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Researchers at University of Glasgow Release New Data on Genomic Research (YuGene: A simple approach to scale gene expression data derived from...

July 8, 2014



Researchers at University of Glasgow Release New Data on Genomic Research (YuGene: A simple approach to scale gene expression data derived from different platforms for integrated analyses)

By a News Reporter-Staff News Editor at Life Science Weekly -- New research on Life Science Research is the subject of a report. According to news originating from Glasgow, United Kingdom, by NewsRx correspondents, research stated, "Gene expression databases contain invaluable information about a range of cell states, but the question 'Where is my gene of interest expressed?' remains one of the most difficult to systematically assess when relevant data is derived on different platforms. Barriers to integrating this data include disparities in data formats and scale, a lack of common identifiers, and the disproportionate contribution of a platform to the 'batch effect."

Our news journalists obtained a quote from the research from the University of Glasgow, "There are few purpose-built cross-platform normalization strategies, and most of these fit data to an idealized data structure, which in turn may compromise gene expression comparisons between different platforms. YuGene addresses this gap by providing a simple transform that assigns a modified cumulative proportion value to each measurement, without losing essential underlying information on data distributions or experimental correlates. The Yugene transform is applied to individual samples and is suitable to apply to data with different distributions. Yugene is robust to combining datasets of different sizes, does not require global renormalization as new data is added, and does not require a common identifier. YuGene was benchmarked against commonly used normalization approaches, performing favorably in comparison to quantile (RMA), Z-score or rank methods. Implementation in the www.stemformatics.org resource provides users with expression queries across stem cell related datasets. Probe performance statistics including poorly performing (never expressed) probes, and examples of probes/genes expressed in a sample-restricted manner are provided."

According to the news editors, the research concluded: "The YuGene software is implemented as an R package available from CRAN."

For more information on this research see: YuGene: A simple approach to scale gene expression data derived from different platforms for integrated analyses. Genomics, 2014;103(4):239-251. Genomics can be contacted at: Academic Press Inc Elsevier Science, 525 B St, Ste 1900, San Diego, CA 92101-4495, USA. (Elsevier - www.elsevier.com; Genomics - www.elsevier.com/wps/product/cws_home/622838)

The news correspondents report that additional information may be obtained from K.A.L. Cao, University of Glasgow, Coll Med Vet & Life Sci, Inst Infect Immun & Inflammat, Glasgow G12 8TA, Lanark, United Kingdom. Additional authors for this research include F. Rohart, L. McHugh, O. Korn and C.A. Wells (see also Life Science Research).

Keywords for this news article include: Europe, Glasgow, United Kingdom, Life Science Research

Our reports deliver fact-based news of research and discoveries from around the world. Copyright 2014, NewsRx LLC


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Source: Life Science Weekly


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