Trends in microarray analysis

Stears, Robin L.; Martinsky, Todd; Schena, Mark

doi:10.1038/nm0103-140

Cited by 250 publications

(141 citation statements)

References 54 publications

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“…Evaluation of complex patterns of gene expression is now feasible by the use of microarray analysis [23]. We have previously used high-density oligonucleotide arrays to analyse FACS-purified rat beta cells exposed for 6 or 24 h to IL-1β + IFN-γ [24,25].…”

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confidence: 99%

Global profiling of double stranded RNA- and IFN-?-induced genes in rat pancreatic beta cells

et al. 2003

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Aims/hypothesis. Viral infections and local production of IFN-γ might contribute to beta-cell dysfunction/ death in Type 1 Diabetes. Double stranded RNA (dsRNA) accumulates in the cytosol of viral-infected cells, and exposure of purified rat beta cells to dsRNA (tested in the form of polyinosinic-polycytidylic acid, PIC) in combination with IFN-γ results in beta-cell dysfunction and apoptosis. To elucidate the molecular mechanisms involved in PIC + IFN-γ-effects, we determined the global profile of genes modified by these agents in primary rat beta cells. Methods. FACS-purified rat beta cells were cultured for 6 or 24 h in control condition or with IFN-γ, PIC or a combination of both agents. The gene expression profile was analysed in duplicate by high-density oligonucleotide arrays representing 5000 full-length genes and 3000 EST's. Changes of greater than or equal to 2.5-fold were considered as relevant.Results. Following a 6-or 24-h treatment with IFN-γ, PIC or IFN-γ and PIC, we observed changes in the expression of 51 to 189 genes. IFN-γ modified the expression of MHC-related genes, and also of genes involved in beta-cell metabolism, protein processing, cytokines and signal transduction. PIC affected preferentially the expression of genes related to cell adhesion, cytokines and dsRNA signal transduction, transcription factors and MHC. PIC and/or IFN-γ up-regulated the expression of several chemokines and cytokines that could contribute to mononuclear cell homing and activation during viral infection, while IFN-γ induced a positive feedback on its own signal transduction. PIC + IFN-γ inhibited insulin and GLUT-2 expression without modifying pdx-1 mRNA expression. Conclusion/interpretation. This study provides the first comprehensive characterization of the molecular responses of primary beta cells to dsRNA + IFN-γ, two agents that are probably present in the beta cell milieu during the course of virally-induced insulitis and Type 1 Diabetes. Based on these findings, we propose an integrated model for the molecular mechanisms involved in dsRNA + IFN-γ induced beta-cell dysfunction and death. [Diabetologia (2003[Diabetologia ( ) 46:1641[Diabetologia ( -1657

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confidence: 99%

Global profiling of double stranded RNA- and IFN-?-induced genes in rat pancreatic beta cells

et al. 2003

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“…Finally, we summarize the current body of literature evaluating the potential ability of biomarkers to correlate with disease progression, predict mortality, and identify exacerbations. genes or proteins one-by-one; (2) discovery-based studies that use high-throughput techniques to screen large portions of the genome or proteome, such as RNA expression microarrays or mass spectroscopy of an entire proteome of serum 7,18 ; and (3) pattern-based exploration using expression signatures or algorithminterpreted proteomic patterns while not needing to understand precisely which genes or proteins account for the pattern. 16,18 Although signifi cant progress has occurred in the fi eld of biomarkers, important limitations must be considered.…”

Section: Potential Biomarker Applicationsmentioning

confidence: 99%

“…genes or proteins one-by-one; (2) discovery-based studies that use high-throughput techniques to screen large portions of the genome or proteome, such as RNA expression microarrays or mass spectroscopy of an entire proteome of serum 7,18 ; and (3) pattern-based exploration using expression signatures or algorithminterpreted proteomic patterns while not needing to understand precisely which genes or proteins account for the pattern. 16,18 Although signifi cant progress has occurred in the fi eld of biomarkers, important limitations must be considered. General limitations of biomarker research include threats to validity, including chance, generalizability, bias, reproducibility, overfi tting, confounding, 7,14 analytical issues, 19 concerns regarding processing/storage, and false-positive fi ndings due to multiple hypothesis testing, as well as failure to establish incremental utility beyond existing markers 15 and other clinical tools.…”

