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Microarray scanner calibration curves: characteristics and implications

Leming Shi, Weida Tong, Zhenqiang Su, Tao Han, Jing Han, Raj K Puri, Hong Fang, Felix W Frueh, Federico M Goodsaid, Lei Guo, William S Branham, James J Chen (+6 others)
2005 BMC Bioinformatics  
Results: By scanning a microarray scanner calibration slide containing known concentrations of fluorescent dyes under 18 PMT gains, we were able to evaluate the differences in calibration characteristics  ...  Microarray-based measurement of mRNA abundance assumes a linear relationship between the fluorescence intensity and the dye concentration. In reality, however, the calibration curve can be nonlinear.  ...  Yaping Zong and Dr. Youxiang Wang of Full Moon Biosystems for stimulating discussions regarding the calibration and validation of microarray scanners.  ... 
doi:10.1186/1471-2105-6-s2-s11 pmid:16026596 pmcid:PMC1637029 fatcat:tf2osgyhqrbang6yu5numdonaq

Microarray scanner performance over a five-week period as measured with Cy5 and Cy3 serial dilution slides

Mary B. Satterfield, Katrice Lippa, Z. Q. Lu, Marc L. Salit
2008 Journal of Research of the National Institute of Standards and Technology  
The scanner is usually assumed to work in a consistent and predictable manner over a wide range of operating settings.  ...  The instrument used to measure the fluorescent signal of the hybridized sample, the microarray scanner, should not be overlooked as a source of variability in microarray experiments.  ...  Acknowledgments Improvements were made in the study and manuscript based on discussions and reviews by David Duewer, Jennifer McDaniel, Walter Liggett, and Steve Choquette.  ... 
doi:10.6028/jres.113.012 fatcat:qppoany2djejvbrumizbjrftiq

Plasmonic substrates for multiplexed protein microarrays with femtomolar sensitivity and broad dynamic range

Scott M. Tabakman, Lana Lau, Joshua T. Robinson, Jordan Price, Sarah P. Sherlock, Hailiang Wang, Bo Zhang, Zhuo Chen, Stephanie Tangsombatvisit, Justin A. Jarrell, Paul J. Utz, Hongjie Dai
2011 Nature Communications  
Further, we demonstrate a multiplexed autoantigen array for human autoantibodies implicated in a range of autoimmune diseases with superior signal-to-noise ratios and broader dynamic range compared with  ...  commercial nitrocellulose and glass substrates.  ...  µArray/Au assay substrate with serum from a different Ls174T tumourbearing mouse and a uniquely generated calibration curve.  ... 
doi:10.1038/ncomms1477 pmid:21915108 pmcid:PMC3402035 fatcat:v55vm4lakne7tmone75vr3e35i

Proceedings of the Second Annual Conference of the MidSouth Computational Biology and Bioinformatics Society

Jonathan D Wren, William Slikker
2005 BMC Bioinformatics  
The MCBIOS 2004 conference brought together regional researchers and students in biology, computer science and bioinformatics on October 7th-9th 2004 to present their latest work.  ...  This editorial describes the conference itself and introduces the twelve peer-reviewed manuscripts accepted for publication in the Proceedings of the MCBIOS 2004 Conference.  ...  By scanning a microarray scanner calibration slide containing known concentrations of fluorescent dyes under various PMT gains, Leming Shi et al.  ... 
doi:10.1186/1471-2105-6-s2-s1 pmid:16026594 pmcid:PMC1637027 fatcat:mlohvyw4hzgflnjfdhmfmfpede

The impact of quantitative optimization of hybridization conditions on gene expression analysis

Peter Sykacek, David P Kreil, Lisa A Meadows, Richard P Auburn, Bettina Fischer, Steven Russell, Gos Micklem
2011 BMC Bioinformatics  
While probe-design is a major research area, relatively little work has been reported on the optimization of microarray protocols.  ...  With the growing availability of entire genome sequences, an increasing number of scientists can exploit oligonucleotide microarrays for genome-scale expression studies.  ...  Funding for work was provided by the Vienna Science and Technology  ... 
doi:10.1186/1471-2105-12-73 pmid:21401920 pmcid:PMC3065421 fatcat:clh4zdpypbewhpws7umlmtv2hq

