{"id":"https://openalex.org/W1606733169","doi":"https://doi.org/10.17169/refubium-15330","title":"Co-occurrence of transcription factor binding sites","display_name":"Co-occurrence of transcription factor binding sites","publication_year":2010,"publication_date":"2010-01-01","ids":{"openalex":"https://openalex.org/W1606733169","doi":"https://doi.org/10.17169/refubium-15330","mag":"1606733169"},"language":"en","primary_location":{"id":"doi:10.17169/refubium-15330","is_oa":true,"landing_page_url":"https://doi.org/10.17169/refubium-15330","pdf_url":null,"source":{"id":"https://openalex.org/S7407052913","display_name":"Universit\u00e4tsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"type":"dissertation","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.17169/refubium-15330","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5103239938","display_name":"Holger Klein","orcid":"https://orcid.org/0000-0002-6904-2319"},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Klein, Holger","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5103239938"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9988999962806702,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9976999759674072,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5771646499633789},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.354134202003479},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.32246100902557373},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.28912800550460815}],"concepts":[{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5771646499633789},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.354134202003479},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.32246100902557373},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.28912800550460815},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.17169/refubium-15330","is_oa":true,"landing_page_url":"https://doi.org/10.17169/refubium-15330","pdf_url":null,"source":{"id":"https://openalex.org/S7407052913","display_name":"Universit\u00e4tsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"},{"id":"mag:1606733169","is_oa":false,"landing_page_url":"https://refubium.fu-berlin.de/handle/fub188/11132","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"doi:10.17169/refubium-15330","is_oa":true,"landing_page_url":"https://doi.org/10.17169/refubium-15330","pdf_url":null,"source":{"id":"https://openalex.org/S7407052913","display_name":"Universit\u00e4tsbibliothek der FU Berlin Hochschulschriftenstelle u. Dokumentenserver","issn_l":null,"issn":[],"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[{"score":0.49000000953674316,"id":"https://metadata.un.org/sdg/2","display_name":"Zero hunger"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":258,"referenced_works":["https://openalex.org/W132925206","https://openalex.org/W177874506","https://openalex.org/W1498410508","https://openalex.org/W1531710418","https://openalex.org/W1570782502","https://openalex.org/W1597226907","https://openalex.org/W1644724366","https://openalex.org/W1651302448","https://openalex.org/W1720193968","https://openalex.org/W1720376523","https://openalex.org/W1836845228","https://openalex.org/W1840001167","https://openalex.org/W1853093403","https://openalex.org/W1854431161","https://openalex.org/W1898862743","https://openalex.org/W1919194185","https://openalex.org/W1963646848","https://openalex.org/W1965267927","https://openalex.org/W1967074502","https://openalex.org/W1967270377","https://openalex.org/W1972875048","https