Wyniki wyszukiwania - Biblioteka Nauki

1

How the RNA isolation method can affect microRNA microarray results

100%

Podolska A. , Kaczkowski B. , Litman T. , Fredholm M. , Cirera S.

Acta Biochimica Polonica

|

2011

|

tom 58

|

nr 4

535-540

EN

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.

2

Microarray Inspector: tissue cross contamination detection tool for microarray data

86%

Stępniak P. , Maycock M. , Wojdan K. , Markowska M. , Perun S. , Srivastava A. , Wyrwicz L. , Świrski K.

Acta Biochimica Polonica

|

2013

|

tom 60

|

nr 4

647-655

EN

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.

3

Comparison of gene expression of mitogenic kinin path in adherent and non-adherent CD 34-stem cells using oligonucleotide microarrays

86%

Stojko R. , Witek A. , Glogowska J. , Mazurek U. , Chromy G. , Wilk K. , Witek L. , Bojdys-Szyndlar M. , Machaj K. , Pojda Z.

|

tom 46

|

nr 1

45-50

4

Impact of DNA microarray data transformation on gene expression analysis - comparison of two normalization methods

86%

Schmidt M. T. , Handschuh L. , Zyprych J. , Szabelska A. , Olejnik-Schmidt A. K. , Siatkowski I. , Figlerowicz M.

Acta Biochimica Polonica

|

2011

|

tom 58

|

nr 4

573-580

EN

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.

5

Decision tree approach to microarray data analysis

86%

Grześ M. , Krętowski M.

Biocybernetics and Biomedical Engineering

|

2007

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tom Vol. 27, no. 3

29-42

EN

The classification of gene expression data is still new, difficult and also an interesting field of endeavour. There is a demand for powerful approaches to this problem, which is one of the ultimate goals of modern biological research. Two different techniques for inducing decision trees are discussed and evaluated on well-known and publicly available gene expression datasets. Empirical results are presented.

6

Genomic Virtual Laboratory

86%

Cegielska B. , Kaliszan D. , Handschuh L. , Figlerowicz M. , Meyer N.

Computational Methods in Science and Technology

|

2010

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tom Vol. 16, No. 1

39-49

EN

In contemporary science, virtual laboratories give a chance to improve research by facilitating access to high-throughput technologies and bioinformatics methods. The Genomic Virtual Laboratory (GVL) presented here was developed for automate analysis of data retrieved from a microarray experiment. The system was implemented for R Bioconductor-based analysis of results obtained in the study on human acute myeloid leukaemia (AML). The article extends the theoretical aspects of GVL presented earlier [8] and describes how the particular elements were integrated to establish the advanced system of two-colour microarray data analysis.

7

Microarray of SNPs for diverse applications in Holstein-Friesian cattle breeding

86%

Kaminski S. , Brym P. , Ahman A. , Rusc A. , Wojcik E.

Annals of Animal Science

|

2006

|

tom 06

|

nr 2

8

Smooth muscle contamination analysis in clinical oncology gene expression research

86%

Markowska M. , Stępniak P. , Wojdan K. , Świrski K.

Acta Biochimica Polonica

|

2014

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tom 61

|

nr 2

333-340

EN

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.

9

MicroRNA expression prediction: Regression from regulatory elements

86%

Oğul H. , Tuncer M. E.

Biocybernetics and Biomedical Engineering

|

2016

|

tom Vol. 36, no. 1

89--94

EN

MicroRNAs are known as important actors in post-transcriptional regulation and relevant biological processes. Their expression levels do not only provide information about their own activities but also implicitly explain the behaviors of their targets, thus, in turn, the circuitry of underlying gene regulatory network. In this study, we consider the problem of estimating the expression of a newly discovered microRNA with known promoter sequence in a certain condition where the expression values of some known microRNAs are available. To this end, we offer a regression model to be learnt from the expression levels of other microRNAs obtained through a microarray experiment. To our knowledge, this is the first study that evaluates the predictability of microRNA expression from the regulatory elements found in its promoter sequence. The results obtained through the experiments on real microarray data justify the applicability of the framework in practice.

10

Pathogenesis of middle ear acquired cholesteatoma in the light of the research using high throughput, “omics”, technologies of molecular biology

86%

Makuszewska M. , Bartoszewicz R. , Niemczyk K.

Polski Przegląd Otorynolaryngologiczny

|

2019

|

tom 8(3)

14-19

EN

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.

11

Evaporative edge lithography of a liposomal drug microarray for cell migration assays

86%

Vafai N. , Lowry T. W. , Wilson K. A. , Davidson M. W. , Lenhert S.

Nanofabrication

|

2015

|

tom 2

|

nr 1

EN

Lipid multilayer microarrays are a promising approach to miniaturize laboratory procedures by taking advantage of the microscopic compartmentalization capabilities of lipids. Here, we demonstrate a new method to pattern lipid multilayers on surfaces based on solvent evaporation along the edge where a stencil contacts a surface called evaporative edge lithography (EEL). As an example of an application of this process, we use EEL to make microarrays suitable for a cell-based migration assay. Currently existing cell migration assays require a separate compartment for each drug which is dissolved at a single concentration in solution. An advantage of the lipid multilayer microarray assay is that multiple compounds can be tested on the same surface. We demonstrate this by testing the effect of two different lipophilic drugs, Taxol and Brefeldin A, on collective cell migration into an unpopulated area. This particular assay should be scalable to test of 2000 different lipophilic compounds or dosages on a standard microtiter plate area, or if adapted for individual cell migration, it would allow for high-throughput screening of more than 50,000 compounds per plate.