1α,25-Dihydroxy-vitamin D3 stimulation of bronchial smooth muscle cells induces autocrine, contractility, and remodeling processes

Yohan Bossé, Karim Maghni, Thomas J. Hudson
2007 Physiological Genomics  
remodeling. microarray; real-time PCR; pathways analyses; candidate genes MATERIALS AND METHODS Cell culture.  ...  Microarray experiments were then performed to identify differentially regulated genes and pathways in BMSCs treated or not with 1␣,25(OH) 2D3.  ...  GRANTS Support for the project was available from Genome Canada and Genome Quebec.  ... 
doi:10.1152/physiolgenomics.00134.2006 pmid:17213369 fatcat:t3uw5onv5rdnnfx7fd724brwau

Interferometric silicon biochips for label and label-free DNA and protein microarrays

Marina Cretich, Margo R. Monroe, Alex Reddington, Xirui Zhang, George G. Daaboul, Francesco Damin, Laura Sola, M. Selim Unlu, Marcella Chiari
2012 Proteomics  
Finally, the importance of calibration of protein microarrays through the dual use of labeled and label-free detection schemes on the same chip will be illustrated.  ...  Protein and DNA microarrays hold the promise to revolutionize the field of molecular diagnostics.  ...  receiver-operating characteristic curves [92] .  ... 
doi:10.1002/pmic.201200202 pmid:22930463 fatcat:w47ubjjdfjhtzjjdk2qfoxcz3e

Rosetta error model for gene expression analysis

Lee Weng, Hongyue Dai, Yihui Zhan, Yudong He, Sergey B. Stepaniants, Douglas E. Bassett
2006 Computer applications in the biosciences : CABIOS  
Motivation: In microarray gene expression studies, the number of replicated microarrays is usually small because of cost and sample availability, resulting in unreliable variance estimation and thus unreliable  ...  These technology-specific error models are designed and optimized for different microarray technologies, such as Affymetrix ® and Agilent Technologies.  ...  Authors are grateful to Roger Bumgarner at the University Washington for providing the microarray data demonstrated in this paper.  ... 
doi:10.1093/bioinformatics/btl045 pmid:16522673 fatcat:lus6em3xzbf6ldklyahty4yrkm

A calibration method for estimating absolute expression levels from microarray data

Kristof Engelen, Bart Naudts, Bart De Moor, Kathleen Marchal
2006 Computer applications in the biosciences : CABIOS  
Motivation: We describe an approach to normalize spotted microarray data, based on a physically motivated calibration model.  ...  The model parameters and error distributions are estimated from external control spikes.  ...  Owing to the characteristics of microarray technology, they cannot be dealt with modelwise.  ... 
doi:10.1093/bioinformatics/btl068 pmid:16522672 fatcat:zkb4burb6fa55pxnzmbtvr2r5m

A Head and Neck Cancer Tumor Response-Specific Gene Signature for Cisplatin, 5-Fluorouracil Induction Chemotherapy Fails with Added Taxanes

Céline Tomkiewicz, Stéphane Hans, Marie Hélène Mucchielli, Nicolas Agier, Hervé Delacroix, Laetitia Marisa, Daniel Brasnu, Lawrence P. Aggerbeck, Cécile Badoual, Robert Barouki, Martine Aggerbeck, Andrew Yeudall
2012 PLoS ONE  
microarrays and quantitative reverse transcriptase-PCR (TLDA) cards.  ...  A tengene microarray signature correctly classified 12/13 responders and 7/10 non-responders to PF (92% specificity, 82.6% accuracy).  ...  Acknowledgments We are indebted to all the technicians in the Pathology and Biochemistry departments of the Hôpital Européen Georges Pompidou who helped to process the initial biopsies for further studies  ... 
doi:10.1371/journal.pone.0047170 pmid:23056603 pmcid:PMC3467249 fatcat:vl4ikofkijb4vcofjvqhqxj7qu

Microarray gene expression profiles in dilated and hypertrophic cardiomyopathic end-stage heart failure

