Literature DB >> 26334922

DNA Motif Databases and Their Uses.

Gary D Stormo1.   

Abstract

Transcription factors (TFs) recognize and bind to specific DNA sequences. The specificity of a TF is usually represented as a position weight matrix (PWM). Several databases of DNA motifs exist and are used in biological research to address important biological questions. This overview describes PWMs and some of the most commonly used motif databases, as well as a few of their common applications.
Copyright © 2015 John Wiley & Sons, Inc.

Keywords:  DNA motifs; binding site predictions; position weight matrices; transcription factors

Mesh：

Substances：

Year:  2015        PMID： 26334922     DOI： 10.1002/0471250953.bi0215s51

Source DB:  PubMed          Journal:  Curr Protoc Bioinformatics        ISSN： 1934-3396


  8 in total

1.  Rules of RNA specificity of hnRNP A1 revealed by global and quantitative analysis of its affinity distribution.

Authors:  Niyati Jain; Hsuan-Chun Lin; Christopher E Morgan; Michael E Harris; Blanton S Tolbert
Journal:  Proc Natl Acad Sci U S A       Date:  2017-02-13       Impact factor: 11.205

Review 2.  Past Roadblocks and New Opportunities in Transcription Factor Network Mapping.

Authors:  Michael R Brent
Journal:  Trends Genet       Date:  2016-10-06       Impact factor: 11.639

3.  Single base-pair resolution analysis of DNA binding motif with MoMotif reveals an oncogenic function of CTCF zinc-finger 1 mutation.

Authors:  Benjamin Lebeau; Kaiqiong Zhao; Maika Jangal; Tiejun Zhao; Maria Guerra; Celia M T Greenwood; Michael Witcher
Journal:  Nucleic Acids Res       Date:  2022-08-10       Impact factor: 19.160

4.  HOCOMOCO: expansion and enhancement of the collection of transcription factor binding sites models.

Authors:  Ivan V Kulakovskiy; Ilya E Vorontsov; Ivan S Yevshin; Anastasiia V Soboleva; Artem S Kasianov; Haitham Ashoor; Wail Ba-Alawi; Vladimir B Bajic; Yulia A Medvedeva; Fedor A Kolpakov; Vsevolod J Makeev
Journal:  Nucleic Acids Res       Date:  2015-11-19       Impact factor: 16.971

5.  JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework.

Authors:  Aziz Khan; Oriol Fornes; Arnaud Stigliani; Marius Gheorghe; Jaime A Castro-Mondragon; Robin van der Lee; Adrien Bessy; Jeanne Chèneby; Shubhada R Kulkarni; Ge Tan; Damir Baranasic; David J Arenillas; Albin Sandelin; Klaas Vandepoele; Boris Lenhard; Benoît Ballester; Wyeth W Wasserman; François Parcy; Anthony Mathelier
Journal:  Nucleic Acids Res       Date:  2018-01-04       Impact factor: 16.971

6.  An Enhancer's Length and Composition Are Shaped by Its Regulatory Task.

Authors:  Lily Li; Zeba Wunderlich
Journal:  Front Genet       Date:  2017-05-23       Impact factor: 4.599

7.  JASPAR 2020: update of the open-access database of transcription factor binding profiles.

Authors:  Oriol Fornes; Jaime A Castro-Mondragon; Aziz Khan; Robin van der Lee; Xi Zhang; Phillip A Richmond; Bhavi P Modi; Solenne Correard; Marius Gheorghe; Damir Baranašić; Walter Santana-Garcia; Ge Tan; Jeanne Chèneby; Benoit Ballester; François Parcy; Albin Sandelin; Boris Lenhard; Wyeth W Wasserman; Anthony Mathelier
Journal:  Nucleic Acids Res       Date:  2020-01-08       Impact factor: 16.971

8.  MANTA2, update of the Mongo database for the analysis of transcription factor binding site alterations.

Authors:  Oriol Fornes; Marius Gheorghe; Phillip A Richmond; David J Arenillas; Wyeth W Wasserman; Anthony Mathelier
Journal:  Sci Data       Date:  2018-07-24       Impact factor: 6.444
  8 in total

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