Microarrays最新文献_第10页

The Transcriptomics to Proteomics of Hair Cell Regeneration: Looking for a Hair Cell in a Haystack. 毛细胞再生的转录组学到蛋白质组学:在大海捞针中寻找毛细胞。

Microarrays Pub Date : 2013-07-25 DOI: 10.3390/microarrays2030186

Michael E Smith, Gopinath Rajadinakaran

{"title":"The Transcriptomics to Proteomics of Hair Cell Regeneration: Looking for a Hair Cell in a Haystack.","authors":"Michael E Smith, Gopinath Rajadinakaran","doi":"10.3390/microarrays2030186","DOIUrl":"https://doi.org/10.3390/microarrays2030186","url":null,"abstract":"Mature mammals exhibit very limited capacity for regeneration of auditory hair cells, while all non-mammalian vertebrates examined can regenerate them. In an effort to find therapeutic targets for deafness and balance disorders, scientists have examined gene expression patterns in auditory tissues under different developmental and experimental conditions. Microarray technology has allowed the large-scale study of gene expression profiles (transcriptomics) at whole-genome levels, but since mRNA expression does not necessarily correlate with protein expression, other methods, such as microRNA analysis and proteomics, are needed to better understand the process of hair cell regeneration. These technologies and some of the results of them are discussed in this review. Although there is a considerable amount of variability found between studies owing to different species, tissues and treatments, there is some concordance between cellular pathways important for hair cell regeneration. Since gene expression and proteomics data is now commonly submitted to centralized online databases, meta-analyses of these data may provide a better picture of pathways that are common to the process of hair cell regeneration and lead to potential therapeutics. Indeed, some of the proteins found to be regulated in the inner ear of animal models (e.g., IGF-1) have now gone through human clinical trials. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"2 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-07-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2030186","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"32024035","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: 6

Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data. CNV调用算法的比较分析:文献综述和牛高密度SNP数据的案例研究。

Microarrays Pub Date : 2013-06-25 DOI: 10.3390/microarrays2030171

Lingyang Xu, Yali Hou, Derek M Bickhart, Jiuzhou Song, George E Liu

{"title":"Comparative Analysis of CNV Calling Algorithms: Literature Survey and a Case Study Using Bovine High-Density SNP Data.","authors":"Lingyang Xu, Yali Hou, Derek M Bickhart, Jiuzhou Song, George E Liu","doi":"10.3390/microarrays2030171","DOIUrl":"https://doi.org/10.3390/microarrays2030171","url":null,"abstract":"Copy number variations (CNVs) are gains and losses of genomic sequence between two individuals of a species when compared to a reference genome. The data from single nucleotide polymorphism (SNP) microarrays are now routinely used for genotyping, but they also can be utilized for copy number detection. Substantial progress has been made in array design and CNV calling algorithms and at least 10 comparison studies in humans have been published to assess them. In this review, we first survey the literature on existing microarray platforms and CNV calling algorithms. We then examine a number of CNV calling tools to evaluate their impacts using bovine high-density SNP data. Large incongruities in the results from different CNV calling tools highlight the need for standardizing array data collection, quality assessment and experimental validation. Only after careful experimental design and rigorous data filtering can the impacts of CNVs on both normal phenotypic variability and disease susceptibility be fully revealed. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"2 3","pages":"171-85"},"PeriodicalIF":0.0,"publicationDate":"2013-06-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2030171","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34728499","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: 52

Correction: Gan, L.; Denecke, B. Profiling Pre-MicroRNA and Mature MicroRNA Expressions Using a Single Microarray and Avoiding Separate Sample Preparation. Microarrays 2013, 2, 24-33. 更正:甘，L.;使用单个微阵列分析预MicroRNA和成熟MicroRNA表达，避免单独的样品制备。芯片，2013,22,24-33。

