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Microarrays, Volume 3, Issue 4 (December 2014) , Pages 212-351

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Open AccessArticle
t-Test at the Probe Level: An Alternative Method to Identify Statistically Significant Genes for Microarray Data
Microarrays 2014, 3(4), 340-351; https://doi.org/10.3390/microarrays3040340
Received: 27 October 2014 / Revised: 21 November 2014 / Accepted: 9 December 2014 / Published: 16 December 2014
Cited by 1 | Viewed by 2069 | PDF Full-text (2653 KB) | HTML Full-text | XML Full-text
Abstract
Microarray data analysis typically consists in identifying a list of differentially expressed genes (DEG), i.e., the genes that are differentially expressed between two experimental conditions. Variance shrinkage methods have been considered a better choice than the standard t-test for selecting the DEG because [...] Read more.
Microarray data analysis typically consists in identifying a list of differentially expressed genes (DEG), i.e., the genes that are differentially expressed between two experimental conditions. Variance shrinkage methods have been considered a better choice than the standard t-test for selecting the DEG because they correct the dependence of the error with the expression level. This dependence is mainly caused by errors in background correction, which more severely affects genes with low expression values. Here, we propose a new method for identifying the DEG that overcomes this issue and does not require background correction or variance shrinkage. Unlike current methods, our methodology is easy to understand and implement. It consists of applying the standard t-test directly on the normalized intensity data, which is possible because the probe intensity is proportional to the gene expression level and because the t-test is scale- and location-invariant. This methodology considerably improves the sensitivity and robustness of the list of DEG when compared with the t-test applied to preprocessed data and to the most widely used shrinkage methods, Significance Analysis of Microarrays (SAM) and Linear Models for Microarray Data (LIMMA). Our approach is useful especially when the genes of interest have small differences in expression and therefore get ignored by standard variance shrinkage methods. Full article
(This article belongs to the Special Issue Microarray Gene Expression Data Analysis)
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Open AccessArticle
Variation of RNA Quality and Quantity Are Major Sources of Batch Effects in Microarray Expression Data
Microarrays 2014, 3(4), 322-339; https://doi.org/10.3390/microarrays3040322
Received: 15 September 2014 / Revised: 30 September 2014 / Accepted: 8 December 2014 / Published: 16 December 2014
Cited by 6 | Viewed by 2271 | PDF Full-text (974 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The great utility of microarrays for genome-scale expression analysis is challenged by the widespread presence of batch effects, which bias expression measurements in particular within large data sets. These unwanted technical artifacts can obscure biological variation and thus significantly reduce the reliability of [...] Read more.
The great utility of microarrays for genome-scale expression analysis is challenged by the widespread presence of batch effects, which bias expression measurements in particular within large data sets. These unwanted technical artifacts can obscure biological variation and thus significantly reduce the reliability of the analysis results. It is largely unknown which are the predominant technical sources leading to batch effects. We here quantitatively assess the prevalence and impact of several known technical effects on microarray expression results. Particularly, we focus on important factors such as RNA degradation, RNA quantity, and sequence biases including multiple guanine effects. We find that the common variation of RNA quality and RNA quantity can not only yield low-quality expression results, but that both factors also correlate with batch effects and biological characteristics of the samples. Full article
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Open AccessArticle
Assessing Agreement between miRNA Microarray Platforms
Microarrays 2014, 3(4), 302-321; https://doi.org/10.3390/microarrays3040302
Received: 3 July 2014 / Revised: 24 September 2014 / Accepted: 25 November 2014 / Published: 12 December 2014
Cited by 2 | Viewed by 2384 | PDF Full-text (1389 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Over the last few years, miRNA microarray platforms have provided great insights into the biological mechanisms underlying the onset and development of several diseases. However, only a few studies have evaluated the concordance between different microarray platforms using methods that took into account [...] Read more.
