Title |
Improving stability and understandability of genotype-phenotype mapping in Saccharomyces using regularized variable selection in L-PLS regression
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Published in |
BMC Bioinformatics, December 2012
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DOI | 10.1186/1471-2105-13-327 |
Pubmed ID | |
Authors |
Tahir Mehmood, Jonas Warringer, Lars Snipen, Solve Sæbø |
Abstract |
Multivariate approaches have been successfully applied to genome wide association studies. Recently, a Partial Least Squares (PLS) based approach was introduced for mapping yeast genotype-phenotype relations, where background information such as gene function classification, gene dispensability, recent or ancient gene copy number variations and the presence of premature stop codons or frameshift mutations in reading frames, were used post hoc to explain selected genes. One of the latest advancement in PLS named L-Partial Least Squares (L-PLS), where 'L' presents the used data structure, enables the use of background information at the modeling level. Here, a modification of L-PLS with variable importance on projection (VIP) was implemented using a stepwise regularized procedure for gene and background information selection. Results were compared to PLS-based procedures, where no background information was used. |
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Norway | 1 | 100% |
Demographic breakdown
Type | Count | As % |
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Members of the public | 1 | 100% |
Mendeley readers
Geographical breakdown
Country | Count | As % |
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United States | 1 | 5% |
Australia | 1 | 5% |
Unknown | 18 | 90% |
Demographic breakdown
Readers by professional status | Count | As % |
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Researcher | 6 | 30% |
Student > Ph. D. Student | 3 | 15% |
Professor > Associate Professor | 3 | 15% |
Professor | 2 | 10% |
Student > Master | 1 | 5% |
Other | 2 | 10% |
Unknown | 3 | 15% |
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Agricultural and Biological Sciences | 7 | 35% |
Computer Science | 4 | 20% |
Engineering | 3 | 15% |
Biochemistry, Genetics and Molecular Biology | 2 | 10% |
Chemistry | 1 | 5% |
Other | 0 | 0% |
Unknown | 3 | 15% |