{"id":1719,"date":"2023-04-12T01:32:36","date_gmt":"2023-04-11T16:32:36","guid":{"rendered":"https:\/\/bdsl.jbnu.ac.kr\/blog\/?p=1719"},"modified":"2023-04-12T01:37:15","modified_gmt":"2023-04-11T16:37:15","slug":"patterns-in-tfbs","status":"publish","type":"post","link":"https:\/\/bdsl.jbnu.ac.kr\/blog\/patterns-in-tfbs\/","title":{"rendered":"Patterns in TFBS"},"content":{"rendered":"\n<p class=\"wp-block-paragraph\">\uc804\uc0ac\uc778\uc790(transcription factor, TF)\ub294 \ud2b9\uc815 \uc11c\uc5f4\uc744 \uc9c0\ub2cc DNA\uc5d0 \uacb0\ud569\ud558\uc5ec \uc720\uc804\uc790\uc758 \ubc1c\ud604\uc744 \uc870\uc808\ud55c\ub2e4. \uc804\uc0ac \uc778\uc790\uac00 \uacb0\ud569\ud558\ub294 \ubd80\uc704\ub97c <strong>transcription factor binding site (TFBS)<\/strong>\ub77c\uace0 \ud55c\ub2e4. TFBS\ub294 <strong>CHromosome ImmunoPrecipitation (ChIP)<\/strong> \uc2e4\ud5d8\uc744 \ud1b5\ud574 \ucc3e\uc744 \uc218 \uc788\ub2e4. ChIP\ub294 \ud2b9\uc815 \uc804\uc0ac\uc778\uc790\ub97c \ud2b9\uc774\uc801\uc73c\ub85c \uc778\uc9c0\ud558\uc5ec \uacb0\ud569\ud558\ub294 \ud56d\uccb4\ub97c \uc774\uc6a9\ud558\uc5ec \uc804\uc0ac\uc778\uc790\ub97c \ub18d\ucd95\uc2dc\ud0a4\ub294 \uc2e4\ud5d8 \ubc29\ubc95\uc774\ub2e4. \uc774 \ub54c \uc804\uc0ac\uc778\uc790\uc5d0 \uacb0\ud569\ub418\uc5b4 \uc788\ub294 genomic DNA\ub3c4 \uac19\uc774 \ub18d\ucd95\ub41c\ub2e4. \uc774\ub807\uac8c \ub18d\ucd95\ub41c DNA\uc758 \uc11c\uc5f4\uc744 <strong>next generation sequencing (NGS)<\/strong> \uae30\ubc95\uc744 \uc774\uc6a9\ud574 \ucc3e\uc744 \uc218 \uc788\ub2e4. \uc774\ub807\uac8c ChIP \ubc29\ubc95\uacfc NGS \uae30\ubc95\uc744 \uac19\uc774 \uc0ac\uc6a9\ud558\ub294 \uac83\uc744 <strong>ChIP-Seq<\/strong>\uc774\ub77c \ud55c\ub2e4. \uc774\ub807\uac8c \uc5bb\uc740 \uc11c\uc5f4\uc5d0\uc11c \ubc18\ubcf5\ub418\ub294 \uc11c\uc5f4 \ud639\uc740 <strong>pattern (sequence motif<\/strong>)\uc740 <strong>MEME(Multiple Em for Motif Elicitation)<\/strong>\uc640 \uac19\uc740  \ud504\ub85c\uadf8\ub7a8\uc744 \uc774\uc6a9\ud574 \ucc3e\uc744 \uc218 \uc788\ub2e4. <\/p>\n\n\n\n<h2 class=\"wp-block-heading\">\uc5f0\uc2b5 \uc608\uc81c<\/h2>\n\n\n\n<p class=\"wp-block-paragraph\">\uc5ec\uae30\uc11c\ub294 \uac04\ub2e8\ud55c \uc608\uc81c\ub97c \uc774\uc6a9\ud574 DNA \uc11c\uc5f4\uc5d0\uc11c pattern\uc744 \ucc3e\ub294 \uacfc\uc815\uc744 \uc9c4\ud589\ud55c\ub2e4. <\/p>\n\n\n\n<h3 class=\"wp-block-heading\">1. \uc11c\uc5f4 \ub370\uc774\ud130 \ud655\ubcf4\ud558\uae30<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">\uc804\uc0ac\uc778\uc790 \uacb0\ud569 DNA\uc758 \uc11c\uc5f4\uc744 \uc54c\uae30\uc704\ud574\uc11c\ub294 ChIP-Seq\uacfc \uac19\uc740 \uc2e4\ud5d8\uc774 \ud544\uc694\ud558\ub2e4. \uc5ec\uae30\uc11c\ub294 \uc2e4\ud5d8 \uacb0\uacfc\ub97c \ubaa8\uc544\ub454 ENCODE database\uc5d0 \uc788\ub294 \ub370\uc774\ud130\ub97c \uc774\uc6a9\ud55c\ub2e4. \uc608\uc81c\ub85c \uc0ac\uc6a9\ud558\ub294 \ub370\uc774\ud130\ub294 \uc804\uc0ac\uc778\uc9c0 MYC\uc5d0 \ub300\ud55c \uc2e4\ud5d8\uacb0\uacfc(https:\/\/www.encodeproject.org\/experiments\/ENCSR784BVD\/) \uc911 500\uac1c\uc758 \uc11c\uc5f4\ub9cc \ub530\ub85c \ubaa8\uc740 \ub370\uc774\ud130\ub85c \uc544\ub798\uc640 \uac19\uc774 FASTA \ud3ec\uba67\uc73c\ub85c \uc11c\uc5f4 \uc815\ubcf4\uac00 \uae30\uc785\ub418\uc5b4 \uc788\ub2e4.<\/p>\n\n\n\n<pre class=\"wp-block-code\"><code lang=\"vim\" class=\"language-vim\">&gt;NS500343:231:H33YLBGX3:1:11101:17526:1038 1:N:0:TGGGAGT\nCCTGANCTAGGTAGTTCCAAAGCTGCACTCCTGGAGCTTTTGCCCTCACAGCTGGCGTGGCTTTTTGGTTAATACT\n&gt;NS500343:231:H33YLBGX3:1:11101:24028:1038 1:N:0:TGGGAGT\nGGAGGNTGCAGTGAGCCGAGATCGCACCACTGCACTCTAGCCTGGGGGACAGAGCGAGACTCCGTCTCAAAGATCG\n&gt;NS500343:231:H33YLBGX3:1:11101:9331:1040 1:N:0:TGGGAGT\nCCCTTNCTGCTCACCTGGCAGCAGCTGCTTGTTAGACCCTGGAGGAACTCCAAGAGGAGAGCCACAGAGTCTGACA\n&gt;NS500343:231:H33YLBGX3:1:11101:21757:1040 1:N:0:TGGGAGA\nCTTTGNGCCTGGGGGAGTTGCACAGGTGAGCTGGGGCCTCACCACTTGCAGCAGGTCAGGAGTTTGGGTCCTAGCA\n&gt;NS500343:231:H33YLBGX3:1:11101:13759:1042 1:N:0:TGGGAGT\nCGAGGNGCGGGCTCCGGCCTGGGCAAGCGGGTACGCGGCGGAGGCCCCGCAGCGGGGCGGGGAGGGAGGCGTGCGG\n<\/code><\/pre>\n\n\n\n<p class=\"wp-block-paragraph\"><strong>Example file<\/strong><\/p>\n\n\n\n<p class=\"wp-block-paragraph\">\uc544\ub798 \uc608\uc81c \ud30c\uc77c\uc744 \ub2e4\uc6b4\ubc1b\ub294\ub2e4. <\/p>\n\n\n\n<div class=\"wp-block-file\"><a id=\"wp-block-file--media-87ed931e-39a6-4b30-a72d-38bfdf46a1f8\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/MYC_500_reads.txt\" target=\"_blank\" rel=\"noreferrer noopener\">MYC_500_reads<\/a><a href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/MYC_500_reads.txt\" class=\"wp-block-file__button wp-element-button\" download aria-describedby=\"wp-block-file--media-87ed931e-39a6-4b30-a72d-38bfdf46a1f8\">Download<\/a><\/div>\n\n\n\n<h3 class=\"wp-block-heading\">2. MEME-Chip\uc744 \uc774\uc6a9\ud55c motif \ucc3e\uae30<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">\ub2e4\uc218\uc758 \uc11c\uc5f4\uc774 \uc9c0\ub2cc <strong>pattern <\/strong>\ud639\uc740 <strong>sequence motif<\/strong>\ub294 MEME(Multiple Em for Motif Elicitation)\uc640 \uac19\uc740 \ud504\ub85c\uadf8\ub7a8\uc744 \uc774\uc6a9\ud558\uc5ec \ucc3e\uc744 \uc218 \uc788\ub2e4. MEME\ub294 web\uc744 \ud1b5\ud574 \uc2e4\ud589\ud560 \uc218 \uc788\ub2e4. \uc5ec\uae30\uc11c\ub294 ChIP\uc5d0 \ud2b9\ud654\ub41c MEME-ChIP\ub97c \uc774\uc6a9\ud55c\ub2e4. \uc544\ub798\uc758 \uacfc\uc815\uc744 \ud1b5\ud574 DNA motif\ub97c \ucc3e\ub294\ub2e4.<\/p>\n\n\n\n<ol class=\"wp-block-list\">\n<li>MEME-ChIP web site\uc5d0 \uc811\uc18d\ud55c\ub2e4\n<ul class=\"wp-block-list\">\n<li><a href=\"https:\/\/meme-suite.org\/meme\/tools\/meme-chip\">https:\/\/meme-suite.org\/meme\/tools\/meme-chip<\/a><\/li>\n<\/ul>\n<\/li>\n\n\n\n<li>\ud30c\uc77c\uc744 \uc5c5\ub85c\ub4dc \ud55c\ub2e4. (MYC_500_reads.txt)<\/li>\n\n\n\n<li>\uc2e4\ud589 \ubc84\ud2bc(Start Search)\ub97c \ud074\ub9ad\ud55c\ub2e4.