ArticleNature genetics2004
Rapid analysis of the DNA-binding specificities of transcription factors with DNA microarrays.
Article in Nature genetics, 2004. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 191 papers, 1 of them a synthesis that pooled it.
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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
191 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Meta-analysis discovery of tissue-specific DNA sequence motifs from mammalian gene expression data.BMC bioinformatics · 2006Pooled it
- TF2TG: an online resource mining the potential gene targets of transcription factors in Drosophila.Genetics · 2026Article
- Chemical Engineering of Transcription Factors Uncovered Cell-Permeable μMax Modulators.Journal of the American Chemical Society · 2025Article
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- Ultra-fast variant effect prediction using biophysical transcription factor binding models.Nucleic acids research · 2025Article
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- NKX2-5 congenital heart disease mutations show diverse loss and gain of epigenomic, biochemical and chromatin search functions underpinning pathogenicity.bioRxiv : the preprint server for biology · 2025Article
- Multisite λ-Dynamics for Protein-DNA Binding Affinity Prediction.Journal of chemical theory and computation · 2025Article
- Experimental approaches to investigate biophysical interactions between homeodomain transcription factors and DNA.Biochimica et biophysica acta. Gene regulatory mechanisms · 2025Review
- Genome-wide single-cell and single-molecule footprinting of transcription factors with deaminase.Proceedings of the National Academy of Sciences of the United States of America · 2024Article
- Comprehensive analysis of computational approaches in plant transcription factors binding regions discovery.Heliyon · 2024Article
- Site-Specific Acetylation of the Transcription Factor Protein Max Modulates Its DNA Binding Activity.ACS central science · 2024Article
- Machine Learning and Deep Learning in Synthetic Biology: Key Architectures, Applications, and Challenges.ACS omega · 2024Review
- Mechanisms and biotechnological applications of transcription factors.Synthetic and systems biotechnology · 2023Review
- KaScape: a sequencing-based method for global characterization of protein‒DNA binding affinity.Scientific reports · 2023Article
- Zinc cluster transcription factors frequently activate target genes using a non-canonical half-site binding mode.Nucleic acids research · 2023Article
- Primate protein-ligand interfaces exhibit significant conservation and unveil human-specific evolutionary drivers.PLoS computational biology · 2023Article
- Applications of deep learning in understanding gene regulation.Cell reports methods · 2023Review
- Databases and prospects of dynamic gene regulation in eukaryotes: A mini review.Computational and structural biotechnology journal · 2023Review
- Cis-regulatory sequences in plants: Their importance, discovery, and future challenges.The Plant cell · 2022Review
131 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
8 authors.
Funding
Abstract
We developed a new DNA microarray-based technology, called protein binding microarrays (PBMs), that allows rapid, high-throughput characterization of the in vitro DNA binding-site sequence specificities of transcription factors in a single day. Using PBMs, we identified the DNA binding-site sequence specificities of the yeast transcription factors Abf1, Rap1 and Mig1. Comparison of these proteins' in vitro binding sites with their in vivo binding sites indicates that PBM-derived sequence specificities can accurately reflect in vivo DNA sequence specificities. In addition to previously identified targets, Abf1, Rap1 and Mig1 bound to 107, 90 and 75 putative new target intergenic regions, respectively, many of which were upstream of previously uncharacterized open reading frames. Comparative sequence analysis indicated that many of these newly identified sites are highly conserved across five sequenced sensu stricto yeast species and, therefore, are probably functional in vivo binding sites that may be used in a condition-specific manner. Similar PBM experiments should be useful in identifying new cis regulatory elements and transcriptional regulatory networks in various genomes.
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