://openalex.org/W1973468493","https://openalex.org/W1974279777","https://openalex.org/W1974725278","https://openalex.org/W1975574765","https://openalex.org/W1976260744","https://openalex.org/W1977186059","https://openalex.org/W1978173716","https://openalex.org/W1980507776","https://openalex.org/W1980809845","https://openalex.org/W1982267716","https://openalex.org/W1984765576","https://openalex.org/W1986772154","https://openalex.org/W1987122345","https://openalex.org/W1988267054","https://openalex.org/W1988496202","https://openalex.org/W1989080074","https://openalex.org/W1990601349","https://openalex.org/W1991758223","https://openalex.org/W1996598520","https://openalex.org/W1997633477","https://openalex.org/W1997794074","https://openalex.org/W1999966058","https://openalex.org/W2000758249","https://openalex.org/W2001577201","https://openalex.org/W2003463914","https://openalex.org/W2003967338","https://openalex.org/W2004563262","https://openalex.org/W2006439752","https://openalex.org/W2008491350","https://openalex.org/W2008900336","https://openalex.org/W2009358682","https://openalex.org/W2011282682","https://openalex.org/W2013213258","https://openalex.org/W2013782479","https://openalex.org/W2015502807","https://openalex.org/W2015900846","https://openalex.org/W2016923471","https://openalex.org/W2017200304","https://openalex.org/W2017560054","https://openalex.org/W2018527742","https://openalex.org/W2019916144","https://openalex.org/W2021389024","https://openalex.org/W2025289680","https://openalex.org/W2026199611","https://openalex.org/W2026882865","https://openalex.org/W2027349221","https://openalex.org/W2027662098","https://openalex.org/W2029454659","https://openalex.org/W2029667189","https://openalex.org/W2029873987","https://openalex.org/W2030337983","https://openalex.org/W2032548898","https://openalex.org/W2037036397","https://openalex.org/W2038012561","https://openalex.org/W2039220873","https://openalex.org/W2041877620","https://openalex.org/W2041905891","https://openalex.org/W2042543706","https://openalex.org/W2044648447","https://openalex.org/W2046222637","https://openalex.org/W2046374070","https://openalex.org/W2048523814","https://openalex.org/W2049260878","https://openalex.org/W2050218740","https://openalex.org/W2051333589","https://openalex.org/W2052408008","https://openalex.org/W2053126761","https://openalex.org/W2053283145","https://openalex.org/W2054624670","https://openalex.org/W2055214702","https://openalex.org/W2057692691","https://openalex.org/W2057885377","https://openalex.org/W2058267750","https://openalex.org/W2060443980","https://openalex.org/W2060460012","https://openalex.org/W2061680337","https://openalex.org/W2065304353","https://openalex.org/W2065579185","https://openalex.org/W2066718232","https://openalex.org/W2068286667","https://openalex.org/W2070340804","https://openalex.org/W2070360032","https://openalex.org/W2071726755","https://openalex.org/W2073727170","https://openalex.org/W2073931970","https://openalex.org/W2074426357","https://openalex.org/W2074644609","https://openalex.org/W2075793022","https://openalex.org/W2077609634","https://openalex.org/W2078757082","https://openalex.org/W2079321730","https://openalex.org/W2080498142","https://openalex.org/W2080922074","https://openalex.org/W2082397309","https://openalex.org/W2082684425","https://openalex.org/W2083193728","https://openalex.org/W2084748297","https://openalex.org/W2085439932","https://openalex.org/W2085442947","https://openalex.org/W2087401860","https://openalex.org/W2087892194","