Over the last few years, miRNA microarray platforms have provided great insights into the biological mechanisms underlying the onset and development of several diseases. However, only a few studies have evaluated the concordance between different microarray platforms using methods that took into account measurement error in the data. In this work, we propose the use of a modified version of the Bland–Altman plot to assess agreement between microarray platforms. To this aim, two samples, one renal tumor cell line and a pool of 20 different human normal tissues, were profiled using three different miRNA platforms (Affymetrix, Agilent, Illumina) on triplicate arrays. Intra-platform reliability was assessed by calculating pair-wise concordance correlation coefficients (CCC) between technical replicates and overall concordance correlation coefficient (OCCC) with bootstrap percentile confidence intervals, which revealed moderate-to-good repeatability of all platforms for both samples. Modified Bland–Altman analysis revealed good patterns of concordance for Agilent and Illumina, whereas Affymetrix showed poor-to-moderate agreement for both samples considered. The proposed method is useful to assess agreement between array platforms by modifying the original Bland–Altman plot to let it account for measurement error and bias correction and can be used to assess patterns of concordance between other kinds of arrays other than miRNA microarrays. Full article
(This article belongs to the Special Issue Advances in Data Analysis Methods and Tools)
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Open AccessArticle
Fabrication of Homogeneous High-Density Antibody Microarrays for Cytokine Detection
Microarrays 2014, 3(4), 282-301; https://doi.org/10.3390/microarrays3040282
Received: 6 June 2014 / Revised: 15 November 2014 / Accepted: 1 December 2014 / Published: 9 December 2014
Cited by 1 | Viewed by 3256 | PDF Full-text (3444 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Cytokine proteins are known as biomarker molecules, characteristic of a disease or specific body condition. Monitoring of the cytokine pattern in body fluids can contribute to the diagnosis of diseases. Here we report on the development of an array comprised of different anti-cytokine [...] Read more.
Cytokine proteins are known as biomarker molecules, characteristic of a disease or specific body condition. Monitoring of the cytokine pattern in body fluids can contribute to the diagnosis of diseases. Here we report on the development of an array comprised of different anti-cytokine antibodies on an activated solid support coupled with a fluorescence readout mechanism. Optimization of the array preparation was done in regard of spot homogeneity and spot size. The proinflammatory cytokines Tumor Necrosis Factor alpha (TNFα) and Interleukin 6 (IL-6) were chosen as the first targets of interest. First, the solid support for covalent antibody immobilization and an adequate fluorescent label were selected. Three differently functionalized glass substrates for spotting were compared: amine and epoxy, both having a two-dimensional structure, and the NHS functionalized hydrogel (NHS-3D). The NHS-hydrogel functionalization of the substrate was best suited to antibody immobilization. Then, the optimization of plotting parameters and geometry as well as buffer media were investigated, considering the ambient analyte theory of Roger Ekins. As a first step towards real sample studies, a proof of principle of cytokine detection has been established. Full article
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Open AccessArticle
Expression Comparison of Oil Biosynthesis Genes in Oil Palm Mesocarp Tissue Using Custom Array
Microarrays 2014, 3(4), 263-281; https://doi.org/10.3390/microarrays3040263
Received: 22 August 2014 / Revised: 22 September 2014 / Accepted: 3 November 2014 / Published: 13 November 2014
Cited by 10 | Viewed by 3048 | PDF Full-text (1808 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Gene expression changes that occur during mesocarp development are a major research focus in oil palm research due to the economic importance of this tissue and the relatively rapid increase in lipid content to very high levels at fruit ripeness. Here, we report [...] Read more.
Gene expression changes that occur during mesocarp development are a major research focus in oil palm research due to the economic importance of this tissue and the relatively rapid increase in lipid content to very high levels at fruit ripeness. Here, we report the development of a transcriptome-based 105,000-probe oil palm mesocarp microarray. The expression of genes involved in fatty acid (FA) and triacylglycerol (TAG) assembly, along with the tricarboxylic acid cycle (TCA) and glycolysis pathway at 16 Weeks After Anthesis (WAA) exhibited significantly higher signals compared to those obtained from a cross-species hybridization to the Arabidopsis (p-value < 0.01), and rice (p-value < 0.01) arrays. The oil palm microarray data also showed comparable correlation of expression (r2 = 0.569, p < 0.01) throughout mesocarp development to transcriptome (RNA sequencing) data, and improved correlation over quantitative real-time PCR (qPCR) (r2 = 0.721, p < 0.01) of the same RNA samples. The results confirm the advantage of the custom microarray over commercially available arrays derived from model species. We demonstrate the utility of this custom microarray to gain a better understanding of gene expression patterns in the oil palm mesocarp that may lead to increasing future oil yield. Full article
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Open AccessReview
Particle-Based Microarrays of Oligonucleotides and Oligopeptides
Microarrays 2014, 3(4), 245-262; https://doi.org/10.3390/microarrays3040245
Received: 4 August 2014 / Revised: 15 October 2014 / Accepted: 16 October 2014 / Published: 28 October 2014
Cited by 8 | Viewed by 3323 | PDF Full-text (1324 KB) | HTML Full-text | XML Full-text
Abstract
In this review, we describe different methods of microarray fabrication based on the use of micro-particles/-beads and point out future tendencies in the development of particle-based arrays. First, we consider oligonucleotide bead arrays, where each bead is a carrier of one specific sequence [...] Read more.
