W-ChIPMotifs: A web application tool for de novo motif discovery from ChIP-based high-throughput data

Victor X. Jin, Jeff Apostolos, Naga Satya Venkateswara Ra Nagisetty, Peggy J. Farnham

Research output: Contribution to journalArticle

37 Citations (Scopus)

Abstract

W-ChIPMotifs is a web application tool that provides a user friendly interface for de novo motif discovery. The web tool is based on our previous ChIPMotifs program which is a de novo motif finding tool developed for ChIP-based high-throughput data and incorporated various ab initio motif discovery tools such as MEME, MaMF, Weeder and optimized the significance of the detected motifs by using a bootstrap resampling statistic method and a Fisher test. Use of a randomized statistical model like bootstrap resampling can significantly increase the accuracy of the detected motifs. In our web tool, we have modified the program in two aspects: (i) we have refined the P-value with a Bonferroni correction; (ii) we have incorporated the STAMP tool to infer phylogenetic information and to determine the detected motifs if they are novel and known using the TRANSFAC and JASPAR databases. A comprehensive result file is mailed to users.

Original languageEnglish (US)
Article numberbtp570
Pages (from-to)3191-3193
Number of pages3
JournalBioinformatics
Volume25
Issue number23
DOIs
StatePublished - Oct 1 2009

Fingerprint

Motif Discovery
Statistical Models
Web Application
High Throughput
Chip
Throughput
Databases
Resampling
Bootstrap
Bonferroni
Phylogenetics
User Interface
Statistical Model
User interfaces
Statistic
Statistics

ASJC Scopus subject areas

  • Biochemistry
  • Molecular Biology
  • Computational Theory and Mathematics
  • Computer Science Applications
  • Computational Mathematics
  • Statistics and Probability
  • Medicine(all)

Cite this

Jin, V. X., Apostolos, J., Ra Nagisetty, N. S. V., & Farnham, P. J. (2009). W-ChIPMotifs: A web application tool for de novo motif discovery from ChIP-based high-throughput data. Bioinformatics, 25(23), 3191-3193. [btp570]. https://doi.org/10.1093/bioinformatics/btp570

W-ChIPMotifs : A web application tool for de novo motif discovery from ChIP-based high-throughput data. / Jin, Victor X.; Apostolos, Jeff; Ra Nagisetty, Naga Satya Venkateswara; Farnham, Peggy J.

In: Bioinformatics, Vol. 25, No. 23, btp570, 01.10.2009, p. 3191-3193.

Research output: Contribution to journalArticle

Jin, VX, Apostolos, J, Ra Nagisetty, NSV & Farnham, PJ 2009, 'W-ChIPMotifs: A web application tool for de novo motif discovery from ChIP-based high-throughput data', Bioinformatics, vol. 25, no. 23, btp570, pp. 3191-3193. https://doi.org/10.1093/bioinformatics/btp570
Jin, Victor X. ; Apostolos, Jeff ; Ra Nagisetty, Naga Satya Venkateswara ; Farnham, Peggy J. / W-ChIPMotifs : A web application tool for de novo motif discovery from ChIP-based high-throughput data. In: Bioinformatics. 2009 ; Vol. 25, No. 23. pp. 3191-3193.
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