https://openalex.org/W2088704425","https://openalex.org/W2088990426","https://openalex.org/W2089956843","https://openalex.org/W2091346116","https://openalex.org/W2091607609","https://openalex.org/W2094036688","https://openalex.org/W2094710114","https://openalex.org/W2095901576","https://openalex.org/W2096358531","https://openalex.org/W2097117811","https://openalex.org/W2097353028","https://openalex.org/W2097697746","https://openalex.org/W2098412979","https://openalex.org/W2099035403","https://openalex.org/W2099302179","https://openalex.org/W2100332892","https://openalex.org/W2101654376","https://openalex.org/W2101803429","https://openalex.org/W2102356629","https://openalex.org/W2103148270","https://openalex.org/W2104730528","https://openalex.org/W2105315497","https://openalex.org/W2105581244","https://openalex.org/W2106004801","https://openalex.org/W2106756765","https://openalex.org/W2106760243","https://openalex.org/W2106848313","https://openalex.org/W2107233609","https://openalex.org/W2108011868","https://openalex.org/W2108507302","https://openalex.org/W2109621905","https://openalex.org/W2110312780","https://openalex.org/W2111400482","https://openalex.org/W2113197426","https://openalex.org/W2114459488","https://openalex.org/W2115992869","https://openalex.org/W2116301885","https://openalex.org/W2116405705","https://openalex.org/W2116672274","https://openalex.org/W2117245895","https://openalex.org/W2117398059","https://openalex.org/W2117549173","https://openalex.org/W2117770738","https://openalex.org/W2118360831","https://openalex.org/W2118628540","https://openalex.org/W2119060106","https://openalex.org/W2120006551","https://openalex.org/W2120973253","https://openalex.org/W2121607820","https://openalex.org/W2122107930","https://openalex.org/W2122707830","https://openalex.org/W2122893035","https://openalex.org/W2123223165","https://openalex.org/W2123812291","https://openalex.org/W2124195715","https://openalex.org/W2125286524","https://openalex.org/W2125819516","https://openalex.org/W2125970547","https://openalex.org/W2126466006","https://openalex.org/W2126602684","https://openalex.org/W2127779731","https://openalex.org/W2128114769","https://openalex.org/W2128613007","https://openalex.org/W2128937741","https://openalex.org/W2129061533","https://openalex.org/W2130687290","https://openalex.org/W2130832525","https://openalex.org/W2130919037","https://openalex.org/W2133036743","https://openalex.org/W2133147430","https://openalex.org/W2134193442","https://openalex.org/W2134193463","https://openalex.org/W2135030836","https://openalex.org/W2135704771","https://openalex.org/W2135738422","https://openalex.org/W2135805255","https://openalex.org/W2137505881","https://openalex.org/W2137786672","https://openalex.org/W2138717237","https://openalex.org/W2139025111","https://openalex.org/W2139083403","https://openalex.org/W2141408320","https://openalex.org/W2142460132","https://openalex.org/W2145221987","https://openalex.org/W2145427519","https://openalex.org/W2146312020","https://openalex.org/W2146450812","https://openalex.org/W2146517458","https://openalex.org/W2146539504","https://openalex.org/W2148711195","https://openalex.org/W2148753315","https://openalex.org/W2149310258","https://openalex.org/W2149769193","https://openalex.org/W2149841955","https://openalex.org/W2150452800","https://openalex.org/W2150612336","https://openalex.org/W2150934340","https://openalex.org/W2152142189","https://openalex.org/W2152568394","https://openalex.org/W2153392439","https://openalex.org/W2154447604","https://openalex.org/W2154882611","https://openalex.org/W2155717510","https://openalex.org/W2156153879","https://openalex.org/W2156885385","https://openalex.org/W2157825442","https://openalex.org/W2158266834","https://openalex.org/W2158698691","https://openalex.org/W2158995353","https://openalex.org/W2159164310","https://openalex.org/W2160238006","https://openalex.org/W2161838765","https://openalex.org/W2164154631","https://openalex.org/W2165228646","https://openalex.org/W2165853529","https://openalex.org/W2166043581","https://openalex.org/W2166103265","https://openalex.org/W2166894044","https://openalex.org/W2167084099","https://openalex.org/W2167331352","https://openalex.org/W2167869241","https://openalex.org/W2169056802","https://openalex.org/W2169351355","https://openalex.org/W2170698318","https://openalex.org/W2177510297","https://openalex.org/W2222512263","https://openalex.org/W2260318604","https://openalex.org/W2323302721","https://openalex.org/W2340616476","https://openalex.org/W2409931811","https://openalex.org/W2411975710","https://openalex.org/W2427045451","https://openalex.org/W2440331430","https://openalex.org/W2441941171","https://openalex.org/W2570870491","https://openalex.org/W2612812586"],"related_works":["https://openalex.org/W1993149298","https://openalex.org/W2224922780","https://openalex.org/W1494380318","https://openalex.org/W165169846","https://openalex.org/W203861128","https://openalex.org/W2621025264","https://openalex.org/W3045161314","https://openalex.org/W183958491","https://openalex.org/W2999199371","https://openalex.org/W2040319456","https://openalex.org/W1608068936","https://openalex.org/W2522296551","https://openalex.org/W2093094564","https://openalex.org/W2616876512","https://openalex.org/W3038827303","https://openalex.org/W2110464997","https://openalex.org/W2035432773","https://openalex.org/W2582615587","https://openalex.org/W2976515480","https://openalex.org/W2000863793"],"abstract_inverted_index":{"Motivation":[0],"and":[1,23,57,89,126,151,156,227,244,266,271,327,335,357,365,390,424,499,508,578,608,645,681,793,854,909,927,951,981,1068,1131,1140,1197,1226,1279,1311,1317,1323,1378],"Thesis":[2],"Structure":[3],"Transcriptional":[4],"Regulation":[5],"Gene":[6],"regulation":[7],"deals":[8],"with":[9,197,415,538,849,894,918,996,1200],"the":[10,27,44,64,68,85,101,105,109,117,140,154,160,164,174,185,212,238,298,317,328,346,349,351,358,393,396,402,413,416,427,453,472,482,489,500,513,516,536,547,553,568,605,609,662,669,716,771,787,796,819,859,871,884,906,910,930,942,973,993,997,1007,1016,1021,1037,1043,1081,1089,1102,1106,1112,1136,1150,1155,1166,1201,1218,1229,1253,1261,1266,1269,1275,1285,1293,1334,1341,1348],"processes,":[11],"that":[12,99,149,451,582,611,720,773,778,929,953,1332],"enable":[13],"an":[14,113,292,479,1318,1324],"organism":[15,341],"to":[16,153,163,207,247,291,345,381,401,474,525,546,761,847,934,944,964,968,1009,1027,1119,1148,1162,1184,1255,1360],"create":[17],"a":[18,55,58,82,132,170,199,215,221,310,339,440,583,589,600,623,647,749,828,833,868,890,954,1046,1121,1160,1169,1185,1338,1352],"large":[19,216,222,359,483,648,750,955],"variety":[20,223,484,649],"of":[21,43,70,87,116,139,159,178,189,202,214,218,224,232,256,275,286,297,313,330,333,348,353,361,385,422,426,443,467,481,485,491,502,515,520,535,549,555,563,570,586,588,618,630,650,664,715,726,740,752,789,798,804,821,861,875,886,921,957,975,978,985,1020,1024,1083,1092,1108,1114,1135,1173,1231,1233,1263,1265,1274,1295,1301,1309,1343,1351,1366],"cells":[22,1065],"cell