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Cold Spring Harbor Protocols Oct 2016Protein microarrays have emerged as a powerful tool for the scientific community, and their greatest advantage lies in the fact that thousands of reactions can be... (Review)
Review
Protein microarrays have emerged as a powerful tool for the scientific community, and their greatest advantage lies in the fact that thousands of reactions can be performed in a parallel and unbiased manner. The first high-density protein microarray, dubbed the "yeast proteome array," consisted of approximately 5800 full-length yeast proteins and was initially used to identify protein-lipid interactions. Further assays were subsequently developed to allow measurement of protein-DNA, protein-RNA, and protein-protein interactions, as well as four well-known posttranslational modifications: phosphorylation, acetylation, ubiquitylation, and SUMOylation. In this introduction, we describe the advent of high-density protein microarrays, as well as current methods for assessing a wide variety of protein interactions and posttranslational modifications.
Topics: Microarray Analysis; Protein Array Analysis
PubMed: 27698245
DOI: 10.1101/pdb.top081471 -
Histopathology Jan 2006Array technologies (gene array, tissue microarray and others) are being used in a growing number of research projects involving soft tissue tumours. Gene array... (Review)
Review
Array technologies (gene array, tissue microarray and others) are being used in a growing number of research projects involving soft tissue tumours. Gene array techniques allow for measurements of RNA expression levels or gene copy number changes for a large number of genes in a single specimen. A complementary technique, tissue microarrays, allows for the measurement of expression of a single gene in a large number of specimens. These techniques and similar ones have created a fundamentally new approach to the investigation of soft tissue tumours. This review addresses some of the advantages, problems, and solutions to those problems that come with these technologies.
Topics: Cluster Analysis; Gene Expression Profiling; Humans; Microarray Analysis; Oligonucleotide Array Sequence Analysis; Soft Tissue Neoplasms
PubMed: 16359534
DOI: 10.1111/j.1365-2559.2005.02286.x -
Progress in Brain Research 2007Microarray analysis of gene expression at the level of RNA has generated new insights into the relationship between cellular responses to acute heat shock in vitro,... (Review)
Review
Microarray analysis of gene expression at the level of RNA has generated new insights into the relationship between cellular responses to acute heat shock in vitro, exercise, and exertional heat illness. Here we discuss the systemic physiology of exertional hyperthermia and exertional heat illness, and compare the results of several recent microarray studies performed in vitro on human cells subjected to heat shock and in vivo on samples obtained from subjects performing exercise or suffering from exertional heat injury. From these comparisons, a concept of overlapping component responses emerges. Namely, some of the gene expression changes observed in peripheral blood mononuclear cells during exertional heat injury can be accounted for by normal cellular responses to heat, exercise, or both; others appear to be specific to the disease state itself. If confirmed in future studies, these component responses might provide a better understanding of adaptive and pathological responses to exercise and exercise-induced hyperthermia, help find new ways of identifying individuals at risk for exertional heat illness, and perhaps even help find rational molecular targets for therapeutic intervention.
Topics: Gene Expression; Gene Expression Profiling; Heat Stress Disorders; Humans; Microarray Analysis; Oligonucleotide Array Sequence Analysis; Physical Exertion
PubMed: 17645926
DOI: 10.1016/S0079-6123(06)62016-5 -
Briefings in Bioinformatics Mar 2010High-throughput biotechnologies, such as gene expression microarrays or mass-spectrometry-based proteomic assays, suffer from frequent missing values due to various... (Review)
Review
High-throughput biotechnologies, such as gene expression microarrays or mass-spectrometry-based proteomic assays, suffer from frequent missing values due to various experimental reasons. Since the missing data points can hinder downstream analyses, there exists a wide variety of ways in which to deal with missing values in large-scale data sets. Nowadays, it has become routine to estimate (or impute) the missing values prior to the actual data analysis. After nearly a decade since the publication of the first missing value imputation methods for gene expression microarray data, new imputation approaches are still being developed at an increasing rate. However, what is lagging behind is a systematic and objective evaluation of the strengths and weaknesses of the different approaches when faced with different types of data sets and experimental questions. In this review, the present strategies for missing value imputation and the measures for evaluating their performance are described. The imputation methods are first reviewed in the context of gene expression microarray data, since most of the methods have been developed for estimating gene expression levels; then, we turn to other large-scale data sets that also suffer from the problems posed by missing values, together with pointers to possible imputation approaches in these settings. Along with a description of the basic principles behind the different imputation approaches, the review tries to provide practical guidance for the users of high-throughput technologies on how to choose the imputation tool for their data and questions, and some additional research directions for the developers of imputation methodologies.
Topics: Algorithms; Gene Expression Profiling; High-Throughput Screening Assays; Humans; Microarray Analysis; Models, Statistical; Research Design; Software
PubMed: 19965979
DOI: 10.1093/bib/bbp059 -
Methods in Molecular Biology (Clifton,... 2016The microarray technology has been a tremendous advance in molecular-based testing methods for biochemical and biomedical applications. As a result, the immobilization... (Review)
Review
The microarray technology has been a tremendous advance in molecular-based testing methods for biochemical and biomedical applications. As a result, the immobilization techniques and grafting chemistries of biochemical molecules have experienced great progress. The particularities of the grafting techniques adapted to the microarray development will be presented here.