Juey-Jen Hwang, Paul D. Allen, George C. Tseng, Ching-Wan Lam, Lameh Fananapazir, Victor J. Dzau, Choong-Chin Liew
2002 Physiological Genomics  
Microarray gene expression profiles in dilated and hypertrophic cardiomyopathic end-stage heart failure. .  ...  We demonstrated that normalization for cDNA microarray data is slide-dependent and nonlinear.  ...  David Barrans, Leonard Anderson, and Richard E. Pratt for insight on analyzing microarray data, and Isolde Prince for manuscript preparation.  ... 
doi:10.1152/physiolgenomics.00122.2001 pmid:12118103 fatcat:geivevvoa5agziwvb4vrllcdv4

A novel quantitative microarray antibody capture assay identifies an extremely high hepatitis delta virus prevalence among hepatitis B virus-infected mongolians

Xiaohua Chen, Odgerel Oidovsambuu, Ping Liu, Rosslyn Grosely, Menashe Elazar, Virginia D. Winn, Benjamin Fram, Zhang Boa, Hongjie Dai, Bekhbold Dashtseren, Dahgwahdorj Yagaanbuyant, Zulkhuu Genden (+4 others)
2017 Hepatology  
Conclusion: The quantitative microarray antibody capture assay's unique performance characteristics make it ideal for population screening; its application to the Mongolian HBV surface antigen-positive  ...  We developed a high-throughput quantitative microarray antibody capture assay for anti-HDV immunoglobulin G wherein recombinant HDV delta antigen is printed by microarray on slides coated with a noncontinuous  ...  (C) Calibration curve for captured anti-HDV quantification.  ... 
doi:10.1002/hep.28957 pmid:27880976 fatcat:ihsq3a7z6vfq7jwrmtoy7ygwfe

Association of Neovascular Age-Related Macular Degeneration with Specific Gene Expression Patterns in Peripheral White Blood Cells

Michal Lederman, Avraham Weiss, Itay Chowers
2010 Investigative Ophthalmology and Visual Science  
Posthybridization washes were performed, followed by scanning with the Axon scanner and the image analysis software (GenePix Pro 4.1 Microarray; Axon Instruments Inc., Union City, CA).  ...  ROC Analysis Receiver operating characteristic (ROC) curves assist in evaluating the feasibility of using a certain test for diagnostic purposes by measuring the area under the ROC curve (AUC).  ... 
doi:10.1167/iovs.08-3019 pmid:19684010 fatcat:47m7wjccdjeondyyj6n4yovcye

Cytokine detection and simultaneous assessment of rheumatoid factor interference in human serum and synovial fluid using high-sensitivity protein arrays on plasmonic gold chips

Manfè Valentina, Fleckner Jan, Nørby Lisby Peder, Zhang Bo, Dai Hongjie, Keller Pernille
2015 BMC Biotechnology  
Plasmonic protein microarrays are, as other immunoassays, affected by the presence of heterophilic antibodies and rheumatoid factor may lead to analytical errors with serious implications for patient care  ...  The protein microarray platform allowed for the detection of human IL-20 at levels <1 pg/ml with reliable IL-20 quantification over a 5-log dynamic range.  ...  Funding This work was supported by Novo Nordisk R&D Science, Talent, Attraction and Recruitment (STAR) and by a Stanford Bio-X Fellowship. Received: 19 January 2015 Accepted: 24 July 2015  ... 
doi:10.1186/s12896-015-0186-0 pmid:26268325 pmcid:PMC4535377 fatcat:ttjxtcfrsncifohnrilq3uv4cy

Gene expression of inflammatory molecules in circulating lymphocytes from arsenic-exposed human subjects

Meei-Maan Wu, Hung-Yi Chiou, I-Ching Ho, Chien-Jen Chen, Te-Chang Lee
2003 Environmental Health Perspectives  
The eight individuals were age-, sex,-and smokingfrequency-matched among groups. b Quantification of each individual gene in one group was standardized to a calibration curve established from serial dilutions  ...  The eight individuals were age-, sex,-and smoking-frequencymatched among groups. b Quantification of each individual gene in one group was standardized to a calibration curve established from serial dilutions  ... 
doi:10.1289/ehp.6396 pmid:12928151 pmcid:PMC1241636 fatcat:p3b3haovynflvaqs5svw6nmq2u
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