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
Externally publishedYes

Fingerprint

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

ASJC Scopus subject areas

  • Statistics and Probability
  • Biochemistry
  • Molecular Biology
  • Computer Science Applications
  • Computational Theory and Mathematics
  • Computational Mathematics

Cite this

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, 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.
@article{ae7a5b9a58a240869e8f1b3552f8fa82,
title = "W-ChIPMotifs: A web application tool for de novo motif discovery from ChIP-based high-throughput data",
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.",
author = "Jin, {Victor X} and Jeff Apostolos and {Ra Nagisetty}, {Naga Satya Venkateswara} and Farnham, {Peggy J.}",
year = "2009",
month = "10",
day = "1",
doi = "10.1093/bioinformatics/btp570",
language = "English (US)",
volume = "25",
pages = "3191--3193",
journal = "Bioinformatics",
issn = "1367-4803",
publisher = "Oxford University Press",
number = "23",

}

TY - JOUR

T1 - W-ChIPMotifs

T2 - A web application tool for de novo motif discovery from ChIP-based high-throughput data

AU - Jin, Victor X

AU - Apostolos, Jeff

AU - Ra Nagisetty, Naga Satya Venkateswara

AU - Farnham, Peggy J.

PY - 2009/10/1

Y1 - 2009/10/1

N2 - 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.

AB - 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.

UR - http://www.scopus.com/inward/record.url?scp=75949114262&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=75949114262&partnerID=8YFLogxK

U2 - 10.1093/bioinformatics/btp570

DO - 10.1093/bioinformatics/btp570

M3 - Article

VL - 25

SP - 3191

EP - 3193

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 23

M1 - btp570

ER -