{"id":258,"date":"2013-05-21T20:22:27","date_gmt":"2013-05-21T18:22:27","guid":{"rendered":"http:\/\/jloliverlab.wordpress.com\/?page_id=258"},"modified":"2013-05-21T20:22:27","modified_gmt":"2013-05-21T18:22:27","slug":"cpg-island-database","status":"publish","type":"page","link":"https:\/\/alu.ugr.es\/bioinfo\/?page_id=258","title":{"rendered":"CpG island DB"},"content":{"rendered":"<p><a href=\"http:\/\/bioinfo2.ugr.es\/CpGislands\/\" target=\"_blank\">CpG island database<\/a><\/p>\n<div>\n<p>Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed\/expected ratio and length thresholds as main parameters. Recently, clustering methods directly detect clusters of CpG dinucleotides as a statistical property of the genome sequence.<\/p>\n<p>We compare sliding-window to clustering (i.e. <a href=\"http:\/\/bioinfo2.ugr.es\/CpGcluster\/\" target=\"_blank\"><em>CpGcluster<\/em><\/a>) predictions by applying new ways to detect putative functionality of CpG islands. Analyzing the co-localization with several genomic regions as a function of window size <em>vs<\/em>. statistical significance (<em>p-value<\/em>), <em>CpGcluster <\/em>shows a higher overlap with promoter regions and highly conserved elements, at the same time showing less overlap with <em>Alu <\/em>retrotransposons. The major difference in the prediction was found for short islands (CpG islets), often exclusively predicted by <em>CpGcluster<\/em>. Many of these islets seem to be functional, as they are unmethylated, highly conserved and\/or located within the promoter region. Finally, we show that window-based islands can spuriously overlap several, differentially regulated promoters as well as different methylation domains, which might indicate a wrong merge of several CpG islands into a single, very long island. The shorter <em>CpGcluster <\/em>islands seem to be much more specific when concerning the overlap with alternative transcription start sites or the detection of homogenous methylation domains.<\/p>\n<p>The main difference between sliding-window approaches and clustering methods is the length of the predicted islands. Short islands, often differentially methylated, are almost exclusively predicted by <em>CpGcluster<\/em>. This suggests that <em>CpGcluster <\/em>may be the algorithm of choice to explore the function of these short, but putatively functional CpG islands.<\/p>\n<p>[1] Hackenberg M, Previti C, Luque-Escamilla PL, Carpena P, Mart\u00ednez-Aroza J, Oliver JL. 2006.<br \/>\nCpGcluster: A distance-based algorithm for CpG-island detection.<br \/>\n<strong>BMC Bioinformatics 7: 446<\/strong><br \/>\n<a href=\"http:\/\/dx.doi.org\/10.1186\/1471-2105-7-446\" target=\"_blank\">http:\/\/dx.doi.org\/10.1186\/1471-2105-7-446<\/a><\/p>\n<p>[2] <a href=\"http:\/\/bioinfo2.ugr.es\/CpGcluster\/\" target=\"_blank\">http:\/\/bioinfo2.ugr.es\/CpGcluster\/<\/a><\/p>\n<\/div>\n","protected":false},"excerpt":{"rendered":"<p>CpG island database Unmethylated stretches of CpG dinucleotides (CpG islands) are an outstanding property of mammal genomes. Conventionally, these regions are detected by sliding window approaches using %G + C, CpG observed\/expected ratio and length thresholds as main parameters. Recently, clustering methods directly detect clusters of CpG dinucleotides as a statistical property of the genome [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"parent":0,"menu_order":38,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"class_list":["post-258","page","type-page","status-publish","hentry"],"blocksy_meta":[],"_links":{"self":[{"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=\/wp\/v2\/pages\/258","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=258"}],"version-history":[{"count":0,"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=\/wp\/v2\/pages\/258\/revisions"}],"wp:attachment":[{"href":"https:\/\/alu.ugr.es\/bioinfo\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=258"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}