Microarrays最新文献

A New Distribution Family for Microarray Data † 微阵列数据的新分布族†

Microarrays Pub Date : 2017-02-10 DOI: 10.3390/microarrays6010005

D. Kelmansky, L. Ricci

{"title":"A New Distribution Family for Microarray Data †","authors":"D. Kelmansky, L. Ricci","doi":"10.3390/microarrays6010005","DOIUrl":"https://doi.org/10.3390/microarrays6010005","url":null,"abstract":"The traditional approach with microarray data has been to apply transformations that approximately normalize them, with the drawback of losing the original scale. The alternative standpoint taken here is to search for models that fit the data, characterized by the presence of negative values, preserving their scale; one advantage of this strategy is that it facilitates a direct interpretation of the results. A new family of distributions named gpower-normal indexed by p∈R is introduced and it is proven that these variables become normal or truncated normal when a suitable gpower transformation is applied. Expressions are given for moments and quantiles, in terms of the truncated normal density. This new family can be used to model asymmetric data that include non-positive values, as required for microarray analysis. Moreover, it has been proven that the gpower-normal family is a special case of pseudo-dispersion models, inheriting all the good properties of these models, such as asymptotic normality for small variances. A combined maximum likelihood method is proposed to estimate the model parameters, and it is applied to microarray and contamination data. R codes are available from the authors upon request.","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-02-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays6010005","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"43199979","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 3

DNA Microarray-Based Screening and Characterization of Traditional Chinese Medicine 基于DNA微阵列的中药筛选与表征

Microarrays Pub Date : 2017-01-30 DOI: 10.3390/microarrays6010004

R. Kiyama

{"title":"DNA Microarray-Based Screening and Characterization of Traditional Chinese Medicine","authors":"R. Kiyama","doi":"10.3390/microarrays6010004","DOIUrl":"https://doi.org/10.3390/microarrays6010004","url":null,"abstract":"The application of DNA microarray assay (DMA) has entered a new era owing to recent innovations in omics technologies. This review summarizes recent applications of DMA-based gene expression profiling by focusing on the screening and characterization of traditional Chinese medicine. First, herbs, mushrooms, and dietary plants analyzed by DMA along with their effective components and their biological/physiological effects are summarized and discussed by examining their comprehensive list and a list of representative effective chemicals. Second, the mechanisms of action of traditional Chinese medicine are summarized by examining the genes and pathways responsible for the action, the cell functions involved in the action, and the activities found by DMA (silent estrogens). Third, applications of DMA for traditional Chinese medicine are discussed by examining reported examples and new protocols for its use in quality control. Further innovations in the signaling pathway-based evaluation of beneficial effects and the assessment of potential risks of traditional Chinese medicine are expected, just as are observed in other closely related fields, such as the therapeutic, environmental, nutritional, and pharmacological fields.","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-01-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays6010004","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"48985319","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 19

Microarray Technology Applied to Human Allergic Disease. 微阵列技术在人类变态反应性疾病中的应用

Microarrays Pub Date : 2017-01-28 DOI: 10.3390/microarrays6010003

Robert G Hamilton

{"title":"Microarray Technology Applied to Human Allergic Disease.","authors":"Robert G Hamilton","doi":"10.3390/microarrays6010003","DOIUrl":"10.3390/microarrays6010003","url":null,"abstract":"IgE antibodies serve as the gatekeeper for the release of mediators from sensitized (IgE positive) mast cells and basophils following a relevant allergen exposure which can lead to an immediate-type hypersensitivity (allergic) reaction. Purified recombinant and native allergens were combined in the 1990s with state of the art chip technology to establish the first microarray-based IgE antibody assay. Triplicate spots to over 100 allergenic molecules are immobilized on an amine-activated glass slide to form a single panel multi-allergosorbent assay. Human antibodies, typically of the IgE and IgG isotypes, specific for one or many allergens bind to their respective allergen(s) on the chip. Following removal of unbound serum proteins, bound IgE antibody is detected with a fluorophore-labeled anti-human IgE reagent. The fluorescent profile from the completed slide provides a sensitization profile of an allergic patient which can identify IgE antibodies that bind to structurally similar (cross-reactive) allergen families versus molecules that are unique to a single allergen specificity. Despite its ability to rapidly analyze many IgE antibody specificities in a single simple assay format, the chip-based microarray remains less analytically sensitive and quantitative than its singleplex assay counterpart (ImmunoCAP, Immulite). Microgram per mL quantities of allergen-specific IgG antibody can also complete with nanogram per mL quantities of specific IgE for limited allergen binding sites on the chip. Microarray assays, while not used in clinical immunology laboratories for routine patient IgE antibody testing, will remain an excellent research tool for defining sensitization profiles of populations in epidemiological studies.","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2017-01-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374363/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"47147023","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Acknowledgement to Reviewers of Microarrays in 2016 感谢2016年微阵列评审员

