ReviewNucleic acids research2010
Genomic repertoires of DNA-binding transcription factors across the tree of life.
Review in Nucleic acids research, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 82 papers, 1 of them a synthesis that pooled it.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
82 citing papers in PubMed, 1 synthesis or guideline pooled it, 175 citations in OpenAlex.
- Advances in the Application of Protein Language Modeling for Nucleic Acid Protein Binding Site Prediction.Genes · 2024Pooled it
- xBind: an integrated webserver for large language model-enabled cross-molecular protein binding site prediction.Nucleic acids research · 2026Article
- DeepPANB: integrating protein language model with PaiNN equivariant graph neural networks for prediction of protein-nucleic acid binding sites.Briefings in bioinformatics · 2026Article
- The allostery principle supports the symbolic character of signaling circuits: gene regulation provides a form of intelligence to living systems.Theory in biosciences = Theorie in den Biowissenschaften · 2026Article
- Graph-based deep learning approach for high-throughput protein-DNA interaction scoring.Acta pharmacologica Sinica · 2026Article
- Comprehensive multi-omics analysis reveals RUNX1's prognostic value, immune associations, and MUC13-Mediated mechanistic role in hepatocellular carcinoma pathogenesis.Biochemistry and biophysics reports · 2026Article
- Properties of Putative APSES Transcription Factor AfpA inJournal of fungi (Basel, Switzerland) · 2025Article
- SHIP identifies genomic safe harbors in eukaryotic organisms using genomic general feature annotation.Scientific reports · 2025Article
- Chromatin enables precise and scalable gene regulation with factors of limited specificity.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The Velvet transcription factor PnVeA regulates necrotrophic effectors and secondary metabolism in the wheat pathogen Parastagonospora nodorum.BMC microbiology · 2024Article
- Genome sequencing of Elaeocarpus spp. stem blight pathogen Pseudocryphonectria elaeocarpicola reveals potential adaptations to colonize woody bark.BMC genomics · 2024Article
- EPDRNA: A Model for Identifying DNA-RNA Binding Sites in Disease-Related Proteins.The protein journal · 2024Article
- EGPDI: identifying protein-DNA binding sites based on multi-view graph embedding fusion.Briefings in bioinformatics · 2024Article
- Role of Natural Binding Proteins in Therapy and Diagnostics.Life (Basel, Switzerland) · 2024Article
- Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis.Nature communications · 2024Article
- EquiPNAS: improved protein-nucleic acid binding site prediction using protein-language-model-informed equivariant deep graph neural networks.Nucleic acids research · 2024Article
- Protein-protein and protein-nucleic acid binding site prediction via interpretable hierarchical geometric deep learning.GigaScience · 2024Article
- Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis.Research square · 2023Article
- Genetically encoded transcriptional plasticity underlies stress adaptation in Mycobacterium tuberculosis.bioRxiv : the preprint server for biology · 2023Article
- Evolution of sex in crops: recurrent scrap and rebuild.Breeding science · 2023Article
22 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
3 authors at 1 institution in 1 country.
Funding
Abstract
Sequence-specific transcription factors (TFs) are important to genetic regulation in all organisms because they recognize and directly bind to regulatory regions on DNA. Here, we survey and summarize the TF resources available. We outline the organisms for which TF annotation is provided, and discuss the criteria and methods used to annotate TFs by different databases. By using genomic TF repertoires from ∼700 genomes across the tree of life, covering Bacteria, Archaea and Eukaryota, we review TF abundance with respect to the number of genes, as well as their structural complexity in diverse lineages. While typical eukaryotic TFs are longer than the average eukaryotic proteins, the inverse is true for prokaryotes. Only in eukaryotes does the same family of DNA-binding domain (DBD) occur multiple times within one polypeptide chain. This potentially increases the length and diversity of DNA-recognition sequence by reusing DBDs from the same family. We examined the increase in TF abundance with the number of genes in genomes, using the largest set of prokaryotic and eukaryotic genomes to date. As pointed out before, prokaryotic TFs increase faster than linearly. We further observe a similar relationship in eukaryotic genomes with a slower increase in TFs.
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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.