CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments

Publication type:
Journal article
Metadata:
Autoren
  • Lakshmi Kuttippurathu
  • Michael Hsing
  • Yongchao Liu
  • Bertil Schmidt
  • Douglas L Maskell
  • Kyungjoon Lee
  • Aibin He
  • William T Pu
  • Sek Won Kong
Autoren-URL
https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000287758400018&DestLinkType=FullRecord&DestApp=WOS_CPL
DOI
10.1093/bioinformatics/btq707
eISSN
1460-2059
Externe Identifier
  • Clarivate Analytics Document Solution ID: 726WU
  • PubMed Identifier: 21183585
ISSN
1367-4803
Ausgabe der Veröffentlichung
5
Zeitschrift
BIOINFORMATICS
Paginierung
715 - 717
Datum der Veröffentlichung
2011
Status
Published
Titel
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments
Sub types
  • Article
Ausgabe der Zeitschrift
27

Data source: Web of Science (Lite)

Other metadata sources:
Abstract
<jats:title>Abstract</jats:title> <jats:p>Summary:CompleteMOTIFs (cMOTIFs) is an integrated web tool developed to facilitate systematic discovery of overrepresented transcription factor binding motifs from high-throughput chromatin immunoprecipitation experiments. Comprehensive annotations and Boolean logic operations on multiple peak locations enable users to focus on genomic regions of interest for de novo motif discovery using tools such as MEME, Weeder and ChIPMunk. The pipeline incorporates a scanning tool for known motifs from TRANSFAC and JASPAR databases, and performs an enrichment test using local or precalculated background models that significantly improve the motif scanning result. Furthermore, using the cMOTIFs pipeline, we demonstrated that multiple transcription factors could cooperatively bind to the upstream of important stem cell differentiation regulators.</jats:p> <jats:p>Availability:  http://cmotifs.tchlab.org</jats:p> <jats:p>Contact:  sekwon.kong@childrens.harvard.edu</jats:p> <jats:p>Supplementary information:  Supplementary data are available at Bioinformatics online.</jats:p>
Autoren
  • Lakshmi Kuttippurathu
  • Michael Hsing
  • Yongchao Liu
  • Bertil Schmidt
  • Douglas L Maskell
  • Kyungjoon Lee
  • Aibin He
  • William T Pu
  • Sek Won Kong
DOI
10.1093/bioinformatics/btq707
eISSN
1367-4811
ISSN
1367-4803
Ausgabe der Veröffentlichung
5
Zeitschrift
Bioinformatics
Sprache
en
Online publication date
2010
Paginierung
715 - 717
Datum der Veröffentlichung
2011
Status
Published
Herausgeber
Oxford University Press (OUP)
Herausgeber URL
http://dx.doi.org/10.1093/bioinformatics/btq707
Datum der Datenerfassung
2023
Titel
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments
Ausgabe der Zeitschrift
27

Data source: Crossref

Abstract
<h4>Unlabelled</h4>CompleteMOTIFs (cMOTIFs) is an integrated web tool developed to facilitate systematic discovery of overrepresented transcription factor binding motifs from high-throughput chromatin immunoprecipitation experiments. Comprehensive annotations and Boolean logic operations on multiple peak locations enable users to focus on genomic regions of interest for de novo motif discovery using tools such as MEME, Weeder and ChIPMunk. The pipeline incorporates a scanning tool for known motifs from TRANSFAC and JASPAR databases, and performs an enrichment test using local or precalculated background models that significantly improve the motif scanning result. Furthermore, using the cMOTIFs pipeline, we demonstrated that multiple transcription factors could cooperatively bind to the upstream of important stem cell differentiation regulators.<h4>Availability</h4>http://cmotifs.tchlab.org.
Addresses
  • Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA 02115, USA.
Autoren
  • Lakshmi Kuttippurathu
  • Michael Hsing
  • Yongchao Liu
  • Bertil Schmidt
  • Douglas L Maskell
  • Kyungjoon Lee
  • Aibin He
  • William T Pu
  • Sek Won Kong
DOI
10.1093/bioinformatics/btq707
eISSN
1367-4811
Externe Identifier
  • PubMed Identifier: 21183585
  • PubMed Central ID: PMC3105477
Funding acknowledgements
  • NHLBI NIH HHS: HL098166
  • NHLBI NIH HHS: UM1 HL098166
  • NHLBI NIH HHS: U01 HL098166
Open access
false
ISSN
1367-4803
Ausgabe der Veröffentlichung
5
Zeitschrift
Bioinformatics (Oxford, England)
Schlüsselwörter
  • Transcription Factors
  • DNA
  • Models, Statistical
  • Sequence Analysis, DNA
  • Binding Sites
  • Protein Binding
  • Algorithms
  • Internet
  • Databases, Nucleic Acid
  • Protein Interaction Domains and Motifs
  • Molecular Sequence Annotation
Sprache
eng
Medium
Print-Electronic
Online publication date
2010
Paginierung
715 - 717
Datum der Veröffentlichung
2011
Status
Published
Datum der Datenerfassung
2010
Titel
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments.
Sub types
  • Research Support, Non-U.S. Gov't
  • research-article
  • Journal Article
  • Research Support, N.I.H., Extramural
Ausgabe der Zeitschrift
27