Microarrays Pub Date : 2017-01-11 DOI: 10.3390/microarrays6010002

Microarrays Editorial Office

引用次数: 0

Droplet Microarray Based on Superhydrophobic-Superhydrophilic Patterns for Single Cell Analysis. 基于超疏水-超亲水模式的微滴芯片单细胞分析。

Microarrays Pub Date : 2016-12-09 DOI: 10.3390/microarrays5040028

Gabriella E Jogia, Tina Tronser, Anna A Popova, Pavel A Levkin

{"title":"Droplet Microarray Based on Superhydrophobic-Superhydrophilic Patterns for Single Cell Analysis.","authors":"Gabriella E Jogia, Tina Tronser, Anna A Popova, Pavel A Levkin","doi":"10.3390/microarrays5040028","DOIUrl":"https://doi.org/10.3390/microarrays5040028","url":null,"abstract":"Single-cell analysis provides fundamental information on individual cell response to different environmental cues and is a growing interest in cancer and stem cell research. However, current existing methods are still facing challenges in performing such analysis in a high-throughput manner whilst being cost-effective. Here we established the Droplet Microarray (DMA) as a miniaturized screening platform for high-throughput single-cell analysis. Using the method of limited dilution and varying cell density and seeding time, we optimized the distribution of single cells on the DMA. We established culturing conditions for single cells in individual droplets on DMA obtaining the survival of nearly 100% of single cells and doubling time of single cells comparable with that of cells cultured in bulk cell population using conventional methods. Our results demonstrate that the DMA is a suitable platform for single-cell analysis, which carries a number of advantages compared with existing technologies allowing for treatment, staining and spot-to-spot analysis of single cells over time using conventional analysis methods such as microscopy.","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-12-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays5040028","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39981760","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 27

SNPConvert: SNP Array Standardization and Integration in Livestock Species. SNPConvert:家畜SNP阵列标准化与整合。

Microarrays Pub Date : 2016-06-09 DOI: 10.3390/microarrays5020017

Ezequiel Luis Nicolazzi, Gabriele Marras, Alessandra Stella

{"title":"SNPConvert: SNP Array Standardization and Integration in Livestock Species.","authors":"Ezequiel Luis Nicolazzi, Gabriele Marras, Alessandra Stella","doi":"10.3390/microarrays5020017","DOIUrl":"https://doi.org/10.3390/microarrays5020017","url":null,"abstract":"One of the main advantages of single nucleotide polymorphism (SNP) array technology is providing genotype calls for a specific number of SNP markers at a relatively low cost. Since its first application in animal genetics, the number of available SNP arrays for each species has been constantly increasing. However, conversely to that observed in whole genome sequence data analysis, SNP array data does not have a common set of file formats or coding conventions for allele calling. Therefore, the standardization and integration of SNP array data from multiple sources have become an obstacle, especially for users with basic or no programming skills. Here, we describe the difficulties related to handling SNP array data, focusing on file formats, SNP allele coding, and mapping. We also present SNPConvert suite, a multi-platform, open-source, and user-friendly set of tools to overcome these issues. This tool, which can be integrated with open-source and open-access tools already available, is a first step towards an integrated system to standardize and integrate any type of raw SNP array data. The tool is available at: https://github. com/nicolazzie/SNPConvert.git. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-06-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays5020017","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34366387","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7

Evaluation of Solid Supports for Slide- and Well-Based Recombinant Antibody Microarrays. 载玻片和孔基重组抗体微阵列固体载体的评价。

Microarrays Pub Date : 2016-06-08 DOI: 10.3390/microarrays5020016

Anna S Gerdtsson, Linda Dexlin-Mellby, Payam Delfani, Erica Berglund, Carl A K Borrebaeck, Christer Wingren

{"title":"Evaluation of Solid Supports for Slide- and Well-Based Recombinant Antibody Microarrays.","authors":"Anna S Gerdtsson, Linda Dexlin-Mellby, Payam Delfani, Erica Berglund, Carl A K Borrebaeck, Christer Wingren","doi":"10.3390/microarrays5020016","DOIUrl":"https://doi.org/10.3390/microarrays5020016","url":null,"abstract":"Antibody microarrays have emerged as an important tool within proteomics, enabling multiplexed protein expression profiling in both health and disease. The design and performance of antibody microarrays and how they are processed are dependent on several factors, of which the interplay between the antibodies and the solid surfaces plays a central role. In this study, we have taken on the first comprehensive view and evaluated the overall impact of solid surfaces on the recombinant antibody microarray design. The results clearly demonstrated the importance of the surface-antibody interaction and showed the effect of the solid supports on the printing process, the array format of planar arrays (slide- and well-based), the assay performance (spot features, reproducibility, specificity and sensitivity) and assay processing (degree of automation). In the end, two high-end recombinant antibody microarray technology platforms were designed, based on slide-based (black polymer) and well-based (clear polymer) arrays, paving the way for future large-scale protein expression profiling efforts. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-06-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays5020016","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34366386","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 12

Enhancing Interpretability of Gene Signatures with Prior Biological Knowledge. 利用先验生物学知识增强基因特征的可解释性。

Microarrays Pub Date : 2016-06-08 DOI: 10.3390/microarrays5020015

Margherita Squillario, Matteo Barbieri, Alessandro Verri, Annalisa Barla

引用次数: 3

Retrospective Proteomic Analysis of Cellular Immune Responses and Protective Correlates of p24 Vaccination in an HIV Elite Controller Using Antibody Arrays. 使用抗体阵列对HIV精英控制者中p24疫苗接种的细胞免疫应答和保护性相关因素进行回顾性蛋白质组学分析。

Microarrays Pub Date : 2016-06-02 DOI: 10.3390/microarrays5020014

Suneth S Perera, Bin Wang, Arturo Damian, Wayne Dyer, Li Zhou, Viviane Conceicao, Nitin K Saksena

{"title":"Retrospective Proteomic Analysis of Cellular Immune Responses and Protective Correlates of p24 Vaccination in an HIV Elite Controller Using Antibody Arrays.","authors":"Suneth S Perera, Bin Wang, Arturo Damian, Wayne Dyer, Li Zhou, Viviane Conceicao, Nitin K Saksena","doi":"10.3390/microarrays5020014","DOIUrl":"https://doi.org/10.3390/microarrays5020014","url":null,"abstract":"Background: HIV p24 is an extracellular HIV antigen involved in viral replication. Falling p24 antibody responses are associated with clinical disease progression and their preservation with non-progressive disease. Stimulation of p24 antibody production by immunization to delay progression was the basis of discontinued p24 vaccine. We studied a therapy-naive HIV+ man from Sydney, Australia, infected in 1988. He received the HIV-p24-virus like particle (VLP) vaccine in 1993, and continues to show vigorous p24 antigen responses (>4% p24-specific CD4⁺ T cells), coupled with undetectable plasma viremia. We defined immune-protective correlates of p24 vaccination at the proteomic level through parallel retrospective analysis of cellular immune responses to p24 antigen in CD4⁺ and CD8⁺ T cells and CD14⁺ monocytes at viremic and aviremic phases using antibody-array. We found statistically significant coordinated up-regulation by all three cell-types with high fold-changes in fractalkine, ITAC, IGFBP-2, and MIP-1α in the aviremic phase. TECK and TRAIL-R4 were down-regulated in the viremic phase and up-regulated in the aviremic phase. The up-regulation of fractalkine in all three cell-types coincided with protective effect, whereas the dysfunction in anti-apoptotic chemokines with the loss of immune function. This study highlights the fact that induction of HIV-1-specific helper cells together with coordinated cellular immune response (p < 0.001) might be important in immunotherapeutic interventions and HIV vaccine development.","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-06-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays5020014","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34366384","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5

Advantages of Array-Based Technologies for Pre-Emptive Pharmacogenomics Testing. 预先药物基因组学检测的阵列技术优势

Microarrays Pub Date : 2016-05-28 DOI: 10.3390/microarrays5020012

Al Shahandeh, Daniel M Johnstone, Joshua R Atkins, Jean-Marie Sontag, Moones Heidari, Nilofar Daneshi, Elvis Freeman-Acquah, Elizabeth A Milward

{"title":"Advantages of Array-Based Technologies for Pre-Emptive Pharmacogenomics Testing.","authors":"Al Shahandeh, Daniel M Johnstone, Joshua R Atkins, Jean-Marie Sontag, Moones Heidari, Nilofar Daneshi, Elvis Freeman-Acquah, Elizabeth A Milward","doi":"10.3390/microarrays5020012","DOIUrl":"https://doi.org/10.3390/microarrays5020012","url":null,"abstract":"As recognised by the National Institutes of Health (NIH) Precision Medicine Initiative (PMI), microarray technology currently provides a rapid, inexpensive means of identifying large numbers of known genomic variants or gene transcripts in experimental and clinical settings. However new generation sequencing techniques are now being introduced in many clinical genetic contexts, particularly where novel mutations are involved. While these methods can be valuable for screening a restricted set of genes for known or novel mutations, implementation of whole genome sequencing in clinical practice continues to present challenges. Even very accurate high-throughput methods with small error rates can generate large numbers of false negative or false positive errors due to the high numbers of simultaneous readings. Additional validation is likely to be required for safe use of any such methods in clinical settings. Custom-designed arrays can offer advantages for screening for common, known mutations and, in this context, may currently be better suited for accredited, quality-controlled clinical genetic screening services, as illustrated by their successful application in several large-scale pre-emptive pharmacogenomics programs now underway. Excessive, inappropriate use of next-generation sequencing may waste scarce research funds and other resources. Microarrays presently remain the technology of choice in applications that require fast, cost-effective genome-wide screening of variants of known importance, particularly for large sample sizes. This commentary considers some of the applications where microarrays continue to offer advantages over next-generation sequencing technologies. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2016-05-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays5020012","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34366383","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 7