ArticleNucleic acids research2012
ScerTF: a comprehensive database of benchmarked position weight matrices for Saccharomyces species.
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 53 papers.
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Who cites it
53 citing papers in PubMed, 86 citations in OpenAlex.
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- Differential Hsp90-dependent gene expression is strain-specific and common among yeast strains.iScience · 2023Article
- Chance promoter activities illuminate the origins of eukaryotic intergenic transcriptions.Nature communications · 2023Article
- Origin recognition complex harbors an intrinsic nucleosome remodeling activity.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- TFLink: an integrated gateway to access transcription factor-target gene interactions for multiple species.Database : the journal of biological databases and curation · 2022Article
- Nucleosome-directed replication origin licensing independent of a consensus DNA sequence.Nature communications · 2022Article
- Predicting which genes will respond to transcription factor perturbations.G3 (Bethesda, Md.) · 2022Article
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- Inferring TF activities and activity regulators from gene expression data with constraints from TF perturbation data.Bioinformatics (Oxford, England) · 2021Article
- Thermodynamic modeling of genome-wide nucleosome depleted regions in yeast.PLoS computational biology · 2021Article
- Systematic identification ofeLife · 2020Article
- The relation between crosstalk and gene regulation form revisited.PLoS computational biology · 2020Article
- Homotypic cooperativity and collective binding are determinants of bHLH specificity and function.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- ChIPulate: A comprehensive ChIP-seq simulation pipeline.PLoS computational biology · 2019Article
- Intrinsic cooperativity potentiates paralleleLife · 2018Article
- Systematic Study of Nucleosome-Displacing Factors in Budding Yeast.Molecular cell · 2018Article
- Comprehensive, high-resolution binding energy landscapes reveal context dependencies of transcription factor binding.Proceedings of the National Academy of Sciences of the United States of America · 2018Article
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Saccharomyces cerevisiae is a primary model for studies of transcriptional control, and the specificities of most yeast transcription factors (TFs) have been determined by multiple methods. However, it is unclear which position weight matrices (PWMs) are most useful; for the roughly 200 TFs in yeast, there are over 1200 PWMs in the literature. To address this issue, we created ScerTF, a comprehensive database of 1226 motifs from 11 different sources. We identified a single matrix for each TF that best predicts in vivo data by benchmarking matrices against chromatin immunoprecipitation and TF deletion experiments. We also used in vivo data to optimize thresholds for identifying regulatory sites with each matrix. To correct for biases from different methods, we developed a strategy to combine matrices. These aligned matrices outperform the best available matrix for several TFs. We used the matrices to predict co-occurring regulatory elements in the genome and identified many known TF combinations. In addition, we predict new combinations and provide evidence of combinatorial regulation from gene expression data. The database is available through a web interface at http://ural.wustl.edu/ScerTF. The site allows users to search the database with a regulatory site or matrix to identify the TFs most likely to bind the input sequence.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.