Files

https://academic.oup.com/bioinformatics/article-pdf/27/5/715/48866565/bioinformatics_27_5_715.pdf http://bioinformatics.oxfordjournals.org/cgi/reprint/27/5/715 https://www.ncbi.nlm.nih.gov/pmc/articles/pmid/21183585/pdf/?tool=EBI https://europepmc.org/articles/PMC3105477?pdf=render

Data source: Europe PubMed Central

Abstract
UNLABELLED: CompleteMOTIFs (cMOTIFs) is an integrated web tool developed to facilitate systematic discovery of overrepresented transcription factor binding motifs from high-throughput chromatin immunoprecipitation experiments. Comprehensive annotations and Boolean logic operations on multiple peak locations enable users to focus on genomic regions of interest for de novo motif discovery using tools such as MEME, Weeder and ChIPMunk. The pipeline incorporates a scanning tool for known motifs from TRANSFAC and JASPAR databases, and performs an enrichment test using local or precalculated background models that significantly improve the motif scanning result. Furthermore, using the cMOTIFs pipeline, we demonstrated that multiple transcription factors could cooperatively bind to the upstream of important stem cell differentiation regulators. AVAILABILITY: http://cmotifs.tchlab.org.
Autoren
  • Lakshmi Kuttippurathu
  • Michael Hsing
  • Yongchao Liu
  • Bertil Schmidt
  • Douglas L Maskell
  • Kyungjoon Lee
  • Aibin He
  • William T Pu
  • Sek Won Kong
Autoren-URL
https://www.ncbi.nlm.nih.gov/pubmed/21183585
DOI
10.1093/bioinformatics/btq707
eISSN
1367-4811
Externe Identifier
  • PubMed Central ID: PMC3105477
Funding acknowledgements
  • NHLBI NIH HHS: U01 HL098166
  • NHLBI NIH HHS: UM1 HL098166
  • NHLBI NIH HHS: HL098166
Ausgabe der Veröffentlichung
5
Zeitschrift
Bioinformatics
Schlüsselwörter
  • Algorithms
  • Binding Sites
  • DNA
  • Databases, Nucleic Acid
  • Internet
  • Models, Statistical
  • Molecular Sequence Annotation
  • Protein Binding
  • Protein Interaction Domains and Motifs
  • Sequence Analysis, DNA
  • Transcription Factors
Sprache
eng
Country
England
Paginierung
715 - 717
PII
btq707
Datum der Veröffentlichung
2011
Status
Published
Datum, an dem der Datensatz öffentlich gemacht wurde
2011
Titel
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments.
Sub types
  • Journal Article
  • Research Support, N.I.H., Extramural
  • Research Support, Non-U.S. Gov't
Ausgabe der Zeitschrift
27

Data source: PubMed

Autoren
  • Lakshmi Kuttippurathu
  • Michael Hsing
  • Yongchao Liu
  • Bertil Schmidt
  • Douglas L Maskell
  • Kyungjoon Lee
  • Aibin He
  • William T Pu
  • Sek Won Kong
Zeitschrift
Bioinform.
Artikelnummer
5
Paginierung
715 - 717
Datum der Veröffentlichung
2011
Titel
CompleteMOTIFs: DNA motif discovery platform for transcription factor binding experiments.
Ausgabe der Zeitschrift
27

Data source: DBLP

Beziehungen:
Property of

Tools