ArticleNucleic acids research2021
SilencerDB: a comprehensive database of silencers.
Article in Nucleic acids research, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 papers.
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Who cites it
35 citing papers in PubMed, 70 citations in OpenAlex.
- Multiple instance fine-mapping: Predicting causal regulatory variants with a deep sequence model.PLoS genetics · 2026Article
- A foundation model for nucleotide sequences.Nucleic acids research · 2026Article
- ATACdb 2.0: a comprehensive chromatin accessibility database of human and mouse.Nucleic acids research · 2026Article
- Pre-training genomic language model with variants for better modeling functional genomics.NPJ artificial intelligence · 2026Article
- Pre-training Genomic Language Model with Variants for Better Modeling Functional Genomics.bioRxiv : the preprint server for biology · 2025Article
- Prediction of target genes and functional types of cis-regulatory modules in the human genome reveals their distinct properties.BMC biology · 2025Article
- CREATE: cell-type-specific cis-regulatory element identification via discrete embedding.Nature communications · 2025Article
- Genome-Wide Silencer Screening Reveals Key Silencer Modulating Reprogramming Efficiency in Mouse Induced Pluripotent Stem Cells.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2025Article
- A mechanism-informed deep neural network enables prioritization of regulators that drive cell state transitions.Nature communications · 2025Article
- Beyond gluten: the multifaceted regulation of MHC class II in celiac disease pathogenesis.Gastroenterology and hepatology from bed to bench · 2025Review
- EpiGePT: a pretrained transformer-based language model for context-specific human epigenomics.Genome biology · 2024Article
- TFTG: A comprehensive database for human transcription factors and their targets.Computational and structural biotechnology journal · 2024Article
- VCAT: an integrated variant function annotation tools.Human genetics · 2024Article
- Deep learning approaches for non-coding genetic variant effect prediction: current progress and future prospects.Briefings in bioinformatics · 2024Review
- CREdb: A comprehensive database of Cis-Regulatory Elements and their activity in human cells and tissues.Epigenetics & chromatin · 2024Article
- Review
- Accurate cell type annotation for single-cell chromatin accessibility data via contrastive learning and reference guidance.Quantitative biology (Beijing, China) · 2024Article
- TSCRE: a comprehensive database for tumor-specificNAR cancer · 2024Article
- MethMarkerDB: a comprehensive cancer DNA methylation biomarker database.Nucleic acids research · 2024Article
- OpenAnnotateApi: Python and R packages to efficiently annotate and analyze chromatin accessibility of genomic regions.Bioinformatics advances · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene regulatory elements, including promoters, enhancers, silencers, etc., control transcriptional programs in a spatiotemporal manner. Though these elements are known to be able to induce either positive or negative transcriptional control, the community has been mostly studying enhancers which amplify transcription initiation, with less emphasis given to silencers which repress gene expression. To facilitate the study of silencers and the investigation of their potential roles in transcriptional control, we developed SilencerDB (http://health.tsinghua.edu.cn/silencerdb/), a comprehensive database of silencers by manually curating silencers from 2300 published articles. The current version, SilencerDB 1.0, contains (1) 33 060 validated silencers from experimental methods, and (ii) 5 045 547 predicted silencers from state-of-the-art machine learning methods. The functionality of SilencerDB includes (a) standardized categorization of silencers in a tree-structured class hierarchy based on species, organ, tissue and cell line and (b) comprehensive annotations of silencers with the nearest gene and potential regulatory genes. SilencerDB, to the best of our knowledge, is the first comprehensive database at this scale dedicated to silencers, with reliable annotations and user-friendly interactive database features. We believe this database has the potential to enable advanced understanding of silencers in regulatory mechanisms and to empower researchers to devise diverse applications of silencers in disease development.
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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.