Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments

Brian A. Kennedy, Xun Lan, Hui-ming Huang, Peggy J. Farnham, Victor X Jin

Research output: Chapter in Book/Report/Conference proceedingChapter

1 Citation (Scopus)

Abstract

DNA motifs are short sequences varying from 6 to 25 bp and can be highly variable and degenerated. One major approach for predicting transcription factor (TF) binding is using position weight matrix (PWM) to represent information content of regulatory sites; however, when used as the sole means of identifying binding sites suffers from the limited amount of training data available and a high rate of false-positive predictions. ChIPMotifs program is a de novo motif finding tool developed for ChIP-based high-throughput data, and W-ChIPMotifs is a Web application tool for ChIPMotifs. It composes various ab initio motif discovery tools such as MEME, MaMF, Weeder and optimizes the significance of the detected motifs by using bootstrap re-sampling error estimation and a Fisher test. Using these techniques, we determined a PWM for OCT4 which is similar to canonical OCT4 consensus sequence. In a separate study, we also use de novo motif discovery to suggest that ZNF263 binds to a 24-nt site that differs from the motif predicted by the zinc finger code in several positions.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
Pages323-334
Number of pages12
Volume802
DOIs
StatePublished - 2012
Externally publishedYes

Publication series

NameMethods in Molecular Biology
Volume802
ISSN (Print)10643745

Fingerprint

Position-Specific Scoring Matrices
Nucleotide Motifs
Selection Bias
Zinc Fingers
Consensus Sequence
Transcription Factors
Binding Sites

Keywords

  • ChIP
  • Motif
  • OCT4
  • Position weight matrix
  • ZNF263

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Kennedy, B. A., Lan, X., Huang, H., Farnham, P. J., & Jin, V. X. (2012). Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments. In Methods in Molecular Biology (Vol. 802, pp. 323-334). (Methods in Molecular Biology; Vol. 802). https://doi.org/10.1007/978-1-61779-400-1_21

Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments. / Kennedy, Brian A.; Lan, Xun; Huang, Hui-ming; Farnham, Peggy J.; Jin, Victor X.

Methods in Molecular Biology. Vol. 802 2012. p. 323-334 (Methods in Molecular Biology; Vol. 802).

Research output: Chapter in Book/Report/Conference proceedingChapter

Kennedy, BA, Lan, X, Huang, H, Farnham, PJ & Jin, VX 2012, Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments. in Methods in Molecular Biology. vol. 802, Methods in Molecular Biology, vol. 802, pp. 323-334. https://doi.org/10.1007/978-1-61779-400-1_21
Kennedy BA, Lan X, Huang H, Farnham PJ, Jin VX. Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments. In Methods in Molecular Biology. Vol. 802. 2012. p. 323-334. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-61779-400-1_21
Kennedy, Brian A. ; Lan, Xun ; Huang, Hui-ming ; Farnham, Peggy J. ; Jin, Victor X. / Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments. Methods in Molecular Biology. Vol. 802 2012. pp. 323-334 (Methods in Molecular Biology).
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