Microarrays Pub Date : 2013-06-24 DOI: 10.3390/microarrays2030170

Lin Gan, Bernd Denecke

引用次数: 1

Challenges for MicroRNA Microarray Data Analysis. MicroRNA微阵列数据分析的挑战。

Microarrays Pub Date : 2013-06-01 DOI: 10.3390/microarrays2020034

Bin Wang, Yaguang Xi

{"title":"Challenges for MicroRNA Microarray Data Analysis.","authors":"Bin Wang, Yaguang Xi","doi":"10.3390/microarrays2020034","DOIUrl":"https://doi.org/10.3390/microarrays2020034","url":null,"abstract":"Microarray is a high throughput discovery tool that has been broadly used for genomic research. Probe-target hybridization is the central concept of this technology to determine the relative abundance of nucleic acid sequences through fluorescence-based detection. In microarray experiments, variations of expression measurements can be attributed to many different sources that influence the stability and reproducibility of microarray platforms. Normalization is an essential step to reduce non-biological errors and to convert raw image data from multiple arrays (channels) to quality data for further analysis. In general, for the traditional microarray analysis, most established normalization methods are based on two assumptions: (1) the total number of target genes is large enough (>10,000); and (2) the expression level of the majority of genes is kept constant. However, microRNA (miRNA) arrays are usually spotted in low density, due to the fact that the total number of miRNAs is less than 2,000 and the majority of miRNAs are weakly or not expressed. As a result, normalization methods based on the above two assumptions are not applicable to miRNA profiling studies. In this review, we discuss a few representative microarray platforms on the market for miRNA profiling and compare the traditional methods with a few novel strategies specific for miRNA microarrays. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":" ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2020034","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"40269467","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: 42

Microarray for Identification of the Chiropteran Host Species of Rabies Virus in Canada. 用微阵列技术鉴定加拿大狂犬病病毒翼类宿主。

Microarrays Pub Date : 2013-05-31 DOI: 10.3390/microarrays2020153

Oliver Lung, Susan Nadin-Davis, Mathew Fisher, Anthony Erickson, M Kimberly Knowles, Tara Furukawa-Stoffer, Aruna Ambagala

{"title":"Microarray for Identification of the Chiropteran Host Species of Rabies Virus in Canada.","authors":"Oliver Lung, Susan Nadin-Davis, Mathew Fisher, Anthony Erickson, M Kimberly Knowles, Tara Furukawa-Stoffer, Aruna Ambagala","doi":"10.3390/microarrays2020153","DOIUrl":"https://doi.org/10.3390/microarrays2020153","url":null,"abstract":"Species identification through genetic barcoding can augment traditional taxonomic methods, which rely on morphological features of the specimen. Such approaches are especially valuable when specimens are in poor condition or comprise very limited material, a situation that often applies to chiropteran (bat) specimens submitted to the Canadian Food Inspection Agency for rabies diagnosis. Coupled with phenotypic plasticity of many species and inconclusive taxonomic keys, species identification using only morphological traits can be challenging. In this study, a microarray assay with associated PCR of the mitochondrial cytochrome c oxidase subunit I (COI) gene was developed for differentiation of 14 bat species submitted to the Canadian Food Inspection Agency from 1985-2012 for rabies diagnosis. The assay was validated with a reference collection of DNA from 153 field samples, all of which had been barcoded previously. The COI gene from 152 samples which included multiple specimens of each target species were successfully amplified by PCR and accurately identified by the microarray. One sample that was severely decomposed failed to amplify with PCR primers developed in this study, but amplified weakly after switching to alternate primers and was accurately typed by the microarray. Thus, the chiropteran microarray was able to accurately differentiate between the 14 species of Canadian bats targeted. This PCR and microarray assay would allow unequivocal identification to species of most, if not all, bat specimens submitted for rabies diagnosis in Canada. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"2 2","pages":"153-69"},"PeriodicalIF":0.0,"publicationDate":"2013-05-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2020153","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34728497","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 Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes. 涉及微小变化的Illumina基因表达微阵列数据的不同归一化和分析方法的评价。

Microarrays Pub Date : 2013-05-21 DOI: 10.3390/microarrays2020131

Daniel M Johnstone, Carlos Riveros, Moones Heidari, Ross M Graham, Debbie Trinder, Regina Berretta, John K Olynyk, Rodney J Scott, Pablo Moscato, Elizabeth A Milward

