ArticleProceedings of the National Academy of Sciences of the United States of America2008
Discovering gapped binding sites of yeast transcription factors.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
14 citing papers in PubMed, 48 citations in OpenAlex.
- Mechanisms and biotechnological applications of transcription factors.Synthetic and systems biotechnology · 2023Review
- abc4pwm: affinity based clustering for position weight matrices in applications of DNA sequence analysis.BMC bioinformatics · 2022Article
- Setting boundaries for genome-wide heterochromatic DNA deletions through flanking inverted repeats in Tetrahymena thermophila.Nucleic acids research · 2019Article
- DIpartite: A tool for detecting bipartite motifs by considering base interdependencies.PloS one · 2019Article
- Aiolos collaborates with Blimp-1 to regulate the survival of multiple myeloma cells.Cell death and differentiation · 2016Article
- Comprehensive genome-wide transcription factor analysis reveals that a combination of high affinity and low affinity DNA binding is needed for human gene regulation.BMC genomics · 2015Article
- Evaluation of methods for modeling transcription factor sequence specificity.Nature biotechnology · 2013Article
- Article
- Efficient motif search in ranked lists and applications to variable gap motifs.Nucleic acids research · 2012Article
- Predicting DNA-binding locations and orientation on proteins using knowledge-based learning of geometric properties.Proteome science · 2011Article
- Predicting RNA-binding residues from evolutionary information and sequence conservation.BMC genomics · 2010Article
- The spatial distribution of cis regulatory elements in yeast promoters and its implications for transcriptional regulation.BMC genomics · 2010Article
- The effect of prior assumptions over the weights in BayesPI with application to study protein-DNA interactions from ChIP-based high-throughput data.BMC bioinformatics · 2010Article
- BayesPI - a new model to study protein-DNA interactions: a case study of condition-specific protein binding parameters for Yeast transcription factors.BMC bioinformatics · 2009Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors at 4 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A gapped transcription factor-binding site (TFBS) contains one or more highly degenerate positions. Discovering gapped motifs is difficult, because allowing highly degenerate positions in a motif greatly enlarges the search space and complicates the discovery process. Here, we propose a method for discovering TFBSs, especially gapped motifs. We use ChIP-chip data to judge the binding strength of a TF to a putative target promoter and use orthologous sequences from related species to judge the degree of evolutionary conservation of a predicted TFBS. Candidate motifs are constructed by growing compact motif blocks and by concatenating two candidate blocks, allowing 0-15 degenerate positions in between. The resultant patterns are statistically evaluated for their ability to distinguish between target and nontarget genes. Then, a position-based ranking procedure is proposed to enhance the signals of true motifs by collecting position concurrences. Empirical tests on 32 known yeast TFBSs show that the method is highly accurate in identifying gapped motifs, outperforming current methods, and it also works well on ungapped motifs. Predictions on additional 54 TFs successfully discover 11 gapped and 38 ungapped motifs supported by literature. Our method achieves high sensitivity and specificity for predicting experimentally verified TFBSs.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.