ArticleNature2004
Transcriptional regulatory code of a eukaryotic genome.
Article in Nature, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1,130 papers.
What it found
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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.
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Who cites it
1,130 citing papers in PubMed, 2,177 citations in OpenAlex.
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- Design and Testing of Root-Specific Synthetic Promoters by Machine Learning.International journal of molecular sciences · 2026Article
- Counting Subnetworks Under Gene Duplication in Genetic Regulatory Networks.Bulletin of mathematical biology · 2026Article
- UBIQUITOUS FUNCTIONAL SYNERGY PARTIALLY EXPLAINS WHY MOST TRANSCRIPTION FACTOR BINDING IS NON-FUNCTIONAL.bioRxiv : the preprint server for biology · 2026Article
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- The Binding Landscape of an Essential Nuclear Hormone Receptor inbioRxiv : the preprint server for biology · 2025Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.Research square · 2025Article
- Mapping transcription factor binding sites by learning UV damage fingerprints.Nucleic acids research · 2025Article
- Stage-resolved gene regulatory network analysis reveals developmental reprogramming and genes with robust stem-preferred expression in sorghum.BMC plant biology · 2025Article
- Mapping the transcriptional regulatory network of a fungal pathogen by exploiting transcription factor perturbation.bioRxiv : the preprint server for biology · 2025Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.bioRxiv : the preprint server for biology · 2025Article
- ChIP-exo and CRISPRi/a illuminate the role of Pdr1 and Yap1 in acetic acid tolerance inApplied and environmental microbiology · 2025Article
- When HSFs bring the heat-mapping the transcriptional circuitries of HSF-type regulators inmSphere · 2025Review
- Inferring differential protein binding from time-series chromatin accessibility data.Bioinformatics advances · 2025Article
- Identification of co-localised transcription factors based on paired motifs analysis.IET systems biology · 2024Article
1,070 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
20 authors at 4 institutions in 1 country.
Funding
Abstract
DNA-binding transcriptional regulators interpret the genome's regulatory code by binding to specific sequences to induce or repress gene expression. Comparative genomics has recently been used to identify potential cis-regulatory sequences within the yeast genome on the basis of phylogenetic conservation, but this information alone does not reveal if or when transcriptional regulators occupy these binding sites. We have constructed an initial map of yeast's transcriptional regulatory code by identifying the sequence elements that are bound by regulators under various conditions and that are conserved among Saccharomyces species. The organization of regulatory elements in promoters and the environment-dependent use of these elements by regulators are discussed. We find that environment-specific use of regulatory elements predicts mechanistic models for the function of a large population of yeast's transcriptional regulators.
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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.