{"id":10168,"date":"2020-06-29T09:36:52","date_gmt":"2020-06-29T09:36:52","guid":{"rendered":"https:\/\/bgrssb.icgbio.ru\/2020\/2020\/06\/29\/analysis-of-short-and-long-range-interactions-within-potential-binding-sites-notably-extends-the-fraction-of-verified-peaks-in-chip-seq-data\/"},"modified":"2020-07-07T08:27:19","modified_gmt":"2020-07-07T08:27:19","slug":"analysis-of-short-and-long-range-interactions-within-potential-binding-sites-notably-extends-the-fraction-of-verified-peaks-in-chip-seq-data","status":"publish","type":"post","link":"https:\/\/bgrssb.icgbio.ru\/2020\/2020\/06\/29\/analysis-of-short-and-long-range-interactions-within-potential-binding-sites-notably-extends-the-fraction-of-verified-peaks-in-chip-seq-data\/","title":{"rendered":"Analysis of short- and long-range interactions within potential binding sites notably extends the fraction of verified peaks in ChIP-seq data"},"content":{"rendered":"<p>Poster (<a href=\"https:\/\/bgrssb.icgbio.ru\/wp-content\/uploads\/2020\/07\/299.pdf\">download<\/a>)<\/p>\n<a href=\"https:\/\/bgrssb.icgbio.ru\/wp-content\/uploads\/2020\/07\/299.pdf\" class=\"pdfemb-viewer\" style=\"\" data-width=\"max\" data-height=\"max\"  data-toolbar=\"bottom\" data-toolbar-fixed=\"off\">299<br\/><\/a>\n<p>Anton Tsukanov<sup>1<\/sup>, Victor Levitsky<sup>2<\/sup>, Tatyana Merkulova<sup>3<\/sup><br \/><sup>1<\/sup>ICG SB RAS, Novosibirsk, Russia, tsukanov@bionet.nsc.ru<br \/><sup>2<\/sup>ICG SB RAS, Novosibirsk, Russia, levitsky@bionet.nsc.ru<br \/><sup>3<\/sup>ICG SB RAS, Novosibirsk, Russia, merkulova@bionet.nsc.ru<\/p>\n<p class=\"western\" lang=\"ru-RU\" align=\"justify\"><span style=\"font-size: small\"><span lang=\"en-US\"><b>We developed pipeline for integrative application of various de novo motif search tools to massive sequencing data. While traditional position weight matrices (PWMs) neglect dependencies between positions of motifs, the short-range interactions\u0432 markov models BAMM\/InMode permit only local dependencies, the long-range interaction model SiteGA allows dependencies between arbitrary positions. The massive analysis of ChIP-seq data have shown that the models BAMM\/InMode and PWMs recognized similar and significantly overlapped peaks; but the notable fractions of peaks predicted by SiteGA model were not predicted by other models. <\/b><\/span><\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>Poster (download) Anton Tsukanov1, Victor Levitsky2, Tatyana Merkulova31ICG SB RAS, Novosibirsk, Russia, tsukanov@bionet.nsc.ru2ICG SB RAS, Novosibirsk, Russia, levitsky@bionet.nsc.ru3ICG SB RAS, Novosibirsk, Russia, merkulova@bionet.nsc.ru We developed pipeline for integrative application of various de novo motif search tools to massive sequencing data. While traditional position weight matrices (PWMs) neglect dependencies between positions of motifs, the short-range interactions\u0432 markov models BAMM\/InMode permit only local dependencies, the long-range interaction model SiteGA allows dependencies between arbitrary positions. The massive analysis of ChIP-seq data have shown that the models BAMM\/InMode and PWMs recognized similar and significantly overlapped peaks; but the notable fractions of peaks predicted by SiteGA model were not predicted by other models.<\/p>\n","protected":false},"author":9,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":[],"categories":[2171],"tags":[1754,1756,1755],"_links":{"self":[{"href":"https:\/\/bgrssb.icgbio.ru\/2020\/wp-json\/wp\/v2\/posts\/10168"}],"collection":[{"href":"https:\/\/bgrssb.icgbio.ru\/2020\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/bgrssb.icgbio.ru\/2020\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2020\/wp-json\/wp\/v2\/users\/9"}],"replies":[{"embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2020\/wp-json\/wp\/v2\/comments?post=10168"}],"version-history":[{"count":1,"href":"https:\/\/bgrssb.icgbio.ru\/2020\/wp-json\/wp\/v2\/posts\/10168\/revisions"}],"predecessor-version":[{"id":12193,"href":"https:\/\/bgrssb.icgbio.ru\/2020\/wp-json\/wp\/v2\/posts\/10168\/revisions\/12193"}],"wp:attachment":[{"href":"https:\/\/bgrssb.icgbio.ru\/2020\/wp-json\/wp\/v2\/media?parent=10168"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2020\/wp-json\/wp\/v2\/categories?post=10168"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/bgrssb.icgbio.ru\/2020\/wp-json\/wp\/v2\/tags?post=10168"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}