{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,26]],"date-time":"2026-08-26T03:22:01Z","timestamp":1787714521805,"version":"build-2784847793"},"reference-count":24,"publisher":"Oxford University Press (OUP)","issue":"3","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2005,2,1]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Motivation: Transcription-factor binding sites (TFBS) in promoter sequences of higher eukaryotes are commonly modeled using position frequency matrices (PFM). The ability to compare PFMs representing binding sites is especially important for de novo sequence motif discovery, where it is desirable to compare putative matrices to one another and to known matrices.<\/jats:p><jats:p>Results: We describe a PFM similarity quantification method based on product multinomial distributions, demonstrate its ability to identify PFM similarity and show that it has a better false positive to false negative ratio compared to existing methods.<\/jats:p><jats:p>We grouped TFBS frequency matrices from two libraries into matrix families and identified the matrices that are common and unique to these libraries. We identified similarities and differences between the skeletal-muscle-specific and non-muscle-specific frequency matrices for the binding sites of Mef-2, Myf, Sp-1, SRF and TEF of Wasserman and Fickett. We further identified known frequency matrices and matrix families that were strongly similar to the matrices given by Wasserman and Fickett. We provide methodology and tools to compare and query libraries of frequency matrices for TFBSs.<\/jats:p><jats:p>Availability: Software is available to use over the Web at http:\/\/rulai.cshl.edu\/MatCompare<\/jats:p><jats:p>Contact: \u00a0dschones@cshl.edu<\/jats:p><jats:p>Supplementary information: Database and clustering statistics, matrix families and representatives are available at http:\/\/rulai.cshl.edu\/MatCompare\/Supplementary<\/jats:p>","DOI":"10.1093\/bioinformatics\/bth480","type":"journal-article","created":{"date-parts":[[2004,8,20]],"date-time":"2004-08-20T02:54:50Z","timestamp":1092970490000},"page":"307-313","source":"Crossref","is-referenced-by-count":82,"title":["Similarity of position frequency matrices for transcription factor binding sites"],"prefix":"10.1093","volume":"21","author":[{"given":"Dustin E.","family":"Schones","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pavel","family":"Sumazin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Michael Q.","family":"Zhang","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2004,8,19]]},"reference":[{"key":"2023051305563581800_B1","doi-asserted-by":"crossref","unstructured":"Agresti, A. 1992A survey of exact inference for contingency tables. Stat. Sci.7131\u2013177","DOI":"10.1214\/ss\/1177011454"},{"key":"2023051305563581800_B2","unstructured":"Berg, O.G. and von Hippel, P. 1987Selection of DNA binding sites by regulatory proteins. Statistical-mechanical theory and application to operators and promoters. J. Mol. Bio.193723\u2013750"},{"key":"2023051305563581800_B3","unstructured":"Berg, O.G. and von Hippel, P. 1988Selection of DNA binding sites by regulatory proteins II: the binding specificity of cyclic AMP receptor protein to recognition sites. J. Mol. Biol.200709\u2013723"},{"key":"2023051305563581800_B4","doi-asserted-by":"crossref","unstructured":"Eisen, M., Spellman, P., Brown, P., Botstein, D. 1998Cluster analysis and display of genome-wide expression patterns. Proc. Natl Acad. Sci. USA9514863\u201314868","DOI":"10.1073\/pnas.95.25.14863"},{"key":"2023051305563581800_B5","doi-asserted-by":"crossref","unstructured":"Fleiss, J.L., Levin, B., Paik, M.C. Statistical Methods for Rates and Proportions2003, NY John Wiley & Sons","DOI":"10.1002\/0471445428"},{"key":"2023051305563581800_B6","doi-asserted-by":"crossref","unstructured":"Hertz, G., Hartzell, G., III, Stormo, G. 1990Identification of consensus patterns in unaligned DNA sequences known to be functionally related. Comput. Appl. Biosci.6, pp. 81\u201392","DOI":"10.1093\/bioinformatics\/6.2.81"},{"key":"2023051305563581800_B7","doi-asserted-by":"crossref","unstructured":"Hertz, G. and Stormo, G. 1999Identifying DNA and protein patterns with statistically significant alignments of multiple sequences. Bioinformatics15563\u2013577","DOI":"10.1093\/bioinformatics\/15.7.563"},{"key":"2023051305563581800_B8","unstructured":"Hughes, J.D., Estep, P.W., Tavozoie, S., Church, G.M. 2000Computational identification of Cis-regulatory elements associated with groups of functionally related genes in Saccharomyces cerevisiae . J. Mol. Biol.2961205\u20131214"},{"key":"2023051305563581800_B9","doi-asserted-by":"crossref","unstructured":"Kaufman, L. and Rousseeuw, P.J. Finding Groups in Data\u2014An Introduction to Cluster Analysis1990, NY John Wiley & Sons","DOI":"10.1002\/9780470316801"},{"key":"2023051305563581800_B10","doi-asserted-by":"crossref","unstructured":"Knuppel, R., Dietze, P., Lehnberg, W., Frech, K., Wingender, E. 1994TRANSFAC retrieval program: a network model database of eukaryotic transcription regulating sequences and proteins. J. Comput. Biol.1, pp. 191\u2013198","DOI":"10.1089\/cmb.1994.1.191"},{"key":"2023051305563581800_B11","unstructured":"Lenhard, B. and Wasserman, W.W. 2002TFBS: computational framework for transcription factor binding site analysis. Bioinformatics181135\u20131136"},{"key":"2023051305563581800_B12","doi-asserted-by":"crossref","unstructured":"Liu, J.S., Lawrence, C.E., Neuwald, A. 1995Bayesian models for multiple local sequence alignment and its Gibbs sampling strategies. J. Am. Stat. Assoc.901156\u20131170","DOI":"10.2307\/2291508"},{"key":"2023051305563581800_B13","doi-asserted-by":"crossref","unstructured":"Mitsui, K.K., Shirakata, M., Paterson, B.M. 1993Phosphorylation inhibits the DNA-binding activity of MyoD homodimers but not MyoD-E12 heterodimers. J. Biol. Chem.26824415\u201324420","DOI":"10.1016\/S0021-9258(20)80541-9"},{"key":"2023051305563581800_B14","unstructured":"Needleman, S. and Wunsch, C. 1970A general method applicable to the search for similarities in the amino acid sequence of two proteins. J. Mol. Biol.48443\u2013453"},{"key":"2023051305563581800_B15","unstructured":"Pietrokovski, S. 1996Searching databases of conserved sequence regions by aligning protein multiple-alignments. Nucleic Acids Res.243836\u20133845"},{"key":"2023051305563581800_B16","doi-asserted-by":"crossref","unstructured":"Sandelin, A., Alkema, W., Engstr\u00f6m, P., Wasserman, W.W., Lenhard, B. 2004JASPAR: an open access database for eukaryotic transcription factor binding profiles. Nucleic Acids Res.32D91\u2013D94","DOI":"10.1093\/nar\/gkh012"},{"key":"2023051305563581800_B17","doi-asserted-by":"crossref","unstructured":"Sandelin, A. and Wasserman, W.W. 2004Constrained binding site diversity within families of transcription factors enhances pattern discovery bioinformatics. J. Mol. Biol.338207\u2013215","DOI":"10.1016\/j.jmb.2004.02.048"},{"key":"2023051305563581800_B18","doi-asserted-by":"crossref","unstructured":"Schneider, T.D. and Stephens, R.M. 1990Sequence logos: a new way to display consensus sequences. Nucleic Acids Res.186097\u20136100","DOI":"10.1093\/nar\/18.20.6097"},{"key":"2023051305563581800_B19","unstructured":"Schneider, T.D., Stormo, G.D., Gold, L., Ehrenfeucht, A. 1982Use of the \u2018Perceptron\u2019 algorithm to distinguish translational initiation sites in E.coli . Nucleic Acids Res.102997\u20133011"},{"key":"2023051305563581800_B20","unstructured":"Schneider, T.D., Stormo, G.D., Gold, L., Ehrenfeucht, A. 1986Information content of binding sites on nucleotide sequences. J. Mol. Biol.188415\u201331"},{"key":"2023051305563581800_B21","doi-asserted-by":"crossref","unstructured":"Staden, R. 1984Computer methods to locate signals in nucleic acid sequences. Nucleic Acids Res.12505\u2013519","DOI":"10.1007\/978-1-4684-4973-0_4"},{"key":"2023051305563581800_B22","doi-asserted-by":"crossref","unstructured":"Stormo, G.D. and Hartzell, G., III. 1989Identifying protein-binding sites from unaligned DNA fragments. Proc. Natl Acad. Sci. USA861183\u20131187","DOI":"10.1073\/pnas.86.4.1183"},{"key":"2023051305563581800_B23","doi-asserted-by":"crossref","unstructured":"Wang, T. and Stormo, G.D. 2003Combining phylogenetic data with co-regulated genes to identify regulatory motifs. Bioinformatics192369\u20132380","DOI":"10.1093\/bioinformatics\/btg329"},{"key":"2023051305563581800_B24","unstructured":"Wasserman, W.W. and Fickett, J.W. 1998Identification of regulatory regions which confer muscle-specific gene expression. J. Mol. Biol.278167\u2013181"}],"container-title":["Bioinformatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/3\/307\/50305673\/bioinformatics_21_3_307.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article-pdf\/21\/3\/307\/50305673\/bioinformatics_21_3_307.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,12,18]],"date-time":"2024-12-18T09:45:40Z","timestamp":1734515140000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/bioinformatics\/article\/21\/3\/307\/237585"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2004,8,19]]},"references-count":24,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2005,2,1]]}},"URL":"https:\/\/doi.org\/10.1093\/bioinformatics\/bth480","relation":{},"ISSN":["1367-4811","1367-4803"],"issn-type":[{"value":"1367-4811","type":"electronic"},{"value":"1367-4803","type":"print"}],"subject":[],"published-other":{"date-parts":[[2005,2,1]]},"published":{"date-parts":[[2004,8,19]]}}}