{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,4,15]],"date-time":"2026-04-15T14:29:00Z","timestamp":1776263340218,"version":"3.50.1"},"reference-count":51,"publisher":"Cold Spring Harbor Laboratory","issue":"9","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Genome Res."],"published-print":{"date-parts":[[2002,9,1]]},"abstract":"<jats:p>Evolutionarily conserved noncoding genomic sequences represent a potentially rich source for the discovery of gene regulatory regions. However, detecting and visualizing compositionally similar<jats:italic>cis<\/jats:italic>-element clusters in the context of conserved sequences is challenging. We have explored potential solutions and developed an algorithm and visualization method that combines the results of conserved sequence analyses (<jats:monospace>BLASTZ<\/jats:monospace>) with those of transcription factor binding site analyses (<jats:monospace>MatInspector<\/jats:monospace>) (<jats:ext-link xmlns:xlink=\"http:\/\/www.w3.org\/1999\/xlink\" ext-link-type=\"uri\" xlink:href=\"http:\/\/trafac.chmcc.org\" xlink:type=\"simple\">http:\/\/trafac.chmcc.org<\/jats:ext-link>). We define hits as the density of co-occurring <jats:italic>cis<\/jats:italic>-element transcription factor (TF)-binding sites measured within a 200-bp moving average window through phylogenetically conserved regions. The results are depicted as a Regulogram, in which the hit count is plotted as a function of position within each of the two genomic regions of the aligned orthologs. Within a high-scoring region, the relative arrangement of shared<jats:italic>cis<\/jats:italic>-elements within compositionally similar TF-binding site clusters is depicted in a Trafacgram. On the basis of analyses of several training data sets, the approach also allows for the detection of similarities in composition and relative arrangement of<jats:italic>cis<\/jats:italic>-element clusters within nonorthologous genes, promoters, and enhancers that exhibit coordinate regulatory properties. Known functional regulatory regions of nonorthologous and less-conserved orthologous genes frequently showed <jats:italic>cis<\/jats:italic>-element shuffling, demonstrating that compositional similarity can be more sensitive than sequence similarity. These results show that combining sequence similarity with <jats:italic>cis<\/jats:italic>-element compositional similarity provides a powerful aid for the identification of potential control regions.<\/jats:p>","DOI":"10.1101\/gr.255002","type":"journal-article","created":{"date-parts":[[2002,9,4]],"date-time":"2002-09-04T20:34:45Z","timestamp":1031171685000},"page":"1408-1417","source":"Crossref","is-referenced-by-count":72,"title":["Detection and Visualization of Compositionally Similar <i>cis<\/i>-Regulatory Element Clusters in Orthologous and Coordinately Controlled Genes"],"prefix":"10.1101","volume":"12","author":[{"given":"Anil G.","family":"Jegga","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shawn P.","family":"Sherwood","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"James W.","family":"Carman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew T.","family":"Pinski","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jerry L.","family":"Phillips","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"John P.","family":"Pestian","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bruce J.","family":"Aronow","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"246","published-online":{"date-parts":[[2002,9,1]]},"reference":[{"key":"2021111810472117000_12.9.1408.1","first-page":"1857","article-title":"The hard wiring of development: Organization and function of genomic regulatory sequences.","volume":"124","author":"Aronone","year":"1997","journal-title":"Development"},{"key":"2021111810472117000_12.9.1408.2","doi-asserted-by":"publisher","DOI":"10.1101\/gad.3.9.1384"},{"key":"2021111810472117000_12.9.1408.3","first-page":"4170","article-title":"Functional analysis of the human adenosine deaminase gene thymic regulatory region and its ability to generate position-independent transgene expression.","volume":"12","author":"Aronow","year":"1992","journal-title":"Mol. 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