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The balance of reproducibility, sensitivity, and specificity of lists of differentially expressed genes in microarray studies

Leming Shi, Wendell D Jones, Roderick V Jensen, Stephen C Harris, Roger G Perkins, Federico M Goodsaid, Lei Guo, Lisa J Croner, Cecilie Boysen, Hong Fang, Feng Qian, Shashi Amur (+37 others)
2008 BMC Bioinformatics  
The FC criterion enhances reproducibility, whereas the P criterion balances sensitivity and specificity.  ...  as differentially expressed, as is the case in most microarray studies; and (3) the instability of short DEG lists solely based on P-value ranking is an expected mathematical consequence of the high variability  ...  Acknowledgements We thank participants of the MicroArray Quality Control (MAQC) project for generating the large data sets that were used in this study.  ... 
doi:10.1186/1471-2105-9-s9-s10 pmid:18793455 pmcid:PMC2537561 fatcat:p4so4nimdjaztpjf5wfxyyjllu

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Leming Shi, Leming Shi, Wendell Jones, Roderick Jensen, Stephen Harris, Roger Perkins, Federico Goodsaid, Lei Guo, Lisa Croner, Cecilie Boysen, Hong Fang, Shashi Amur (+39 others)
2007 Nature Precedings  
The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity.  ...  Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs).  ...  The focus of our work is the reproducibility of lists of putatively differentially expressed genes in microarray studies.  ... 
doi:10.1038/npre.2007.306.1 fatcat:fmwwmybip5fvpiyefeesud2lgy

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Leming Shi, Wendell Jones, Roderick Jensen, Stephen Harris, Roger Perkins, Federico Goodsaid, Lei Guo, Lisa Croner, Cecilie Boysen, Hong Fang, Shashi Amur, Wenjun Bao (+37 others)
2007 Nature Precedings  
The FC criterion enhances reproducibility while the P criterion balances sensitivity and specificity.  ...  Recent publications raise concerns about the reliability of microarray technology because of the apparent lack of agreement between lists of differentially expressed genes (DEGs).  ...  The focus of our work is the reproducibility of lists of putatively differentially expressed genes in microarray studies.  ... 
doi:10.1038/npre.2007.306.2 fatcat:62gqmwcefbhm7prmdjfogf4cfm

Investigation of reproducibility of differentially expressed genes in DNA microarrays through statistical simulation

Xiaohui Fan, Leming Shi, Hong Fang, Stephen Harris, Roger Perkins, Weida Tong
2009 BMC Proceedings  
Recent publications have raised concerns about the reliability of microarray technology because of the lack of reproducibility of differentially expressed genes (DEGs) from highly similar studies across  ...  In this study, we generate a set of simulated microarray datasets to compare gene selection/ranking rules, including P-value, FC and their combinations, using the percentage of overlapping genes between  ...  Acknowledgements Xiaohui Fan thanks the support by ORISE research fellowship.  ... 
doi:10.1186/1753-6561-3-s2-s4 pmid:19278560 pmcid:PMC2654487 fatcat:hfgbpuwie5hj7j5vlbbapmzc5y

Genes Selection Comparative Study in Microarray Data Analysis
English

Ouafae Kaissi, Eric Nimpaye, Tiratha Raj Singh, Brigitte Vannier, Azeddine Ibrahimi, Abdellatif Amrani Ghacham, Ahmed Moussa
2013 Bioinformation  
In response to the rapid development of DNA Microarray Technologies, many differentially expressed genes selection algorithms have been developed, and different comparison studies of these algorithms have  ...  The results, in terms of sensitivity and specificity, indicate that the behavior of SAM is better compared to Fold Change and T-test using R/BioConductor.  ...  This work was supported by a grant from the NIH for H3Africa BioNet to AM & AI.  ... 
doi:10.6026/97320630091019 pmid:24497729 pmcid:PMC3910358 fatcat:524tzz3gprafhf4ipwmxqyj67e

