ArticleNucleic acids research2015
RSAT 2015: Regulatory Sequence Analysis Tools.
Article in Nucleic acids research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 155 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
155 citing papers in PubMed, 254 citations in OpenAlex.
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- Patient-Specific Regulatory Network Rewiring in Inflammatory Bowel Disease: How Genetic Polymorphisms Divert Incoming Signals and Contribute to Disease Pathogenesis.Inflammatory bowel diseases · 2025Article
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- A single-cell and spatial wheat root atlas with cross-species annotations delineates conserved tissue-specific marker genes and regulators.Cell reports · 2025Article
- Clinically-observed FOXA1 mutations upregulate SEMA3C through transcriptional derepression in prostate cancer.Scientific reports · 2024Article
- Crosstalk between chromatin and Shavenbaby defines transcriptional output along the Drosophila intestinal stem cell lineage.iScience · 2024Article
- Review
- Characterization of immunoglobulinFrontiers in immunology · 2023Article
- RSAT 2022: regulatory sequence analysis tools.Nucleic acids research · 2022Article
- Evolution of miRNA-Binding Sites and Regulatory Networks in Cichlids.Molecular biology and evolution · 2022Article
- Z-DNA is remodelled by ZBTB43 in prospermatogonia to safeguard the germline genome and epigenome.Nature cell biology · 2022Article
- Regulatory Evolution of theJournal of bacteriology · 2022Article
- A systems genomics approach to uncover patient-specific pathogenic pathways and proteins in ulcerative colitis.Nature communications · 2022Article
- Dynamics of nuclear matrix attachment regions during 5BMC genomics · 2022Article
- A novel SCARECROW-LIKE3 transcription factorPhysiology and molecular biology of plants : an international journal of functional plant biology · 2022Article
- Cross-species transcriptomic analyses reveals common and opposite responses in Arabidopsis, rice and barley following oxidative stress and hormone treatment.BMC plant biology · 2022Article
95 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
18 authors at 5 institutions in 4 countries.
Funding
Abstract
RSAT (Regulatory Sequence Analysis Tools) is a modular software suite for the analysis of cis-regulatory elements in genome sequences. Its main applications are (i) motif discovery, appropriate to genome-wide data sets like ChIP-seq, (ii) transcription factor binding motif analysis (quality assessment, comparisons and clustering), (iii) comparative genomics and (iv) analysis of regulatory variations. Nine new programs have been added to the 43 described in the 2011 NAR Web Software Issue, including a tool to extract sequences from a list of coordinates (fetch-sequences from UCSC), novel programs dedicated to the analysis of regulatory variants from GWAS or population genomics (retrieve-variation-seq and variation-scan), a program to cluster motifs and visualize the similarities as trees (matrix-clustering). To deal with the drastic increase of sequenced genomes, RSAT public sites have been reorganized into taxon-specific servers. The suite is well-documented with tutorials and published protocols. The software suite is available through Web sites, SOAP/WSDL Web services, virtual machines and stand-alone programs at http://www.rsat.eu/.
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.