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

@article{citeulike:5892010, abstract = {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. Availability: http://motif.bmi.ohio-state.edu/ChIPMotifs. Data used in the article may be downloaded from http://motif.bmi.ohio-state.edu/ChIPMotifs/examples.shtml. Contact: victor.jin@osumc.edu 10.1093/bioinformatics/btp570}, author = {Jin, Victor X. and Apostolos, Jeff and Nagisetty, Naga S. and Farnham, Peggy J.}, booktitle = {Bioinformatics}, citeulike-article-id = {5892010}, citeulike-linkout-0 = {http://dx.doi.org/10.1093/bioinformatics/btp570}, citeulike-linkout-1 = {http://bioinformatics.oxfordjournals.org/content/btp570v1/.abstract}, citeulike-linkout-2 = {http://bioinformatics.oxfordjournals.org/content/btp570v1/.full.pdf}, citeulike-linkout-3 = {http://bioinformatics.oxfordjournals.org/cgi/content/abstract/25/23/3191}, citeulike-linkout-4 = {http://view.ncbi.nlm.nih.gov/pubmed/19797408}, citeulike-linkout-5 = {http://www.hubmed.org/display.cgi?uids=19797408}, day = {1}, doi = {10.1093/bioinformatics/btp570}, issn = {1460-2059}, journal = {Bioinformatics}, keywords = {chip, motif}, month = {December}, number = {23}, pages = {3191--3193}, posted-at = {2009-10-08 10:06:32}, priority = {2}, title = {W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data}, url = {http://dx.doi.org/10.1093/bioinformatics/btp570}, volume = {25}, year = {2009} }

TY - JOUR ID - citeulike:5892010 L3 - citeulike-article-id:5892010 N2 - 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. Availability: http://motif.bmi.ohio-state.edu/ChIPMotifs. Data used in the article may be downloaded from http://motif.bmi.ohio-state.edu/ChIPMotifs/examples.shtml. Contact: victor.jin@osumc.edu 10.1093/bioinformatics/btp570 IS - 23 JF - Bioinformatics SN - 1460-2059 EP - 3193 TI - W-ChIPMotifs: a web application tool for de novo motif discovery from ChIP-based high-throughput data VL - 25 T2 - Bioinformatics SP - 3191 KW - chip KW - motif AU - Jin, Victor AU - Apostolos, Jeff AU - Nagisetty, Naga AU - Farnham, Peggy PY - 2009/12/01/ UR - http://dx.doi.org/10.1093/bioinformatics/btp570 ER -