{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T10:12:50Z","timestamp":1760955170504,"version":"3.37.0"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"23","license":[{"start":{"date-parts":[[2016,10,2]],"date-time":"2016-10-02T00:00:00Z","timestamp":1475366400000},"content-version":"vor","delay-in-days":2558,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/2.0\/uk\/"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2009,12,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Summary: 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.<\/jats:p><jats:p>Availability: \u00a0http:\/\/motif.bmi.ohio-state.edu\/ChIPMotifs. Data used in the article may be downloaded from http:\/\/motif.bmi.ohio-state.edu\/ChIPMotifs\/examples.shtml.<\/jats:p><jats:p>Contact: \u00a0victor.jin@osumc.edu<\/jats:p>","DOI":"10.1093\/bioinformatics\/btp570","type":"journal-article","created":{"date-parts":[[2009,10,2]],"date-time":"2009-10-02T01:23:54Z","timestamp":1254446634000},"page":"3191-3193","source":"Crossref","is-referenced-by-count":37,"title":["W-ChIPMotifs: a web application tool for<i>de novo<\/i>motif discovery from ChIP-based high-throughput data"],"prefix":"10.1093","volume":"25","author":[{"given":"Victor X.","family":"Jin","sequence":"first","affiliation":[{"name":"1 Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, 2 Bioinformatics Program, The University of Memphis, Memphis, TN 38152 and 3 The Genome Center, The University of California, Davis, CA 95616, USA"}]},{"given":"Jeff","family":"Apostolos","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, 2 Bioinformatics Program, The University of Memphis, Memphis, TN 38152 and 3 The Genome Center, The University of California, Davis, CA 95616, USA"}]},{"given":"Naga Satya Venkateswara Ra","family":"Nagisetty","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, 2 Bioinformatics Program, The University of Memphis, Memphis, TN 38152 and 3 The Genome Center, The University of California, Davis, CA 95616, USA"}]},{"given":"Peggy J.","family":"Farnham","sequence":"additional","affiliation":[{"name":"1 Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210, 2 Bioinformatics Program, The University of Memphis, Memphis, TN 38152 and 3 The Genome Center, The University of California, Davis, CA 95616, USA"}]}],"member":"286","published-online":{"date-parts":[[2009,10,1]]},"reference":[{"key":"2023013112193566800_B1","first-page":"21","article-title":"The value of prior knowledge in discovering motifs with MEME","volume":"3","author":"Bailey","year":"1995","journal-title":"Proc. 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