Microarrays

Hassan M. Fathallah-Shaykh
2005 Archives of Neurology  
The gene list includes a small fraction of differentially expressed genes (true-positive genes, Ͻ 5%) and a predominant majority of genes that are not differentially expressed (true-negative genes, Ͼ 95%  ...  They report inconsistencies in sequence fidelity of the spotted microarrays, variability of differential expression, low specificity of cDNA probes, discrepancy in fold-change calculations, and lack of  ... 
doi:10.1001/archneur.62.11.1669 pmid:16286538 fatcat:2f5ijjrxnjb4dn6pkwgptau6ii

Performance comparison of one-color and two-color platforms within the Microarray Quality Control (MAQC) project

Tucker A Patterson, Edward K Lobenhofer, Stephanie B Fulmer-Smentek, Patrick J Collins, Tzu-Ming Chu, Wenjun Bao, Hong Fang, Ernest S Kawasaki, Janet Hager, Irina R Tikhonova, Stephen J Walker, Liang Zhang (+6 others)
2006 Nature Biotechnology  
The data were evaluated in terms of reproducibility, specificity, sensitivity and accuracy to determine if the two approaches provide comparable results.  ...  For each of the three microarray platforms tested, the results show good agreement with high correlation coefficients and high concordance of differentially expressed gene lists within each platform.  ...  list results for one-versus two-color microarray data based on differentially expressed genes Test site Fold change Number of differentially expressed genes Number of differentially expressed genes  ... 
doi:10.1038/nbt1242 pmid:16964228 fatcat:flc6h5nienao3h7ceagi3vmh64

Large scale real-time PCR validation on gene expression measurements from two commercial long-oligonucleotide microarrays

Yulei Wang, Catalin Barbacioru, Fiona Hyland, Wenming Xiao, Kathryn L Hunkapiller, Julie Blake, Frances Chan, Carolyn Gonzalez, Lu Zhang, Raymond R Samaha
2006 BMC Genomics  
and accuracy in detection of differential expression.  ...  In the absence of a "gold standard"/"reference method" for the gene expression measurements, studies evaluating and comparing the performance of various microarray platforms have often yielded subjective  ...  Acknowledgements We thank Eugene Spier and Karl J Guegler for their contributions in designs of TaqMan Gene Expression Assays and helpful discussions.  ... 
doi:10.1186/1471-2164-7-59 pmid:16551369 pmcid:PMC1435885 fatcat:shufbmnu2ne45lfcmj4y3lmebm

A comparison on effects of normalisations in the detection of differentially expressed genes

Monica Chiogna, Maria Sofia Massa, Davide Risso, Chiara Romualdi
2009 BMC Bioinformatics  
Conclusion: Although we found a limited difference of sensitivities and specificities for the test after each normalisation, the study highlights a strong impact in terms of gene ranking agreement, resulting  ...  The aim of this paper is to discuss the impact of normalisation techniques for two-channel array technology on the process of identification of differentially expressed genes.  ...  ", and by Fondazione Cassa di Risparmio di Padova e Rovigo under the grant "A computational approach to the study of skeletal muscle genomic expression in health and disease".  ... 
doi:10.1186/1471-2105-10-61 pmid:19216778 pmcid:PMC2680204 fatcat:mi7lfu6fbzat5kluv5wms7iofi

Differential Gene Expression Patterns Revealed by Oligonucleotide Versus Long cDNA Arrays

J. Li
2002 Toxicological Sciences  
The sensitivity (fluorescence intensity) and specificity (fold) were very different for selected genes when comparing the two platforms.  ...  According to our results, the data generated from oligonucleotide microarrays is more reliable for interrogating changes in gene expression than data from long cDNA microarrays.  ...  ACKNOWLEDGMENTS We thank Matthew Slattery in the Molecular Biology Facility Core, School of Pharmacy, University of Wisconsin for conducting the Affymetrix gene array hybridization.  ... 
doi:10.1093/toxsci/69.2.383 pmid:12377987 fatcat:se6sqkweybdv5h3il6arb6vzgq

