ArticleNucleic acids research2012
Use of ChIP-Seq data for the design of a multiple promoter-alignment method.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
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- Translocator protein is a marker of activated microglia in rodent models but not human neurodegenerative diseases.Nature communications · 2023Article
- Human Milk Oligosaccharide Utilization in Intestinal Bifidobacteria Is Governed by Global Transcriptional Regulator NagR.mSystems · 2022Article
- Quaternary Structure and Deoxyribonucleic Acid-Binding Properties of the Heme-Dependent, CO-Sensing Transcriptional RegulatorBiochemistry · 2022Article
- Establishment Genes Present on pLS20 Family of Conjugative Plasmids Are Regulated in Two Different Ways.Microorganisms · 2021Article
- Functional characterization of a strong promoter of the early light-inducible protein gene from tomato.Planta · 2019Article
- Myostatin gene promoter: structure, conservation and importance as a target for muscle modulation.Journal of animal science and biotechnology · 2019Review
- Control of seed dormancy in Arabidopsis by a cis-acting noncoding antisense transcript.Proceedings of the National Academy of Sciences of the United States of America · 2016Article
- A Bioinformatics Analysis Reveals a Group of MocR Bacterial Transcriptional Regulators Linked to a Family of Genes Coding for Membrane Proteins.Biochemistry research international · 2016Article
- Csr1/Zap1 Maintains Zinc Homeostasis and Influences Virulence in Candida dubliniensis but Is Not Coupled to Morphogenesis.Eukaryotic cell · 2015Article
- Molecular cloning of doublesex genes of four cladocera (water flea) species.BMC genomics · 2013Article
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Authors and funding
6 authors.
Funding
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Abstract
We address the challenge of regulatory sequence alignment with a new method, Pro-Coffee, a multiple aligner specifically designed for homologous promoter regions. Pro-Coffee uses a dinucleotide substitution matrix estimated on alignments of functional binding sites from TRANSFAC. We designed a validation framework using several thousand families of orthologous promoters. This dataset was used to evaluate the accuracy for predicting true human orthologs among their paralogs. We found that whereas other methods achieve on average 73.5% accuracy, and 77.6% when trained on that same dataset, the figure goes up to 80.4% for Pro-Coffee. We then applied a novel validation procedure based on multi-species ChIP-seq data. Trained and untrained methods were tested for their capacity to correctly align experimentally detected binding sites. Whereas the average number of correctly aligned sites for two transcription factors is 284 for default methods and 316 for trained methods, Pro-Coffee achieves 331, 16.5% above the default average. We find a high correlation between a method's performance when classifying orthologs and its ability to correctly align proven binding sites. Not only has this interesting biological consequences, it also allows us to conclude that any method that is trained on the ortholog data set will result in functionally more informative alignments.
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