis, as its down-regulation may induce oxidative stress possibly resulting in carcinogenesis. The preliminary results of the present study indicate that the up-regulation of three genes EXT1, EIF4H, and PDK1 may play an essential role in osteosarcoma formation, development and proliferation. In our opinion the cross-talk between GLI/Hedgehog and PI3K/AKT pathways may be a key factor to increase tumor proliferation and malignancy.
    Źródło:
    Polish Journal of Veterinary Sciences; 2011, 14, 1
    1505-1773
    Pojawia się w:
    Polish Journal of Veterinary Sciences
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    A stable density approach to probe selection for a custom aCGH design
    Autorzy:
    Gambin, T.
    Stankiewicz, P.
    Gambin, A.
    Powiązania:
    https://bibliotekanauki.pl/articles/81185.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    genomic region
    probe
    copy number alternation
    comparative genomic hybridization
    human genome
    microarray
    wide range application
    gene expression
    methylation
    binding protein
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 3
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Detekcja ekspresji genów drzew leśnych za pomocą mikromacierzy DNA
    Gene-expression in forest-tree species assessed with microarrays as a tool
    Autorzy:
    Nowakowska, J.A.
    Powiązania:
    https://bibliotekanauki.pl/articles/972859.pdf
    Data publikacji:
    2006
    Wydawca:
    Polskie Towarzystwo Leśne
    Tematy:
    mRNA
    ekspresja genow
    genetyka roslin
    mikromacierze DNA
    sekwencja ESTs
    lesnictwo
    wykrywanie
    drzewa lesne
    microarray
    gene−expression
    forest−tree specie
    ESTs
    Opis:
    DNA microarray technology is a powerful tool in functional genomics study of many organisms, the forest−trees included. This method allow to examine simultaneously the changes in expression of thousands of genes and it is based on specific hybridization of cDNA probes from an organism with the DNA library immobilized in an array. The power of this method consists in miniaturization, automation and parallel study of large−scale genome from multiple samples. In forest science, the microarray technology has already been applied in some study of gene−expression in Populus, Pinus and Picea species and the number of new reports is still increasing every year. Since far, some gene−expression have been studied among woody plants in regard of development and growth processes (xylem, adventious−root and zygotic embryo formation, flowering, ripening, shooting of leaves), resistance mechanisms against biotic (fungi, viruses) and abiotic factors (drought, NaCl, elevated CO2 and O3 concentrations). Many practical applications of the microarray technique may concern the early selection in nursery of trees for morphologically valuable traits, the sustainable forest regeneration and the production of genetically transformed species for the chosen trait.
    Źródło:
    Sylwan; 2006, 150, 04; 33-43
    0039-7660
    Pojawia się w:
    Sylwan
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Identification of candidate genes related to aroma in rice by analyzing the microarray data of highly aromatic and nonaromatic recombinant inbred line bulks
    Autorzy:
    Zinati, Z.
    Delavari, A.
    Powiązania:
    https://bibliotekanauki.pl/articles/80716.pdf
    Data publikacji:
    2019
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    rice
    Oryza sativa
    aroma
    aroma-related gene
    gene ontology enrichment analysis
    microarray analysis
    protein-protein interaction
    protein interaction network
    inbred line
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2019, 100, 3
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Progress of medically-related biotechnology in the post-genomic era
    Autorzy:
    Kozlowski, P.
    Powiązania:
    https://bibliotekanauki.pl/articles/80941.pdf
    Data publikacji:
    2011
    Wydawca:
    Polska Akademia Nauk. Czytelnia Czasopism PAN
    Tematy:
    Arabidopsis
    biotechnology
    copy number variation
    enormous progress
    eukaryote
    genetic marker
    genome
    medical biotechnology
    metagenome
    microarray technology
    nematode
    non-coding RNA
    stem cell
    yeast
    Źródło:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology; 2011, 92, 1
    0860-7796
    Pojawia się w:
    BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
    Tytuł:
    Analysis of correlation between transcription activity of estrogen-dependent genes of cytochrome P450 and profile of estrogen receptor in endometrial adenocarcinoma
    Analiza zależności pomiędzy aktywnością transkrypcyjną estrogenozależnych genów cytochromu P450 a profilem receptorów estrogenowych w gruczolakoraku endometrium
    Autorzy:
    Jęda-Golonka, Agnieszka
    Witek, Andrzej
    Paul-Samojedny, Monika
    Kruszniewska-Rajs, Celina
    Powiązania:
    https://bibliotekanauki.pl/articles/1035490.pdf
    Data publikacji:
    2020
    Wydawca:
    Śląski Uniwersytet Medyczny w Katowicach
    Tematy:
    endometrial cancer
    estrogen receptors
    estrogen-dependent genes
    cytochrome p450
    oligonucleotide microarray
    posttranscription modifications
    rak endometrium
    receptory estrogenowe
    estrogenozależne geny
    cytochrom p450
