Written by Oliver Yuan Wei Chan, Bryan Ming Hsun Keng, Maurice Han Tong Ling
Parent Category: Year 2014, Volume 6
Category: Year 2014, Volume 6, Issue 1, January-March 2014
Introduction: Reference genes are assumed to be stably expressed under most circumstances. Previous studies have shown that identification of potential reference genes using common algorithms, such as NormFinder, geNorm, and BestKeeper, are not suitable for microarray-sized datasets. The aim of this study was to evaluate existing methods and develop methods for identifying reference genes from microarray datasets.
Methods: We evaluated the correlation between outputs from 7 published methods for identifying reference genes, including NormFinder, geNorm, and BestKeeper, using subsets of published microarray data. From these results, seven novel combinations of published methods for identifying reference genes were evaluated.
Results: Our results showed that NormFinder’s and geNorm’s indices had high correlations (R2 = 0.987, P < 0.0001), which is consistent with the findings of previous studies. However, NormFinder’s and BestKeeper’s indices (R2 = 0.489, 0.01 < P < 0.05) and NormFinder’s coefficient of variance (CV) suggested a lower correlation (R2 = 0.483, 0.01 < P < 0.05). We developed two novel methods with high correlations with NormFinder (R2 values of both methods were 0.796, P < 0.0001). In addition, computational times required by the two novel methods were linear with the size of the dataset.
Conclusion: Our findings suggested that both of our novel methods can be used as alternatives to NormFinder, geNorm, and BestKeeper for identifying reference genes from large datasets. These methods were implemented as a tool, OLIgonucleotide Variable Expression Ranker (OLIVER), which can be downloaded from http://sourceforge. net/projects/bactome/files/OLIVER/OLIVER_1.zip
Key words: reference standards, computing methodologies
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The worldwide spread of COVID-19 as an emerging, rapidly evolving situation, and the dramatic need of urgent medicine or vaccine, has rapidly brought new hypotheses for pathophysiology and potential medicinal agents to the fore. It is crucial that the research community provide a way to publish this research in a timely manner.
To contribute to this important public health discussion, the Electronic Physician Journal is excited to announce a fast-track procedure to help researchers publish their articles on COVID-19 related subjects that fall under the broad definition of public health, internal medicine, and pharmacology. We are especially welcome to all hypotheses about the pathological basis of the COVID-19 infection and the possible characteristics of potential medicine and vaccine. Submit your manuscript here
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The 6th World Conference on Research Integrity (WCRI) is to be held on June 2-5, 2019 in Hong Kong.
The WCRI is the largest and most significant international conference on research integrity. Since the first conference in Lisbon in 2007, it has given researchers, teachers, funding agencies, government officials, journal editors, senior administrators, and research students opportunities to share experiences and to discuss and promote integrity in research. Read more:
TDR Clinical Research and Development Fellowships
Call for applications
Deadline for submission: 7 March 2019, 16:00 (GMT)
TDR provides fellowships for early- to mid-career researchers and clinical trial staff (e.g. clinicians, pharmacists, medical statisticians, data managers, other health researchers) in low- and middle-income countries (LMICs) to learn how to conduct clinical trials. Read more:
Meta-Analysis Workshops in New York, USA, and London, UK, in April and May 2019
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About the Instructor
Dr. Michael Borenstein, one of the authors of Introduction to Meta-Analysis, is widely recognized for his ability to make statistical concepts accessible to researchers as well as to statisticians. He has lectured widely on meta-analysis, including at the NIH, CDC, and FDA. Read more: