{"id":"https://openalex.org/W2396416563","doi":null,"title":"In Silico Analysis of Cis-Regulatory Elements on Co-Expressed Genes","display_name":"In Silico Analysis of Cis-Regulatory Elements on Co-Expressed Genes","publication_year":2015,"publication_date":"2015-04-07","ids":{"openalex":"https://openalex.org/W2396416563","mag":"2396416563"},"language":"en","primary_location":{"id":"pmh:oai:dergipark.gov.tr:article/438671","doi":null,"is_oa":false,"landing_page_url":"http://dergipark.gov.tr/jbes/issue/37990/438671","pdf_url":null,"source":{"id":"https://openalex.org/S4306401840","display_name":"DergiPark (Istanbul University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67581229","host_organization_name":"Istanbul University","host_organization_lineage":["https://openalex.org/I67581229"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"\\n Volume: 9, Issue: 25\\n \\n","raw_type":"info:eu-repo/semantics/article"},"volume":null,"type":"article","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5088249371","display_name":"Parviz Heidari","orcid":"https://orcid.org/0000-0003-4716-0143","observed_orcids":["https://orcid.org/0000-0003-4716-0143"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Parviz Heidari","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-4716-0143","affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042247983","display_name":"Mostafa Ahmadizadeh","orcid":"https://orcid.org/0000-0001-9593-2561","observed_orcids":["https://orcid.org/0000-0001-9593-2561"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mostafa Ahmadizadeh","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0001-9593-2561","affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5008055191","display_name":"Hamid Najafi-Zarrini","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Hamid Najafi-Zarrini","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.2306,"has_fulltext":false,"cited_by_count":10,"citation_normalized_percentile":{"value":0.49080574,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":97},"biblio":{"volume":"9","issue":"25","first_page":"1","last_page":"9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.8687000274658203,"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":0.8687000274658203,"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/T10184","display_name":"Plant Molecular Biology Research","score":0.03060000017285347,"subfield":{"id":"https://openalex.org/subfields/1110","display_name":"Plant Science"},"field":{"id":"https://openalex.org/fields/11","display_name":"Agricultural and Biological Sciences"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.01759999990463257,"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/cis-regulatory-elements","display_name":"cis-regulatory elements","score":1.0},{"id":"https://openalex.org/keywords/co-expressed-genes","display_name":"co-expressed genes","score":0.9829999804496765},{"id":"https://openalex.org/keywords/transcription-factor-binding-sites","display_name":"transcription factor binding sites","score":0.8059999942779541},{"id":"https://openalex.org/keywords/promoter-analysis","display_name":"promoter analysis","score":0.7170000076293945},{"id":"https://openalex.org/keywords/gene-expression-regulation","display_name":"gene expression regulation","score":0.531000018119812},{"id":"https://openalex.org/keywords/gene-networks","display_name":"gene networks","score":0.5379999876022339},{"id":"https://openalex.org/keywords/stress-response","display_name":"stress response","score":0.6480000019073486},{"id":"https://openalex.org/keywords/transcription-factor-binding-motifs","display_name":"transcription factor binding motifs","score":0.41999998688697815},{"id":"https://openalex.org/keywords/scope","display_name":"scope","score":0.9769999980926514}],"concepts":[{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.8527641296386719},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.6930535435676575},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6891149878501892},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5568787455558777},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5553984642028809},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.5179570913314819},{"id":"https://openalex.org/C68473852","wikidata":"https://www.wikidata.org/wiki/Q18031845","display_name":"TBX1","level":5,"score":0.490774005651474},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.48820191621780396},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.4859984815120697},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.4855217933654785},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.48192620277404785},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.48084744811058044},{"id":"https://openalex.org/C190796033","wikidata":"https://www.wikidata.org/wiki/Q1093165","display_name":"Cis-regulatory module","level":5,"score":0.47980979084968567},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.4666566550731659},{"id":"https://openalex.org/C179926584","wikidata":"https://www.wikidata.org/wiki/Q207714","display_name":"Transcription (linguistics)","level":2,"score":0.43746697902679443},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4373423457145691},{"id":"https://openalex.org/C138885662","wikidata":"https://www.wikidata.org/wiki/Q5891","display_name":"Philosophy","level":0,"score":0.0},{"id":"https://openalex.org/C41895202","wikidata":"https://www.wikidata.org/wiki/Q8162","display_name":"Linguistics","level":1,"score":0.0}],"mesh":[],"locations_count":3,"locations":[{"id":"pmh:oai:dergipark.gov.tr:article/438671","doi":null,"is_oa":false,"landing_page_url":"http://dergipark.gov.tr/jbes/issue/37990/438671","pdf_url":null,"source":{"id":"https://openalex.org/S4306401840","display_name":"DergiPark (Istanbul University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67581229","host_organization_name":"Istanbul University","host_organization_lineage":["https://openalex.org/I67581229"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"\\n Volume: 9, Issue: 25\\n \\n","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:dergipark.org.tr:article/438671","doi":null,"is_oa":false,"landing_page_url":"https://dergipark.org.tr/en/pub/jbes/article/438671","pdf_url":null,"source":{"id":"https://openalex.org/S4306401840","display_name":"DergiPark (Istanbul University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67581229","host_organization_name":"Istanbul University","host_organization_lineage":["https://openalex.org/I67581229"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"mag:2396416563","doi":null,"is_oa":false,"landing_page_url":"https://www.researchgate.net/profile/Mostafa_Ahmadizadeh/publication/276406023_In_Silico_Analysis_of_Cis-Regulatory_Elements_on_Co-Expressed_Genes/links/5558748608ae6943a874dfb0.pdf?disableCoverPage=true","pdf_url":null,"source":{"id":"https://openalex.org/S2764699770","display_name":"Journal of biological and environmental sciences","issn_l":"1308-2019","issn":["1308-2019"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":"Journal of biological and environmental sciences","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":20,"referenced_works":["https://openalex.org/W1645753843","https://openalex.org/W1978409950","https://openalex.org/W1987122345","https://openalex.org/W1993665892","https://openalex.org/W1996149236","https://openalex.org/W2004147186","https://openalex.org/W2006508229","https://openalex.org/W2035908878","https://openalex.org/W2036771037","https://openalex.org/W2046041727","https://openalex.org/W2069749928","https://openalex.org/W2071759147","https://openalex.org/W2089806726","https://openalex.org/W2106548896","https://openalex.org/W2127300419","https://openalex.org/W2135518907","https://openalex.org/W2144710927","https://openalex.org/W2161849959","https://openalex.org/W2163171712","https://openalex.org/W2165702293"],"related_works":["https://openalex.org/W2106848313","https://openalex.org/W2081303346","https://openalex.org/W2045512070","https://openalex.org/W2065716803","https://openalex.org/W2063295686","https://openalex.org/W2028471769","https://openalex.org/W7124461044","https://openalex.org/W2144710927","https://openalex.org/W2981961092","https://openalex.org/W7074009667"],"abstract_inverted_index":{"Cis-regulatory":[0],"elements":[1,170],"(CREs)":[2],"are":[3],"regions":[4],"of":[5,12,31,43,48,59,68,112,114,118,131,136,141,147,186],"non-coding":[6],"DNA":[7,116],"that":[8,95,105,124,171],"regulate":[9,17],"the":[10,79,92,115,182],"transcription":[11,19,26,152],"nearby":[13],"genes.":[14,120],"CREs":[15,60,84],"typically":[16],"gene":[18,33,72,190],"by":[20,90,156],"functioning":[21],"as":[22],"binding":[23],"sites":[24],"for":[25,39,50,54,166],"factors.":[27],"Publicly":[28],"available":[29],"database":[30,94],"co-expressed":[32,97,148,174],"sets":[34],"would":[35],"be":[36],"valuable":[37],"tools":[38],"a":[40,162,178],"wide":[41],"variety":[42],"experimental":[44],"designs,":[45],"including":[46],"targeting":[47],"genes":[49,70,87,98,149,175,188],"functional":[51],"identification":[52],"or":[53],"regulatory":[55],"investigation.":[56],"The":[57,121],"study":[58,76],"effect":[61,172],"on":[62,173],"expression":[63,82],"can":[64],"improve":[65],"our":[66],"understanding":[67],"co-expression":[69,86,119],"and":[71,83,103,129,138,150,184,189],"networks.":[73],"In":[74],"present":[75,160],"we":[77],"compared":[78],"correlation":[80],"between":[81],"in":[85,110,145],"with":[88],"LTP5":[89],"using":[91],"Genevestigator":[93],"provides":[96],"deduced":[99],"from":[100],"microarray":[101],"data,":[102],"SCOPE":[104],"uses":[106],"to":[107,176,180],"find":[108,177],"CRDs":[109],"800bp":[111],"upstream":[113],"sequences":[117],"result":[122],"revealed":[123],"three":[125],"motifs":[126],"(TGSCAB,":[127],"ATWTGYMG":[128],"CBTATC)":[130],"PRISM":[132],"algorithm,":[133],"GCCAC":[134],"motif":[135,140],"BEAM":[137],"ATTGNVANNYGG":[139],"SPACER":[142],"algorithm":[143],"distribute":[144],"promoter":[146],"LUX":[151],"factor":[153],"was":[154],"identified":[155],"UniPROB":[157],"database.":[158],"We":[159],"here":[161],"new":[163],"comparison":[164],"method":[165],"detecting":[167],"key":[168],"cis-regulatory":[169],"relation":[179],"clarify":[181],"function":[183],"regulation":[185],"particular":[187],"networks":[191],"under":[192],"stress":[193],"conditions.":[194]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":4},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1}],"updated_date":"2025-10-10T17:16:08.811792","created_date":"2016-06-24T00:00:00"}