In this review, we describe different methods of microarray fabrication based on the use of micro-particles/-beads and point out future tendencies in the development of particle-based arrays. First, we consider oligonucleotide bead arrays, where each bead is a carrier of one specific sequence of oligonucleotides. This bead-based array approach, appearing in the late 1990s, enabled high-throughput oligonucleotide analysis and had a large impact on genome research. Furthermore, we consider particle-based peptide array fabrication using combinatorial chemistry. In this approach, particles can directly participate in both the synthesis and the transfer of synthesized combinatorial molecules to a substrate. Subsequently, we describe in more detail the synthesis of peptide arrays with amino acid polymer particles, which imbed the amino acids inside their polymer matrix. By heating these particles, the polymer matrix is transformed into a highly viscous gel, and thereby, imbedded monomers are allowed to participate in the coupling reaction. Finally, we focus on combinatorial laser fusing of particles for the synthesis of high-density peptide arrays. This method combines the advantages of particles and combinatorial lithographic approaches. Full article
(This article belongs to the Special Issue New and Old Technologies for Generation of Microarrays)
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Open AccessArticle
DNA Microarray Analysis on the Genes Differentially Expressed in the Liver of the Pufferfish, Takifugu rubripes, Following an Intramuscular Administration of Tetrodotoxin
Microarrays 2014, 3(4), 226-244; https://doi.org/10.3390/microarrays3040226
Received: 25 August 2014 / Revised: 28 September 2014 / Accepted: 15 October 2014 / Published: 27 October 2014
Cited by 2 | Viewed by 2435 | PDF Full-text (910 KB) | HTML Full-text | XML Full-text
Abstract
Pufferfish accumulate tetrodotoxin (TTX) mainly in the liver and ovary. This study aims at investigating the effect of TTX accumulation in the liver of cultured specimens of torafugu Takifugu rubripes on the hepatic gene expression by microarray analysis on Day 5 after the [...] Read more.
Pufferfish accumulate tetrodotoxin (TTX) mainly in the liver and ovary. This study aims at investigating the effect of TTX accumulation in the liver of cultured specimens of torafugu Takifugu rubripes on the hepatic gene expression by microarray analysis on Day 5 after the intramuscular administration of 0.25 mg TTX/kg body weight into the caudal muscle. TTX was detected in the liver, skin and ovary in the TTX-administered individuals. The total amount of TTX accumulated in the body was 67 ± 8% of the administered dose on Day 5. Compared with the buffer-administered control group, a total of 59 genes were significantly upregulated more than two-fold in the TTX-administered group, including those encoding chymotrypsin-like elastase family member 2A, transmembrane protein 168 and Rho GTP-activating protein 29. In contrast, a total of 427 genes were downregulated by TTX administration, including those encoding elongation factor G2, R-spondin-3, nuclear receptor activator 2 and fatty acyl-CoA hydrolase precursor. In conclusion, our results demonstrate that the intramuscular administration of TTX changes the expression of hepatic genes involved in various signaling pathways. Full article
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Open AccessArticle
The Robustness of Pathway Analysis in Identifying Potential Drug Targets in Non-Small Cell Lung Carcinoma
Microarrays 2014, 3(4), 212-225; https://doi.org/10.3390/microarrays3040212
Received: 21 July 2014 / Revised: 4 October 2014 / Accepted: 13 October 2014 / Published: 27 October 2014
Viewed by 2168 | PDF Full-text (513 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The identification of genes responsible for causing cancers from gene expression data has had varied success. Often the genes identified depend on the methods used for detecting expression patterns, or on the ways that the data had been normalized and filtered. The use [...] Read more.
The identification of genes responsible for causing cancers from gene expression data has had varied success. Often the genes identified depend on the methods used for detecting expression patterns, or on the ways that the data had been normalized and filtered. The use of gene set enrichment analysis is one way to introduce biological information in order to improve the detection of differentially expressed genes and pathways. In this paper we show that the use of network models while still subject to the problems of normalization is a more robust method for detecting pathways that are differentially overrepresented in lung cancer data. Such differences may provide opportunities for novel therapeutics. In addition, we present evidence that non-small cell lung carcinoma is not a series of homogeneous diseases; rather that there is a heterogeny within the genotype which defies phenotype classification. This diversity helps to explain the lack of progress in developing therapies against non-small cell carcinoma and suggests that drug development may consider multiple pathways as treatment targets. Full article
(This article belongs to the Special Issue Expression Analyses for Biological Pathway Modeling in Drug Discovery)
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