RSAT peak-motifs statistics

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RSAT peak-motifs specifications

Information


Unique identifier OMICS_00492
Name RSAT peak-motifs
Alternative name Regulatory Sequence Analysis Tools peak-motifs
Interface Web user interface
Restrictions to use None
Input format FASTA, BED, raw, wconsensus, IG, multi, tab
Computer skills Basic
Stability Stable
Maintained Yes

Publications for Regulatory Sequence Analysis Tools peak-motifs

RSAT peak-motifs citations

 (11)
library_books

Convergent roles of ATF3 and CSL in chromatin control of cancer associated fibroblast activation

2017
PMCID: 5551580
PMID: 28684431
DOI: 10.1084/jem.20170724

[…] S11, respectively.MEA was conducted using Regulatory Sequence Analysis Tools (RSAT; ). The ATF3 peak coordinates in the bed format were uploaded onto the RSAT web server (http://floresta.eead.csic.es/rsat/peak-motifs_form.cgi), and the fetched sequences were compared with the discovered motifs using JASPAR CORE vertebrates databases. […]

library_books

Conserved Transcription Factors Steer Growth Related Genomic Programs in Daphnia

2017
Genome Biol Evol
PMCID: 5569996
PMID: 28854641
DOI: 10.1093/gbe/evx127

[…] this requirement and is thus better suited to small-scale gene expression studies.Other existing methods can be used to discover motifs and gene regulatory networks in Daphnia, for example Clover (), RSAT peak-motifs (), or CisFinder (). A comprehensive comparison of the different methods is beyond the scope of this article and we refer the reader to the recent review by . Because of differences i […]

library_books

Gene signature driving invasive mucinous adenocarcinoma of the lung

2017
PMCID: 5376761
PMID: 28255028
DOI: 10.15252/emmm.201606711

[…] The genome distribution of ChIP‐seq peaks was analyzed using CEAS v1.0.0 (Shin et al, ; http://liulab.dfci.harvard.edu/CEAS/) in Cistrome (http://cistrome.org/ap/). Motif analysis was performed using RSAT peak‐motifs (Thomas‐Chollier et al, ,; http://floresta.eead.csic.es/rsat/peak-motifs_form.cgi). For ChIP‐qPCR, DNA was quantified after ChIP using SYBR Green (cat# 4385612, Thermo Fisher Scientif […]

library_books

Concentration dependent chromatin states induced by the bicoid morphogen gradient

2017
eLife
PMCID: 5624782
PMID: 28891464
DOI: 10.7554/eLife.28275.026

[…] to see a higher representation of strong Bcd binding sites in the less sensitive classes, and weaker sites in the more sensitive classes. To test this, we performed de novo motif discovery using the RSAT peak-motifs algorithm (; ). We identified the top motifs in the entire Bcd ChIP peak list, ranked by their e-value, and found that the top three most highly ranked motifs were the consensus bindi […]

library_books

Sequences flanking the core binding site modulate glucocorticoid receptor structure and activity

2016
Nat Commun
PMCID: 5025757
PMID: 27581526
DOI: 10.1038/ncomms12621

[…] son, we extracted a similar number of peaks (532) from genes (688) showing only weak regulation (absolute log2-fold change≤|0.72|). For each group of peaks, we performed de novo motif discovery using RSAT peak motifs (default settings, including dyad-analysis algorithm and the TRANSFAC version 2010.1 motif collection). Peak motifs automatically compare detected motifs to annotated motif collection […]

library_books

PHF13 is a molecular reader and transcriptional co regulator of H3K4me2/3

2016
eLife
PMCID: 4915813
PMID: 27223324
DOI: 10.7554/eLife.10607.094

[…] ich is consistent with an in vivo DNA binding activity to nucleosome free and/or complexed DNA. To further discern whether PHF13 recognizes specific DNA motifs, in silico analysis was performed using RSAT Peak motifs (). This analysis found that PHF13 bound regions were enriched at CpG rich motifs and depleted at AT rich sequences (). This observation prompted us to additionally quantify the overl […]

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RSAT peak-motifs institution(s)
Department of Computational Molecular Biology, Max Planck Institute for Molecular Genetics, Berlin, Germany

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