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Wyświetlanie 1-15 z 33
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:
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:
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:
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, 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:
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:
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:
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:
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:
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:
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:
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:
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:
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:
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
Wyświetlanie 1-15 z 33

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