ArticleNucleic acids research2007
An adaptation of the LMS method to determine expression variations in profiling data.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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Who cites it
6 citing papers in PubMed.
- Involvement of angiopoietin-like 4 in matrix remodeling during chondrogenic differentiation of mesenchymal stem cells.The Journal of biological chemistry · 2014Article
- Promyelocytic leukemia zinc-finger induction signs mesenchymal stem cell commitment: identification of a key marker for stemness maintenance?Stem cell research & therapy · 2014Article
- Differential activity of type I interferon subtypes for dendritic cell differentiation.PloS one · 2013Article
- Sox9-regulated miRNA-574-3p inhibits chondrogenic differentiation of mesenchymal stem cells.PloS one · 2013Article
- Mycobacterium tuberculosis thymidylate synthase gene thyX is essential and potentially bifunctional, while thyA deletion confers resistance to p-aminosalicylic acid.Microbiology (Reading, England) · 2012Article
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
One of the major issues in expression profiling analysis still is to outline proper thresholds to determine differential expression, while avoiding false positives. The problem being that the variance is inversely proportional to the log of signal intensities. Aiming to solve this issue, we describe a model, expression variation (EV), based on the LMS method, which allows data normalization and to construct confidence bands of gene expression, fitting cubic spline curves to the Box-Cox transformation. The confidence bands, fitted to the actual variance of the data, include the genes devoid of significant variation, and allow, based on the confidence bandwidth, to calculate EVs. Each outlier is positioned according to the dispersion space (DS) and a P-value is statistically calculated to determine EV. This model results in variance stabilization. Using two Affymetrix-generated datasets, the sets of differentially expressed genes selected using EV and other classical methods were compared. The analysis suggests that EV is more robust on variance stabilization and on selecting differential expression from both rare and strongly expressed genes.
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Registered trials
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