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Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach

(2013) GENOME RESEARCH. 23(11). p.1928-1937
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Bioinformatics: from nucleotids to networks (N2N)
Abstract
The Gene Promoter Expression Prediction challenge consisted of predicting gene expression from promoter sequences in a previously unknown experimentally generated data set. The challenge was presented to the community in the framework of the sixth Dialogue for Reverse Engineering Assessments and Methods (DREAM6), a community effort to evaluate the status of systems biology modeling methodologies. Nucleotide-specific promoter activity was obtained by measuring fluorescence from promoter sequences fused upstream of a gene for yellow fluorescence protein and inserted in the same genomic site of yeast Saccharomyces cerevisiae. Twenty-one teams submitted results predicting the expression levels of 53 different promoters from yeast ribosomal protein genes. Analysis of participant predictions shows that accurate values for low-expressed and mutated promoters were difficult to obtain, although in the latter case, only when the mutation induced a large change in promoter activity compared to the wild-type sequence. As in previous DREAM challenges, we found that aggregation of participant predictions provided robust results, but did not fare better than the three best algorithms. Finally, this study not only provides a benchmark for the assessment of methods predicting activity of a specific set of promoters from their sequence, but it also shows that the top performing algorithm, which used machine-learning approaches, can be improved by the addition of biological features such as transcription factor binding sites.
Keywords
PATHWAY, BINDING, PROTEIN-STRUCTURE PREDICTION, EUKARYOTIC GENOME, IFH1

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Chicago
Meyer, Pablo, Geoffrey Siwo, Danny Zeevi, Eilon Sharon, Raquel Norel, Eran Segal, Gustavo Stolovitzky, the DREAM6 consortium, Yvan Saeys, and Kathleen Marchal. 2013. “Inferring Gene Expression from Ribosomal Promoter Sequences, a Crowdsourcing Approach.” Genome Research 23 (11): 1928–1937.
APA
Meyer, Pablo, Siwo, G., Zeevi, D., Sharon, E., Norel, R., Segal, E., Stolovitzky, G., et al. (2013). Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. GENOME RESEARCH, 23(11), 1928–1937.
Vancouver
1.
Meyer P, Siwo G, Zeevi D, Sharon E, Norel R, Segal E, et al. Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach. GENOME RESEARCH. 2013;23(11):1928–37.
MLA
Meyer, Pablo, Geoffrey Siwo, Danny Zeevi, et al. “Inferring Gene Expression from Ribosomal Promoter Sequences, a Crowdsourcing Approach.” GENOME RESEARCH 23.11 (2013): 1928–1937. Print.
@article{4416068,
  abstract     = {The Gene Promoter Expression Prediction challenge consisted of predicting gene expression from promoter sequences in a previously unknown experimentally generated data set. The challenge was presented to the community in the framework of the sixth Dialogue for Reverse Engineering Assessments and Methods (DREAM6), a community effort to evaluate the status of systems biology modeling methodologies. Nucleotide-specific promoter activity was obtained by measuring fluorescence from promoter sequences fused upstream of a gene for yellow fluorescence protein and inserted in the same genomic site of yeast Saccharomyces cerevisiae. Twenty-one teams submitted results predicting the expression levels of 53 different promoters from yeast ribosomal protein genes. Analysis of participant predictions shows that accurate values for low-expressed and mutated promoters were difficult to obtain, although in the latter case, only when the mutation induced a large change in promoter activity compared to the wild-type sequence. As in previous DREAM challenges, we found that aggregation of participant predictions provided robust results, but did not fare better than the three best algorithms. Finally, this study not only provides a benchmark for the assessment of methods predicting activity of a specific set of promoters from their sequence, but it also shows that the top performing algorithm, which used machine-learning approaches, can be improved by the addition of biological features such as transcription factor binding sites.},
  author       = {Meyer, Pablo and Siwo, Geoffrey and Zeevi, Danny and Sharon, Eilon and Norel, Raquel and Segal, Eran and Stolovitzky, Gustavo and DREAM6 consortium, the and Saeys, Yvan and Marchal, Kathleen},
  issn         = {1088-9051},
  journal      = {GENOME RESEARCH},
  keyword      = {PATHWAY,BINDING,PROTEIN-STRUCTURE PREDICTION,EUKARYOTIC GENOME,IFH1},
  language     = {eng},
  number       = {11},
  pages        = {1928--1937},
  title        = {Inferring gene expression from ribosomal promoter sequences, a crowdsourcing approach},
  url          = {http://dx.doi.org/10.1101/gr.157420.113},
  volume       = {23},
  year         = {2013},
}

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