    mikromacierz oligonukleotydowa
    modyfikacje potranskrypcyjne
    Opis:
    INTRODUCTION: Studies show that the development of endometrial cancer is associated with the activity of estrogen-dependent genes, whose action is conditioned by the presence of estrogen receptors (ER). Analysis of the transcriptional activity of the genes which code ERs as well as the concentration profile of their isoforms could help to understand the mechanism of estrogen activity on the risk of endometrial cancer occurrence, as well as the mechanisms involved in its development and spread. The aim of the conducted studies was to compare the transcriptional activity of the genes coding ER-alpha and ER-beta estrogen receptors, determine the types of post-transcription modifications of ER mRNA in endometrial adenocarcinoma and normal endometrium as well as determine the transcriptome of estrogen-dependent genes of cytochrome P450. MATERIAL AND METHODS: Extraction of the total RNA from 47 endometrium samples was performed with the TRIzol reagent (Invitrogen). The expression profile of the estrogen-dependent genes of cytochrome P450 was determined using the HG-U133A (Affymetrix) oligonucleotide microarray technique from among 22,283 IDs of mRNA IDs. The QRT-PCR reaction for quantification of the mRNA of estrogen receptors was performed using an ABI PRISMTM 7700 (TaqMan) sequence detector. For the QRT-PCR reaction, oligonucleotide starter sequences to detect the ER-alpha and ER-beta mRNA isoforms were designed using Primer ExpressTM Version 1.0 software. RESULTS: In the presented work, it was found that estrogen receptor gene expression occurs in normal endometrium as well as in endometrial adenocarcinoma, and the dominating type is ER-alpha. The transcriptional activity of the ER-alpha and ER-beta genes decreases in adenocarcinoma with a simultaneous increase in the transcriptional activity ratio. The ER-alpha/delta5 isoform dominates in endometrial cancer. Statistical analysis conducted in the GeneSpring 11.5 programme showed that from the group of 91 mRNA IDs of the genes of cytochrome P450, 5 mRNA IDs differentiate, for p <0.5 and FC(log2) > 1.5. In the presented work, it was found that the expression of estrogen receptor genes occurs in normal endometrium and endometrial adenocarcinoma, and the dominant type is ER-alpha. The transcriptional activity of the ER-alpha and ER-beta genes decreases in adenocarcinoma, while the transcriptional activity index increases. In endometrial cancer, the ER-alpha/delta5 isoform dominates. Statistical analysis conducted in GeneSpring 11.5 showed that from the group 91 ID mRNA of cytochrome P450 genes, 5 ID mRNA is differentiating, for p < 0.5 and FC (log2) > 1.5. CONCLUSIONS: The presence of such a transcriptional profile of the studied genes in endometrial adenocarcinoma may indicate that post-transcriptional modifications of estrogen receptors are associated with changes triggering carcinogenesis.
    WSTĘP: Badania wskazują, że wzrost raka endometrium ma związek z aktywnością genów estrogenozależnych, których działanie jest uwarunkowane obecnością receptorów estrogenowych (ER). Analiza aktywności transkrypcyjnej genów kodujących ERs oraz profilu stężeń ich izoform mogłaby pomóc w zrozumieniu mechanizmów wpływu estrogenów na ryzyko wystąpienia raka endometrium, a także mechanizmów zaangażowanych w jego rozwój i rozprzestrzenianie. Celem prowadzonych badań było porównanie aktywności transkrypcyjnej genów kodujących receptory estrogenowe ER-alfa i ER-beta, wyznaczenie typów modyfikacji potranskrypcyjnych mRNA ERs w gruczolakoraku endometrium i endometrium prawidłowym oraz wyznaczenie transkryptomu estrogenozależnych genów cytochromu P450. MATERIAŁ I METODY: Ekstrakcję całkowitego RNA z 47 próbek endometrium przeprowadzono przy użyciu odczyn-nika TRIzol (Invitrogen). Techniką mikromacierzy oligonukleotydowych HG-U133A (Affymetrix) spośród 22 283 ID mRNA wyznaczono profil ekspresji estrogenozależnych genów cytochromu P450. Reakcję QRT-PCR w celu oznaczenia ilościowego mRNA receptorów estrogenowych wykonano z zastosowaniem detektora sekwencji ABI PRISMTM 7700 (TaqMan). Do reakcji QRT-PCR zaprojektowano sekwencje oligonukleotydowych starterów do detekcji izoform mRNA ER-alfa i ER-beta, wykorzystując program komputerowy Primer ExpressTM Version 1.0. WYNIKI: W przedstawionej pracy stwierdzono, że ekspresja genów receptorów estrogenowych występuje w endometrium prawidłowym oraz gruczolakoraku endometrium, a dominującym typem jest ER-alfa. Aktywność transkrypcyjna genów ER-alfa i ER-beta zmniejsza się w gruczolakoraku, przy równoczesnym wzroście wskaźnika aktywności transkrypcyjnej. W raku endometrium dominuje izoforma ER-alfa/delta5. Analiza statystyczna przeprowadzona w programie GeneSpring 11.5 wykazała, że z grupy 91 ID mRNA genów cytochromu P450 różnicujących jest 5 ID mRNA, dla p < 0,5 i FC(log2) > 1,5. WNIOSKI:Obecność takiego profilu transkrypcyjnego badanych genów w gruczolakoraku endometrium może wskazywać na związek modyfikacji potranskrypcyjnych receptorów estrogenowych ze zmianami uruchamiającymi karcinogenezę.
    Źródło:
    Annales Academiae Medicae Silesiensis; 2020, 74; 24-39
    1734-025X
    Pojawia się w:
    Annales Academiae Medicae Silesiensis
    Dostawca treści:
    Biblioteka Nauki
    Artykuł
      Wyświetlanie 1-33 z 33

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