{"title":"Evaluation of Different Normalization and Analysis Procedures for Illumina Gene Expression Microarray Data Involving Small Changes.","authors":"Daniel M Johnstone, Carlos Riveros, Moones Heidari, Ross M Graham, Debbie Trinder, Regina Berretta, John K Olynyk, Rodney J Scott, Pablo Moscato, Elizabeth A Milward","doi":"10.3390/microarrays2020131","DOIUrl":"https://doi.org/10.3390/microarrays2020131","url":null,"abstract":"While Illumina microarrays can be used successfully for detecting small gene expression changes due to their high degree of technical replicability, there is little information on how different normalization and differential expression analysis strategies affect outcomes. To evaluate this, we assessed concordance across gene lists generated by applying different combinations of normalization strategy and analytical approach to two Illumina datasets with modest expression changes. In addition to using traditional statistical approaches, we also tested an approach based on combinatorial optimization. We found that the choice of both normalization strategy and analytical approach considerably affected outcomes, in some cases leading to substantial differences in gene lists and subsequent pathway analysis results. Our findings suggest that important biological phenomena may be overlooked when there is a routine practice of using only one approach to investigate all microarray datasets. Analytical artefacts of this kind are likely to be especially relevant for datasets involving small fold changes, where inherent technical variation-if not adequately minimized by effective normalization-may overshadow true biological variation. This report provides some basic guidelines for optimizing outcomes when working with Illumina datasets involving small expression changes. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"2 2","pages":"131-52"},"PeriodicalIF":0.0,"publicationDate":"2013-05-21","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2020131","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34728496","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

A Flexible Microarray Data Simulation Model. 一个灵活的微阵列数据仿真模型。

Microarrays Pub Date : 2013-04-17 DOI: 10.3390/microarrays2020115

Doulaye Dembélé

引用次数: 33

Expanding the Diversity of Imaging-Based RNAi Screen Applications Using Cell Spot Microarrays. 利用细胞点微阵列扩展基于成像的RNAi筛选应用的多样性。

Microarrays Pub Date : 2013-04-11 DOI: 10.3390/microarrays2020097

Juha K Rantala, Sunjong Kwon, James Korkola, Joe W Gray

{"title":"Expanding the Diversity of Imaging-Based RNAi Screen Applications Using Cell Spot Microarrays.","authors":"Juha K Rantala, Sunjong Kwon, James Korkola, Joe W Gray","doi":"10.3390/microarrays2020097","DOIUrl":"https://doi.org/10.3390/microarrays2020097","url":null,"abstract":"Over the past decade, great strides have been made in identifying gene aberrations and deregulated pathways that are associated with specific disease states. These association studies guide experimental studies aimed at identifying the aberrant genes and networks that cause the disease states. This requires functional manipulation of these genes and networks in laboratory models of normal and diseased cells. One approach is to assess molecular and biological responses to high-throughput RNA interference (RNAi)-induced gene knockdown. These responses can be revealed by immunofluorescent staining for a molecular or cellular process of interest and quantified using fluorescence image analysis. These applications are typically performed in multiwell format, but are limited by high reagent costs and long plate processing times. These limitations can be mitigated by analyzing cells grown in cell spot microarray (CSMA) format. CSMAs are produced by growing cells on small (~200 mm diameter) spots with each spot carrying an siRNA with transfection reagent. The spacing between spots is only a few hundred micrometers, thus thousands of cell spots can be arranged on a single cell culture surface. These high-density cell cultures can be immunofluorescently stained with minimal reagent consumption and analyzed quickly using automated fluorescence microscopy platforms. This review covers basic aspects of imaging-based CSMA technology, describes a wide range of immunofluorescence assays that have already been implemented successfully for CSMA screening and suggests future directions for advanced RNAi screening experiments. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"2 2","pages":"97-114"},"PeriodicalIF":0.0,"publicationDate":"2013-04-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2020097","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34728494","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: 10

Comparative Analyses of MicroRNA Microarrays during Cardiogenesis: Functional Perspectives. MicroRNA微阵列在心脏发生过程中的比较分析:功能视角。