Section: Potential Biomarker Applicationsmentioning

confidence: 99%

“…General limitations of biomarker research include threats to validity, including chance, generalizability, bias, reproducibility, overfi tting, confounding, 7,14 analytical issues, 19 concerns regarding processing/storage, and false-positive fi ndings due to multiple hypothesis testing, as well as failure to establish incremental utility beyond existing markers 15 and other clinical tools. 16,18 Common limitations in pulmonary biomarker literature include small studies, the lack of replication cohorts, and the paucity of systemic infl ammation, including CRP, SP-D, fi brinogen, IL-6, IL-8, and TNF-a , was associated to changes in FEV 1 over time. However, this study did reveal that Clara cell protein-16 levels were signifi cantly associated with the rate of change of FEV 1 , suggesting a role as a biomarker of COPD.…”

Section: Potential Biomarker Applicationsmentioning

confidence: 99%

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The Expanding Role of Biomarkers in the Assessment of Smoking-Related Parenchymal Lung Diseases

Doyle

Pinto-Plata

Morse

et al. 2012

Chest

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Recent advances in the fi eld of clinical biomarkers suggest that quantifi cation of serum proteins could play an important role in the diagnosis, classifi cation, prognosis, and treatment response of smoking-related parenchymal lung diseases. COPD and idiopathic pulmonary fi brosis (IPF), two common chronic progressive parenchymal lung diseases, share cigarette smoke exposure as a common dominant risk factor for their development. We have recently shown that COPD and interstitial lung disease may represent distinct outcomes of chronic tobacco use, whereas others have demonstrated that both diseases coexist in some individuals . In this perspective, we examine the potential role of peripheral blood biomarkers in predicting which individuals will develop COPD or IPF, as well as their usefulness in tracking disease progression and exacerbations. Additionally, given the current lack of sensitive and effective metrics to determine an individual's response to treatment, we evaluate the potential role of biomarkers as surrogate markers of clinical outcomes. Finally, we examine the possibility that changes in levels of select protein biomarkers can provide mechanistic insight into the common origins and unique individual susceptibilities that lead to the development of smoking-related parenchymal lung diseases. This discussion is framed by a consideration of the properties of ideal biomarkers for different clinical and research purposes and the best uses for those biomarkers that have already been proposed and investigated.CHEST 2012; 142(4):1027-1034Abbreviations: BODE 5 BMI, airfl ow obstruction, dyspnea, and exercise capacity; CCL-18 5 CC-chemokine ligand-18; CRP 5 C-reactive protein; IPF 5 idiopathic pulmonary fi brosis; KL-6 5 Krebs von den Lungen-6; MMP 5 matrix metalloproteinase; SP 5 surfactant protein; TNF-a 5 tumor necrosis factor-a

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“…DNA microarrays can provide highthroughput assays and rapid detection as well as data analysis and modeling through the application of high-density microarray probes, 2-D matrices, multicolor fluorescence marking, and highly specific binding [3,4]. The microarray probes generate photosensitive signals by specifically binding to fluorescently-labeled targets, providing the identity and concentration of the targets in the sample.…”

Section: Introductionmentioning

confidence: 99%

Microarray Multiplex Assay for the Simultaneous Detection and Discrimination of Influenza A and Influenza B Viruses

Tian

et al. 2013

Indian J Microbiol

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In this study, we present a microarray approach for the typing of influenza A and B viruses, and the subtyping of H1 and H3 subtypes. We designed four pairs of specific multiplex RT-PCR primers and eight specific oligonucleotide probes and prepared microarrays to identify the specific subtype of influenza virus. Through amplification and fluorescent marking of the multiplex RT-PCR products on the M gene of influenza A and B viruses and the HA gene of subtypes H1 and H3, the PCR products were hybridized with the microarray, and the results were analyzed using a microarray scanner. The results demonstrate that the chip developed by our research institute can detect influenza A and B viruses specifically and identify the subtypes H1 and H3 at a minimum concentration of 1 9 10 2 copies/lL of viral RNA. We tested 35 clinical samples and our results were identical to other fluorescent methods. The microarray approach developed in this study provides a reliable method for the monitoring and testing of seasonal influenza.

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Trends in microarray analysis

Cited by 250 publications

References 54 publications

Global profiling of double stranded RNA- and IFN-?-induced genes in rat pancreatic beta cells

Global profiling of double stranded RNA- and IFN-?-induced genes in rat pancreatic beta cells

The Expanding Role of Biomarkers in the Assessment of Smoking-Related Parenchymal Lung Diseases

Microarray Multiplex Assay for the Simultaneous Detection and Discrimination of Influenza A and Influenza B Viruses

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