Intensity-based analysis of dual-color gene expression data as an alternative to ratio-based analysis to enhance reproducibility

Koen Bossers, Bauke Ylstra, Ruud H Brakenhoff, Serge J Smeets, Joost Verhaagen, Mark A van de Wiel
2010 BMC Genomics  
gene expression experiments yields 1) more reproducible results, and 2) is more sensitive in the detection of differentially expressed genes.  ...  Conclusions: Intensity-based analysis of dual-color datasets results in more reproducible results and increased sensitivity in the detection of differential gene expression than the analysis of the same  ...  The human brain experiment received funding from the Royal Dutch Academy of Sciences, Innovation Fund and Solvay Pharmaceuticals.  ... 
doi:10.1186/1471-2164-11-112 pmid:20163706 pmcid:PMC2838842 fatcat:khjwhio3zvgi5ce4u4xhazy4ou

Comparing independent microarray studies: the case of human embryonic stem cells

Mayte Suárez-Fariñas, Scott Noggle, Michael Heke, Ali Hemmati-Brivanlou, Marcelo O Magnasco
2005 BMC Genomics  
The upregulated list was subject to rtRTPCR analysis and 75% of the genes were confirmed.  ...  Microarray studies of the same phenomenon in different labs often appear at variance because the published lists of regulated transcripts have disproportionately small intersections.  ...  Acknowledgements M.S.F. acknowledges a Woman in Science fellowship from Rockefeller University. We would like to acknowledge WiCell, the provider of the stem cell line H1.  ... 
doi:10.1186/1471-2164-6-99 pmid:16042783 pmcid:PMC1183205 fatcat:e2rajpgzp5aonjp23iu4hiuxca

A Comprehensive and Universal Method for Assessing the Performance of Differential Gene Expression Analyses

Mikhail G. Dozmorov, Joel M. Guthridge, Robert E. Hurst, Igor M. Dozmorov, Thomas Preiss
2010 PLoS ONE  
The number of methods for pre-processing and analysis of gene expression data continues to increase, often making it difficult to select the most appropriate approach.  ...  Our approach is based on the use of real microarray data in which controlled fold changes are introduced into 20% of the data to provide a metric for comparison with the unmodified data.  ...  Author Contributions Analyzed the data: MGD IMD. Contributed reagents/materials/analysis tools: JMG IMD. Wrote the paper: MGD REH IMD.  ... 
doi:10.1371/journal.pone.0012657 pmid:20844739 pmcid:PMC2936572 fatcat:psinifsm2feddf72r3mdr5agtm

Gene expression arrays as a tool to unravel mechanisms of normal tissue radiation injury and prediction of response

Jacqueline JCM Kruse
2007 World Journal of Gastroenterology  
Over the past 5 years there has been a rapid increase in the use of microarray technology in the field of cancer research.  ...  Differential expression was found in 8% of genes studied.  ...  All genes can be ordered in a ranked list L, according to their differential expression between the classes.  ... 
doi:10.3748/wjg.v13.i19.2669 pmid:17569134 pmcid:PMC4147114 fatcat:6vew6osd7rh2nnwa2o27i6hya4

Modeling the Dynamics of T Helper 17 Induction and Differentiation

Josep BR
2015 MOJ Immunology  
composed of 67 genes involved in induction, function, and maintenance of Th17 differentiation.  ...  Computational simulations highlighted the potential role of IL-24 in shaping IL-17A producing responses, and local sensitivity analysis demonstrated that IL-24 is negatively correlated with FOXP3 expression  ...  Acknowledgement This work was supported in part by a grant from the National Institutes of Health (5R01AT004308) to JBR, NIAID Contract No.  ... 
doi:10.15406/moji.2015.02.00038 fatcat:nflokbp5f5dbtkpwdz4klek724
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