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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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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
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