":[24,31,45,52,83,225,363,366],"states":[25,364],"from":[26,111,193,1073,1193,1203,1284],"same":[28,65],"genome.":[29,66],"A":[30,77,560,810],"uses":[32],"different":[33,51,233,251,354,362,673],"genes":[34,71,219,1059],"under":[35,204],"divergent":[36],"conditions,":[37],"for":[38,134,304,434,448,488,527,552,599,661,765,786,795,813,983,1045,1058,1080,1088,1111,1179,1217,1238,1298],"example":[39],"in":[40,63,73,180,220,237,338,375,410,505,532,539,567,613,657,707,721,901,924,948,961,1012,1050,1052,1061,1144,1159,1168,1245,1340],"two":[41,382,782],"phases":[42],"cycle.":[46],"In":[47,988,1248,1288,1373],"metazoan":[48],"organisms":[49],"completely":[50],"types,":[53],"like":[54,686,1101],"liver":[56],"brain":[59],"cell,":[60],"are":[61,398,576,677,1198],"encoded":[62,236],"However,":[67],"set":[69,1322,1326],"needed":[72],"both":[74],"cases":[75],"differs.":[76],"crucial":[78],"step":[79],"at":[80,104],"which":[81,210,302,438,580,831,1123,1221,1227],"regulates":[84],"production":[86],"proteins":[88,148],"other":[90,533],"gene":[91,102,118,1071,1278],"products":[92],"is":[93,119,123,143,263,289,325,342,419,593,622,746,775,845,932,1042,1124,1347],"transcriptional":[94,106,141,161,165,318,323,417],"regulation.":[95],"The":[96,121,137,229,254,322,429,616,712,738,842,1189],"molecular":[97],"machinery":[98,418],"transcribes":[100],"assembles":[103],"start":[107,166],"site,":[108],"point":[110],"where":[112],"RNA":[114,122],"copy":[115],"transcribed.":[120],"subsequently":[124],"processed":[125],"often":[127,733],"later":[128],"on":[129,457,802,914,1127,1268,1305,1370],"used":[130,1359],"as":[131,445,447,694,867,1055,1057,1165,1176,1314,1327],"blueprint":[133],"protein":[135],"translation.":[136],"assembly":[138],"apparatus":[142,162],"governed":[144],"by":[145,595,736,748,1000],"transcription":[146,179,190,213,234,252,257,277,287,355,372,436,492,496,521,556,571,619,641,728,742,790,805,823,838,965,1234],"factors:":[147],"recognize":[150],"bind":[152,380],"DNA":[155,591],"support":[157],"tethering":[158],"site.":[167],"We":[168,368,477,603,653,703,882,897,904,940,1117,1153,1241,1259,1330],"present":[169,478,594,717,1242],"concise":[171],"overview":[172,480],"about":[173,371,1138],"molec-":[175],"ular":[176],"biology":[177],"Section":[181,376,475,614,658,708,902,925,949,989,1053,1204,1289],"2.1.":[182],"To":[183,777],"date":[184],"known":[186,967,1033,1145,1194,1256,1280],"target":[187],"spectrum":[188],"factors":[191,196,235,258,278,288,315,379,437,522,729,966],"ranges":[192],"very":[194],"specific":[195,449,463,1070],"only":[198,295,680],"tiny":[200],"number":[201,255,329,352,360,585,751,879,885,920,956],"targets":[203],"distinct":[205],"conditions":[206],"ubiquituous":[208],"factors,":[209,356,450],"influence":[211,462],"fraction":[217,231],"types":[226],"conditions.":[228],"estimated":[230],"human":[239,261,1051,1062,1281],"genome":[240,537,1047],"varies":[241],"between":[242,264,671],"6":[243],"8%,":[245],"leading":[246],"more":[248,320,528,732],"than":[249,598,734],"2,500":[250],"factors.":[253,459],"expressed":[259,1060],"per":[260],"tissue":[262,1069],"150":[265],"350.":[267],"Transcription":[268,378,814],"Factor":[269,815],"Interactions":[270],"Regulatory":[272,1084],"Regions":[273,1085],"Aggregates":[274],"several":[276],"can":[279,406,1211],"act":[280],"synergistically":[281],"or":[282,639,689,1096,1105],"antagonistically.":[283],"Using":[284,1206],"combinations":[285,332,1236],"beneficial":[290],"organism,":[293],"not":[294],"because":[296,309,421],"many":[299,672,1032],"possible":[300,331,420],"interactions":[301,337,374,498,621],"allow":[303],"fine-grained":[305],"regulation,":[306],"but":[307],"also":[308,764],"partial":[311],"redundance":[312],"transription":[314],"makes":[316,1133],"response":[319],"stable.":[321],"network":[324,1023],"dynamic,":[326],"factor-factor":[334],"factor-DNA":[336],"complete":[340],"enormous":[343],"due":[344],"size":[347],"genome,":[350],"types.":[367],"summarize":[369,654,1377],"details":[370],"factor":[373,493,497,557,572,620,642,743,791,806,824,839,1235,1336],"2.2.":[377],"major":[383],"classes":[384],"regulatory":[386,468,503,665,722,799,946,1022,1093,1115,1146,1151,1195,1224,1239,1257,1272,1302,1344,1367],"regions":[387,469,504,666,800,947,1094,1147,1196,1273,1283,1303,1313],"\u2014":[388],"promoters":[389,397,430],"enhancers.":[391],"On":[392],"genomic":[394],"sequence":[395,637,678,1099,1161,1321],"located":[399],"close":[400],"regulated":[403],"gene.":[404],"Enhancers":[405,460],"be":[407,762,1163,1358],"far":[408],"away;":[409],"this":[411,544,1207],"case":[412,1044],"interaction":[414],"bending":[423],"looping":[425],"DNA.":[428],"harbor":[431],"binding":[432,494,518,530,558,573,634,643,695,724,744,767,807,840,856,976,1157,1186],"sites":[433,531,644,725,745,977,1158],"general":[435,561,606],"drive":[439],"low":[441,683,936,1128],"level":[442,684,691,1129,1230],"transcription,":[444],"well":[446,1056,1270],"modulate":[452],"expression":[454,631],"strength":[455],"dependent":[456,1126],"various":[458,705,1213],"usually":[461],"expression.":[464],"For":[465,818,858],"properties":[466,1100],"we":[470,757,780,826,865,971,991,1005,1029,1209,1222,1251,1291,1376],"refer":[471],"reader":[473],"3.3.1.":[476],"experimental":[486,633,701],"methods":[487,551,565,627,656,1254],"detection":[490,501,860,1113],"sites,":[495,768],"Sections":[506],"2.3.1":[507],"2.3.3.":[509],"Computational":[510],"Methods":[511],"Already":[512],"knowledge":[514,1137],"first":[517],"motifs":[519],"led":[523],"researchers":[524],"search":[526],"potential":[529],"parts":[534],"silico":[540],"methods.":[541,652],"Over":[542],"time":[543],"lead":[545],"development":[548],"copious":[550],"prediction":[554,617,663,739,788,797,820,1300,1342],"sites.":[559,574,841,857],"problem":[562],"these":[564,655],"lies":[566],"nature":[569],"They":[575],"short":[577],"degenerate,":[579],"means":[581],"high":[584],"occurrences":[587,923],"matching":[590],"motif":[592],"chance,":[596],"rather":[597],"functional":[601,822],"reason.":[602],"explain":[604],"ideas":[607],"problems":[610],"arise":[612],"3.1.":[615],"difficult":[624],"problem.":[625],"Available":[626],"make":[628],"use":[629,1134],"data,":[632,635],"overrepresented":[636,862,958],"motifs,":[638],"predicted":[640,766,1156],"apply":[646,941,1006,1098,1252],"statistical":[651],"3.2.2.":[659],"Also":[660],"one":[667,785,794,1264],"has":[668],"choice":[670],"tools.":[674],"Partly":[675],"they":[676],"based":[679,801,1215,1304,1369],"deploy":[682],"features":[685,692,1130],"GC":[687,1103,1349,1371],"content":[688,1104,1350],"higher":[690,1018],"such":[693],"motifs.":[696],"Other":[697],"tools":[698,1087],"additionally":[699],"utilise":[700],"data.":[702],"review":[704],"approaches":[706],"3.3.":[709],"Working":[710],"Hypothesis":[711],"underlying":[713],"assumption":[714,760],"work":[718],"is,":[719],"regions,":[723],"interacting":[727,979],"co-":[730,911,922],"occur":[731],"expected":[735,878,887],"chance.":[737],"individual":[741],"hampered":[747],"false":[753,1363],"positive":[754,1