title: Using ChIPMotifs for de novo motif discovery of OCT4 and ZNF263 based on ChIP-based high-throughput experiments.
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.
authors: Department of Biomedical Informatics, The Ohio State University, Columbus, OH, USA.
authors: Brian A
authors: BA
authors: Kennedy
authors: Xun
authors: X
authors: Lan
authors: Tim H-M
authors: TH
authors: Huang
authors: Peggy J
authors: PJ
authors: Farnham
authors: Victor X
authors: VX
authors: Jin
mesh_terms: D000818:Animals; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D047369:Chromatin Immunoprecipitation; D004268:DNA-Binding Proteins / Q000378:metabolism*; D006801:Humans; D020407:Internet; D051379:Mice; D059372:Nucleotide Motifs; D050814:Octamer Transcription Factor-3 / Q000378:metabolism*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D016335:Zinc Fingers
chemical_list: D004268:DNA-Binding Proteins; D050814:Octamer Transcription Factor-3