Microarrays Pub Date : 2013-04-03 DOI: 10.3390/microarrays2020081

Fernando Bonet, Francisco Hernandez-Torres, Franciso J Esteban, Amelia Aranega, Diego Franco

{"title":"Comparative Analyses of MicroRNA Microarrays during Cardiogenesis: Functional Perspectives.","authors":"Fernando Bonet, Francisco Hernandez-Torres, Franciso J Esteban, Amelia Aranega, Diego Franco","doi":"10.3390/microarrays2020081","DOIUrl":"https://doi.org/10.3390/microarrays2020081","url":null,"abstract":"Cardiovascular development is a complex process in which several transcriptional pathways are operative, providing instructions to the developing cardiomyocytes, while coping with contraction and morphogenetic movements to shape the mature heart. The discovery of microRNAs has added a new layer of complexity to the molecular mechanisms governing the formation of the heart. Discrete genetic ablation of the microRNAs processing enzymes, such as Dicer and Drosha, has highlighted the functional roles of microRNAs during heart development. Importantly, selective deletion of a single microRNA, miR-1-2, results in an embryonic lethal phenotype in which both morphogenetic, as well as impaired conduction, phenotypes can be observed. In an effort to grasp the variability of microRNA expression during cardiac morphogenesis, we recently reported the dynamic expression profile during ventricular development, highlighting the importance of miR-27 on the regulation of a key cardiac transcription factor, Mef2c. In this review, we compare the microRNA expression profile in distinct models of cardiogenesis, such as ventricular chamber development, induced pluripotent stem cell (iPS)-derived cardiomyocytes and the aging heart. Importantly, out of 486 microRNAs assessed in the developing heart, 11% (55) displayed increased expression, many of which are also differentially expressed in distinct cardiogenetic experimental models, including iPS-derived cardiomyocytes. A review on the functional analyses of these differentially expressed microRNAs will be provided in the context of cardiac development, highlighting the resolution and power of microarrays analyses on the quest to decipher the most relevant microRNAs in the developing, aging and diseased heart. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"2 2","pages":"81-96"},"PeriodicalIF":0.0,"publicationDate":"2013-04-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2020081","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34716721","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: 8

Gene Dosage Analysis in a Clinical Environment: Gene-Targeted Microarrays as the Platform-of-Choice. 临床环境中的基因剂量分析:基因靶向微阵列作为首选平台。

Microarrays Pub Date : 2013-03-27 DOI: 10.3390/microarrays2020051

Renate Marquis-Nicholson, Debra Prosser, Jennifer M Love, Donald R Love

{"title":"Gene Dosage Analysis in a Clinical Environment: Gene-Targeted Microarrays as the Platform-of-Choice.","authors":"Renate Marquis-Nicholson, Debra Prosser, Jennifer M Love, Donald R Love","doi":"10.3390/microarrays2020051","DOIUrl":"https://doi.org/10.3390/microarrays2020051","url":null,"abstract":"The role of gene deletion and duplication in the aetiology of disease has become increasingly evident over the last decade. In addition to the classical deletion/duplication disorders diagnosed using molecular techniques, such as Duchenne Muscular Dystrophy and Charcot-Marie-Tooth Neuropathy Type 1A, the significance of partial or whole gene deletions in the pathogenesis of a large number single-gene disorders is becoming more apparent. A variety of dosage analysis methods are available to the diagnostic laboratory but the widespread application of many of these techniques is limited by the expense of the kits/reagents and restrictive targeting to a particular gene or portion of a gene. These limitations are particularly important in the context of a small diagnostic laboratory with modest sample throughput. We have developed a gene-targeted, custom-designed comparative genomic hybridisation (CGH) array that allows twelve clinical samples to be interrogated simultaneously for exonic deletions/duplications within any gene (or panel of genes) on the array. We report here on the use of the array in the analysis of a series of clinical samples processed by our laboratory over a twelve-month period. The array has proven itself to be robust, flexible and highly suited to the diagnostic environment. ","PeriodicalId":56355,"journal":{"name":"Microarrays","volume":"2 2","pages":"51-62"},"PeriodicalIF":0.0,"publicationDate":"2013-03-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.3390/microarrays2020051","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34716719","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: 2