Topics: Animals; Humans; Microarray Analysis; Molecular Probes
PubMed: 26614065
DOI: 10.1007/978-1-4939-3136-1_2 -
Methods in Molecular Biology (Clifton,... 2022Glycan microarray is an essential tool to study glycan-binding proteins called lectins. Using glycan microarrays, glycan-binding specificity can be analyzed by...
Glycan microarray is an essential tool to study glycan-binding proteins called lectins. Using glycan microarrays, glycan-binding specificity can be analyzed by incubation with an array in which a series of glycans are immobilized. Various research groups in the world have developed glycan microarray. Among them, our glycan microarray has two unique points: one is the incorporation of the evanescent-field fluorescence detection system, and another is the use of multivalent glycopolymers. These two unique properties allow high-sensitive detection from a relatively limited amount of only nanograms of lectins, which could even be applied in crude samples such as cell lysates and cell culture media. Thus, this system is suitable for the first screening of lectins, lectin-like molecules, lectin candidates, and lectin mutants. Here we describe the protocols to analyze glycan-binding specificity of lectins using our glycan microarray system.
Topics: Carrier Proteins; Glycoconjugates; Lectins; Microarray Analysis; Polysaccharides
PubMed: 34972928
DOI: 10.1007/978-1-0716-2148-6_2 -
Methods in Molecular Biology (Clifton,... 2022Glycan microarrays are widely used to elucidate carbohydrate binding specificity and affinity of various analytes including proteins, microorganisms, cells, and tissues....
Glycan microarrays are widely used to elucidate carbohydrate binding specificity and affinity of various analytes including proteins, microorganisms, cells, and tissues. Glycan microarrays comprise a wide variety of platforms, differing in surface chemistry, presentation of carbohydrates, carbohydrate valency, and detection strategies, all of which impact on analyte performance. This chapter describes detailed methods for printing neoglycoprotein and glycoprotein microarrays on hydrogel-coated slides and incubation of these glycan microarrays with fluorescently labeled lectins.
Topics: Glycoproteins; Hydrogels; Lectins; Microarray Analysis; Polysaccharides
PubMed: 34972927
DOI: 10.1007/978-1-0716-2148-6_1 -
Electrophoresis Apr 2018Microwell arrays are widely used for the analysis of fluorescent-labelled biomaterials. For rapid detection and automated analysis of microwell arrays, the computational...
Microwell arrays are widely used for the analysis of fluorescent-labelled biomaterials. For rapid detection and automated analysis of microwell arrays, the computational image analysis is required. Support Vector Machines (SVM) can be used for this task. Here, we present a SVM-based approach for the analysis of microwell arrays consisting of three distinct steps: labeling, training for feature selection, and classification into three classes. The three classes are filled, partially filled, and unfilled microwells. Next, the partially filled wells are analyzed by SVM and their tendency towards filled or unfilled tested through applying a Gaussian filter. Through this, all microwells can be categorized as either filled or unfilled by our algorithm. Therefore, this SVM-based computational image analysis allows for an accurate and simple classification of microwell arrays.
Topics: Algorithms; Biological Assay; Computer Simulation; Fluorescent Dyes; Light; Microarray Analysis; Optical Imaging; Support Vector Machine
PubMed: 29323408
DOI: 10.1002/elps.201700460 -
JAMA Jun 2017
Topics: Algorithms; Child; Chromosome Aberrations; Chromosome Banding; Congenital Abnormalities; Developmental Disabilities; Humans; Intellectual Disability; Microarray Analysis; Neurodevelopmental Disorders; Sequence Analysis, DNA
PubMed: 28654998
DOI: 10.1001/jama.2017.7272 -
Proteomics. Clinical Applications Jan 2023Although several effective treatment modalities have been developed for cancers, the morbidity and mortality associated with cancer continues to increase every year. As... (Review)
Review
Although several effective treatment modalities have been developed for cancers, the morbidity and mortality associated with cancer continues to increase every year. As one of the most exciting emerging technologies, protein microarrays represent a powerful tool in the field of cancer research because of their advantages such as high throughput, small sample usage, more flexibility, high sensitivity and direct readout of results. In this review, we focus on the research progress in four types of protein microarrays (proteome microarray, antibody microarray, lectin microarray and reversed protein array) with emphasis on their application in cancer research. Finally, we discuss the current challenges faced by protein microarrays and directions for future developments. We firmly believe that this novel systems biology research tool holds immense potential in cancer research and will become an irreplaceable tool in this field.
Topics: Protein Array Analysis; Microarray Analysis; Proteome; Lectins; Neoplasms
PubMed: 36316278
DOI: 10.1002/prca.202200036