315,1364],"results.":[755],"Nevertheless":[756],"expect":[758],"our":[759,899,1243,1296,1355,1380],"true":[763],"even":[769],"if":[770],"signal":[772],"emanates":[774],"weakened.":[776],"end":[779],"develop":[781,827],"new":[783],"methods,":[784],"interactions,":[792,825],"commonness":[803],"site":[808,1187],"combinations.":[809],"Co-occurrence":[811],"Score":[812],"Binding":[816,1077],"Sites":[817],"counting":[829,843,907],"method,":[830,1122],"applies":[832],"sliding":[834],"window":[835],"over":[836,877],"annotated":[837],"procedure":[844,893,908],"able":[846,933],"deal":[848],"overlapping":[850,855],"windows,":[851],"homotypic":[852],"clusters,":[853],"TFBS":[863,880,937,959,986,1142],"pairs,":[864],"calculate":[866,1212],"co-occurrence":[869,994,1174,1190],"score":[870,874,913,995],"log":[872],"odds":[873],"observed":[876],"pairs.":[881,987,1040],"estimate":[883],"pairs":[888,960,980,1143,1182],"using":[889],"label":[891],"permutation":[892],"subsequent":[895],"recountings.":[896],"describe":[898],"method":[900,931,943,999,1008,1202,1297,1356],"4.":[903,1205],"assess":[905,1292],"occurrence":[912],"artificially":[915],"generated":[916],"datasets":[917],"defined":[919],"6.1":[926],"show,":[928],"detect":[935],"pair":[938],"enrichments.":[939],"yeast":[945],"6.2,":[950],"find":[952,1031],"fact":[962],"belong":[963],"interact.":[969],"Moreover":[970],"examine":[972],"similarity":[974],"reasons":[982],"underrepresentation":[984],"6.5":[990],"compare":[992],"costat":[998],"Pape":[1001],"et":[1002],"al..":[1003],"Subsequently":[1004],"vertebrate":[1010],"data":[1011],"Chapter":[1013,1246,1249,1374],"6.":[1014],"Despite":[1015],"much":[1017],"complexity":[1019],"vertebrates":[1025],"compared":[1026],"yeast,":[1028],"still":[1030],"inter-":[1034],"actions":[1035],"among":[1036],"top":[1038],"scoring":[1039],"This":[1041],"wide":[1048],"study":[1049],"6.3,":[1054],"embryonic":[1063],"kidney":[1064],"(Section":[1066,1075],"6.4.2),":[1067],"sets":[1072,1316],"mouse":[1074],"6.4.3).":[1076],"Site":[1078],"Graphs":[1079],"Prediction":[1082],"Many":[1086],"pre-":[1090],"diction":[1091],"explicitly":[1095],"implicitly":[1097],"presence":[1107],"CpG":[1109],"islands":[1110],"regions.":[1116,1240,1258],"aim":[1118],"design":[1120],"less":[1125],"hence":[1132],"over-":[1139],"underrepresented":[1141],"measure":[1149],"potential.":[1152],"represent":[1154,1228],"characterised":[1164],"vertices":[1167],"graph.":[1170,1188],"Subsequent":[1171],"assignment":[1172],"scores":[1175,1191,1216,1267],"edge":[1177],"weights":[1178],"all":[1180],"vertex":[1181],"leads":[1183],"originate":[1192],"calculated":[1199],"graph,":[1208],"now":[1210],"edge-weight":[1214],"input":[1219],"sequence,":[1220,1354],"call":[1223],"potentials":[1225],"abundance":[1232],"typical":[1237],"approach":[1244],"5.":[1247],"7":[1250],"show":[1260],"performance":[1262],"examined":[1271],"murine":[1276],"PAX6":[1277],"enhancer":[1282,1312],"VISTA":[1286],"set.":[1287],"7.2":[1290],"reliability":[1294],"genome-wide":[1299],"test":[1306],"sets,":[1307],"consisting":[1308],"promoter":[1310],"artificial,":[1319],"shuffled":[1320],"intergenic":[1325],"negative":[1328],"sets.":[1329],"find,":[1331],"although":[1333],"biggest":[1335],"playing":[1337],"role":[1339],"function":[1345,1368],"again":[1346],"candidate":[1353],"should":[1357],"filter":[1361],"out":[1362],"predictions":[1365],"content.":[1372],"8":[1375],"discuss":[1379],"findings.":[1381]},"counts_by_year":[],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
