ArticleNucleic acids research2012
YeTFaSCo: a database of evaluated yeast transcription factor sequence specificities.
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 128 papers.
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Who cites it
128 citing papers in PubMed.
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- Intergeneric chromosomal transfer in yeast results in improved phenotypes and widespread transcriptional responses.Nature communications · 2026Article
- Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning.Genetics · 2026Article
- Kar4 acts as a Ste12 regulator inbioRxiv : the preprint server for biology · 2025Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.Research square · 2025Article
- A Fkh1/2 binding site array in thebioRxiv : the preprint server for biology · 2025Article
- Nucleotide dependency analysis of genomic language models detects functional elements.Nature genetics · 2025Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.bioRxiv : the preprint server for biology · 2025Article
- In vivo pathway optimization in yeast via loxpsym-mediated shuffling of upstream activating sequences.Nucleic acids research · 2025Article
- A community effort to optimize sequence-based deep learning models of gene regulation.Nature biotechnology · 2025Article
- Variations in flanking or less conserved positions of Reb1 and Abf1 consensus binding sites lead to major changes in their ability to modulate nucleosome sliding activity.Biological research · 2025Article
- Article
- Unraveling the regulatory dynamics of bidirectional promoters for modulating gene co-expression and metabolic flux in Saccharomyces cerevisiae.Nucleic acids research · 2025Article
- Regulation of meiotic gene expression is functional in the human fungal pathogen Candida glabrata.FEMS yeast research · 2025Article
- Improving the generalization of protein expression models with mechanistic sequence information.Nucleic acids research · 2025Article
- Optimization of regulatory DNA with active learning.Computational and structural biotechnology journal · 2025Article
- Most Pleiotropic Effects of Gene Knockouts Are Evolutionarily Transient in Yeasts.Molecular biology and evolution · 2024Article
- Ordered and disordered regions of the Origin Recognition Complex direct differential in vivo binding at distinct motif sequences.Nucleic acids research · 2024Article
68 more citing papers are in PubMed but not listed here.
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2 authors.
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Abstract
The yeast Saccharomyces cerevisiae is a prevalent system for the analysis of transcriptional networks. As a result, multiple DNA-binding sequence specificities (motifs) have been derived for most yeast transcription factors (TFs). However, motifs from different studies are often inconsistent with each other, making subsequent analyses complicated and confusing. Here, we have created YeTFaSCo (The Yeast Transcription Factor Specificity Compendium, http://yetfasco.ccbr.utoronto.ca/), an extensive collection of S. cerevisiae TF specificities. YeTFaSCo differs from related databases by being more comprehensive (including 1709 motifs for 256 proteins or protein complexes), and by evaluating the motifs using multiple objective quality metrics. The metrics include correlation between motif matches and ChIP-chip data, gene expression patterns, and GO terms, as well as motif agreement between different studies. YeTFaSCo also features an index of 'expert-curated' motifs, each associated with a confidence assessment. In addition, the database website features tools for motif analysis, including a sequence scanning function and precomputed genome-browser tracks of motif occurrences across the entire yeast genome. Users can also search the database for motifs that are similar to a query motif.
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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.