<\/li>\n\n\n\n<li>\uacb0\uacfc\uac00 \ub098\uc62c \ub54c \uae4c\uc9c0 \uae30\ub2e4\ub9b0\ub2e4.\n<ul class=\"wp-block-list\">\n<li>\uc11c\ubc84 \uc0c1\ud669\uc5d0 \ub530\ub77c \uacb0\uacfc\uac00 \ub098\uc62c \ub54c\uae4c\uc9c0 \uc2dc\uac04\uc774 \uc18c\uc694\ub41c\ub2e4. <\/li>\n\n\n\n<li>URL \uc8fc\uc18c\ub97c \ubcf5\uc0ac\ud558\uc5ec \ubcf4\uad00\ud558\uba74, \uc2dc\uac04\uc774 \uc9c0\ub09c\ub4a4 URL\uc744 \ud1b5\ud574 \uacb0\uacfc\ub97c \ud655\uc778\ud560 \uc218 \uc788\ub2e4. <\/li>\n\n\n\n<li>\ub2e4\ub9cc, \uc11c\ubc84\uc5d0 \uc800\uc7a5\ub41c \uacb0\uacfc\ub294 \uc77c\uc815\uc2dc\uac04\uc774 \uc9c0\ub098\uba74 \uc0ac\ub77c\uc9c4\ub2e4. (URL\uc744 \ud1b5\ud55c \uc811\uadfc \ubd88\uac00)<\/li>\n<\/ul>\n<\/li>\n<\/ol>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"742\" height=\"872\" src=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/meme_chip_practice.png\" alt=\"\" class=\"wp-image-1728\" srcset=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/meme_chip_practice.png 742w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/meme_chip_practice-255x300.png 255w\" sizes=\"auto, (max-width: 742px) 100vw, 742px\" \/><\/figure>\n\n\n\n<h3 class=\"wp-block-heading\">3. Motif \ubd84\uc11d\ud558\uae30<\/h3>\n\n\n\n<p class=\"wp-block-paragraph\">MEME ChIP-Seq \uc2e4\ud589 \uacb0\uacfc \ubc1c\uacac\ud55c sequence motif(pattern)\ub97c web server\uc5d0\uc11c \ubc14\ub85c \ud655\uc778\ud560 \uc218 \uc788\ub2e4. \uacc4\uc0b0\uc774 \uc644\ub8cc\ub418\uba74 \uc544\ub798\uc640 \uac19\uc774 \ud654\uba74\uc774 \uc804\ud658\ub41c\ub2e4. <\/p>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"879\" height=\"550\" src=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/image.png\" alt=\"\" class=\"wp-image-1733\" srcset=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/image.png 879w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/image-300x188.png 300w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/image-768x481.png 768w\" sizes=\"auto, (max-width: 879px) 100vw, 879px\" \/><\/figure>\n\n\n\n<p class=\"wp-block-paragraph\">\uacb0\uacfc \ud654\uba74\uc5d0\uc11c, MEME-ChIP HTML output link\ub97c \ud074\ub9ad\ud558\uba74 \uc544\ub798\uc640 \uac19\uc774 \uac01\uac01\uc758 \uc704\uce58\uc5d0 \ub530\ub77c \ud2b9\uc815\ud55c nucleotide\uac00 \ub9ce\uc774 \uad00\ucc30\ub418\ub294 \uac83\uc744 \ud655\uc778 \ud560 \uc218 \uc788\ub2e4. DNA \ud639\uc740 protein \uc11c\uc5f4\uc758 pattern\uc744 \ud574\ub2f9 \uc704\uce58\uc758 \uae00\uc790\uc758 \ud06c\uae30\ub85c \ud45c\ud604\ud558\ub294 \ubc29\ubc95\uc744 <strong>WebLogo<\/strong>\ub77c \ud558\uba70, \uc790\uc138\ud55c \uc124\uba85\uc740<a href=\"https:\/\/weblogo.berkeley.edu\/\">https:\/\/weblogo.berkeley.edu\/<\/a>\uc5d0\uc11c \ucc3e\uc744 \uc218 \uc788\ub2e4. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">\ucd1d 4\uac1c\uc758 motif\uac00 \ucc3e\uc544\uc9c4 \uac83\uc744 \ud655\uc778\ud560 \uc218 \uc788\ub2e4. \uc989, \uc804\uc0ac\uc778\uc790 MYC\ub294 \uc544\ub798\uc640 \uac19\uc740 \uc11c\uc5f4\uc5d0 \uacb0\ud569\ud560 \uac00\ub2a5\uc131\uc774 \ub192\ub2e4\uace0 \ud560 \uc218 \uc788\ub2e4. <\/p>\n\n\n\n<p class=\"wp-block-paragraph\">(*) \ud558\uc9c0\ub9cc, \ud574\ub2f9 \uc11c\uc5f4\uc740 ZNF460\uc758 \uacb0\ud569 \uc11c\uc5f4\uc774\uace0, cMYC\uc774 \uacb0\ud569\ud558\ub294 motif\uc5d0 \ud574\ub2f9\ud55c\ub2e4. \ud30c\uc77c \uc900\ube44 \uacfc\uc815\uc5d0 \uc774\uc0c1\uc774 \uc788\uc5c8\ub358 \uac83\uc73c\ub85c \uc0dd\uac01\ud55c\ub2e4. <\/p>\n\n\n\n<figure class=\"wp-block-image size-full is-resized\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/image-1.png\" alt=\"\" class=\"wp-image-1734\" width=\"780\" height=\"648\" srcset=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/image-1.png 937w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/image-1-300x249.png 300w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/image-1-768x638.png 768w\" sizes=\"auto, (max-width: 780px) 100vw, 780px\" \/><\/figure>\n\n\n\n<figure class=\"wp-block-image size-full\"><img loading=\"lazy\" decoding=\"async\" width=\"914\" height=\"400\" src=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/image-2.png\" alt=\"\" class=\"wp-image-1736\" srcset=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/image-2.png 914w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/image-2-300x131.png 300w, https:\/\/bdsl.jbnu.ac.kr\/blog\/wp-content\/uploads\/2023\/04\/image-2-768x336.png 768w\" sizes=\"auto, (max-width: 914px) 100vw, 914px\" \/><\/figure>\n","protected":false},"excerpt":{"rendered":"<p>\uc804\uc0ac\uc778\uc790(transcription factor, TF)\ub294 \ud2b9\uc815 \uc11c\uc5f4\uc744 \uc9c0\ub2cc DNA\uc5d0 \uacb0\ud569\ud558\uc5ec \uc720\uc804\uc790\uc758 \ubc1c\ud604\uc744 \uc870\uc808\ud55c\ub2e4. \uc804\uc0ac \uc778\uc790\uac00 \uacb0\ud569\ud558\ub294 \ubd80\uc704\ub97c transcription factor binding site (TFBS)\ub77c\uace0 \ud55c\ub2e4. TFBS\ub294 CHromosome ImmunoPrecipitation (ChIP) \uc2e4\ud5d8\uc744 \ud1b5\ud574 \ucc3e\uc744 \uc218 \uc788\ub2e4. ChIP\ub294 \ud2b9\uc815 \uc804\uc0ac\uc778\uc790\ub97c \ud2b9\uc774\uc801\uc73c\ub85c \uc778\uc9c0\ud558\uc5ec \uacb0\ud569\ud558\ub294 \ud56d\uccb4\ub97c \uc774\uc6a9\ud558\uc5ec \uc804\uc0ac\uc778\uc790\ub97c \ub18d\ucd95\uc2dc\ud0a4\ub294 \uc2e4\ud5d8 \ubc29\ubc95\uc774\ub2e4. \uc774 \ub54c \uc804\uc0ac\uc778\uc790\uc5d0 \uacb0\ud569\ub418\uc5b4 \uc788\ub294 genomic DNA\ub3c4 \uac19\uc774 \ub18d\ucd95\ub41c\ub2e4. \uc774\ub807\uac8c \ub18d\ucd95\ub41c DNA\uc758 \uc11c\uc5f4\uc744 [&hellip;]<\/p>\n","protected":false},"author":1,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"_uag_custom_page_level_css":"","site-sidebar-layout":"default","site-content-layout":"","ast-site-content-layout":"default","site-content-style":"default","site-sidebar-style":"default","ast-global-header-display":"","ast-banner-title-visibility":"","ast-main-header-display":"","ast-hfb-above-header-display":"","ast-hfb-below-header-display":"","ast-hfb-mobile-header-display":"","site-post-title":"","ast-breadcrumbs-content":"","ast-featured-img":"","footer-sml-layout":"","ast-disable-related-posts":"","theme-transparent-header-meta":"","adv-header-id-meta":"","stick-header-meta":"","header-above-stick-meta":"","header-main-stick-meta":"","header-below-stick-meta":"","astra-migrate-meta-layouts":"default","ast-page-background-enabled":"default","ast-page-background-meta":{"desktop":{"background-color":"var(--ast-global-color-4)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"ast-content-background-meta":{"desktop":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"tablet":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""},"mobile":{"background-color":"var(--ast-global-color-5)","background-image":"","background-repeat":"repeat","background-position":"center center","background-size":"auto","background-attachment":"scroll","background-type":"","background-media":"","overlay-type":"","overlay-color":"","overlay-opacity":"","overlay-gradient":""}},"footnotes":"","_members_access_role":[],"_members_access_error":""},"categories":[33,21],"tags":[],"class_list":["post-1719","post","type-post","status-publish","format-standard","hentry","category-bioinformatics","category-classes"],"yoast_head":"<!-- This site is optimized with the Yoast SEO plugin v28.4 - https:\/\/yoast.com\/product\/yoast-seo-wordpress\/ -->\n<title>Patterns in TFBS - Biomedical Data Science Laboratory<\/title>\n<meta name=\"robots\" content=\"index, follow, max-snippet:-1, max-image-preview:large, max-video-preview:-1\" \/>\n<link rel=\"canonical\" href=\"https:\/\/bdsl.jbnu.ac.kr\/blog\/patterns-in-tfbs\/\" \/>\n<meta property=\"og:locale\" content=\"en_US\" \/>\n<meta property=\"og:type\" content=\"article\" \/>\n<meta property=\"og:title\" content=\"Patterns in TFBS - Biomedical Data Science Laboratory\" \/>\n<meta property=\"og:description\" content=\"\uc804\uc0ac\uc778\uc790(transcription factor, TF)\ub294 \ud2b9\uc815 \uc11c\uc5f4\uc744 \uc9c0\ub2cc DNA\uc5d0 \uacb0\ud569\ud558\uc5ec \uc720\uc804\uc790\uc758 \ubc1c\ud604\uc744 \uc870\uc808\ud55c\ub2e4. \uc804\uc0ac \uc778\uc790\uac00 \uacb0\ud569\ud558\ub294 \ubd80\uc704\ub97c transcription factor binding site (TFBS)\ub77c\uace0 \ud55c\ub2e4. TFBS\ub294 CHromosome ImmunoPrecipitation (ChIP) \uc2e4\ud5d8\uc744 \ud1b5\ud574 \ucc3e\uc744 \uc218 \uc788\ub2e4. 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