12

How the RNA isolation method can affect microRNA microarray results

86%

Podolska A. , Kaczkowski B. , Litman T. , Fredholm M. , Cirera S.

Acta Biochimica Polonica

|

2011

|

tom 58

|

nr 4

EN

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.

13

Analysis of genes involved in response to doxorubicin and a GD2 ganglioside-specific 14G2a monoclonal antibody in IMR-32 human neuroblastoma cells

86%

Horwacik I. , Durbas M. , Boratyn E. , Sawicka A. , Węgrzyn P. , Krzanik S. , Górka A. , Drożniak J. , Augustyniak E. , Kowalczyk A. , Rokita H.

Acta Biochimica Polonica

|

2015

|

tom 62

|

nr 3

423-433

EN

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.

14

Automated modelling of genetic control in Arabidopsis thaliana

86%

Bozek K. , Gambin A. , Wilczynski B. , Tiuryn J.

Journal of Fruit and Ornamental Plant Research

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2006

|

tom 14

|

nr Suppl.1

15

An Extension of TSP-family Algorithms for Microarray Classification

72%

Czajkowski M. , Krętowski M.

Zeszyty Naukowe Politechniki Białostockiej. Informatyka

|

2009

|

tom Z. 4

31-45

EN

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.

PL

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.

16

Transcriptional pattern of TGF-beta1 inhibitory effect on mouse C2C12 myoblasts differentiation

72%

Wicik Z. , Sadkowski T. , Jank M. , Motyl T.

Polish Journal of Veterinary Sciences

|

2010

|

tom 13

|

nr 4

EN

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.

17

Chemical regulation of photorespiratory hydrogen peroxide-induced cell death in catalase deficient (cat2) Arabidopsis plants

72%

Kerchev P. , Denecker J. , Muhlenbock P. , Van Breusegem F.

BioTechnologia. Journal of Biotechnology Computational Biology and Bionanotechnology

|

2013

|

tom 94

|

nr 2

18

Missense mutations in IHH impair Indian hedgehog signaling in C3H10T1-2 cells: implications for brachydactyly type A1, and new targets for hedgehog signaling

72%

Guo S. , Zhou J. , Gao B. , Hu J. , Wang H. , Meng J. , Zhao X. , Ma G. , Lin C. , Xiao Y. , Tang W. , Zhu X. , Cheah K. S. E. , Feng G. , Chan D. , He L.

Cellular and Molecular Biology Letters

|

2010

|

tom 15

|

nr 1

153-176

EN

Heterozygous missense mutations in IHH result in Brachydactyly type A1 (BDA1; OMIM 112500), a condition characterized by the shortening of digits due to hypoplasia/aplasia of the middle phalanx. Indian Hedgehog signaling regulates the proliferation and differentiation of chondrocytes and is essential for endochondral bone formation. Analyses of activated IHH signaling in C3H10T1/2 cells showed that three BDA1-associated mutations (p.E95K, p.D100E and p.E131K) severely impaired the induction of targets such as Ptch1 and Gli1. However, this was not a complete loss of function, suggesting that these mutations may affect the interaction with the receptor PTCH1 or its partners, with an impact on the induction potency. From comparative microarray expression analyses and quantitative real-time PCR, we identified three additional targets, Sostdc1, Penk1 and Igfbp5, which were also severely affected. Penk1 and Igfbp5 were confirmed to be regulated by GLI1, while the induction of Sostdc1 by IHH is independent of GLI1. SOSTDC1 is a BMP antagonist, and altered BMP signaling is known to affect digit formation. The role of Penk1 and Igfbp5 in skeletogenesis is not known. However, we have shown that both Penk1 and Igfbp5 are expressed in the interzone region of the developing joint of mouse digits, providing another link for a role for IHH signaling in the formation of the distal digits.

19

Calculation of reliable transcript levels of annotated genes on the basis of multiple probe-sets in Affymetrix microarrays

72%

Jaksik R. , Polanska J. , Herok R. , Rzeszowska-Wolny J.

Acta Biochimica Polonica

|

2009

|

tom 56

|

nr 2

271-277

EN

Microarray methods have become a basic tool in studies of global gene expression and changes in transcript levels. Affymetrix microarrays from the HGU133 series contain multiple probe-sets complementary to the same gene (4742 genes are represented by more than one probe-set in a microarray HGU133A). Individual probe-sets annotated to the same gene often show different hybridization signals and even opposite trends, which may result from some of them matching transcripts of more than one gene and from the existence of different splice-variant transcripts. Existing methods that redefine probe-sets and develop custom probe-set definitions use mathematical tools such as Matlab or the R statistical environment with the Bioconductor package (Gentleman et al., 2004, Genome Biol. 5: 280) and thus are directed to researchers with a good knowledge of bioinformatics. We propose here a new approach based on the principle that a probe-set which hybridizes to more than one transcript can be recognized because it produces a signal significantly different from others assigned to the particular gene, allowing it to be detected as an outlier in the group and eliminated from subsequent analyses. A simple freeware application has been developed (available at http://www.bioinformatics.aei.polsl.pl) that detects and removes outlying probe-sets and calculates average signal values for individual genes using the latest annotation database provided by Affymetrix. We illustrate this procedure using microarray data from our experiments aiming to study changes of transcription profile induced by ionizing radiation in human cells.

20

Application of the adaptive noise removal technique to the enhancement of cDNA microarray images

72%

Smolka B. , Bieda R.

Journal of Medical Informatics & Technologies

|

2005

|

tom Vol. 9

131--142

EN

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.