{"id":"https://openalex.org/W2398934016","doi":null,"title":"A computational \"genome walk\" technique to identify regulatory interactions in gene networks.","display_name":"A computational \"genome walk\" technique to identify regulatory interactions in gene networks.","publication_year":1998,"publication_date":"1998-01-01","ids":{"openalex":"https://openalex.org/W2398934016","mag":"2398934016","pmid":"https://pubmed.ncbi.nlm.nih.gov/9697188"},"language":"en","primary_location":{"id":"pmid:9697188","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/9697188","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing","raw_type":"Journal Article"},"volume":null,"type":"conference-paper","indexed_in":["pubmed"],"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/A5079730045","display_name":"Andreas Wagner","orcid":"https://orcid.org/0000-0003-4299-3840","observed_orcids":["https://orcid.org/0000-0003-4299-3840"]},"institutions":[{"id":"https://openalex.org/I1308548392","display_name":"Santa Fe Institute","ror":"https://ror.org/01arysc35","country_code":"US","type":"funder","lineage":["https://openalex.org/I1308548392"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"A Wagner","raw_affiliation_strings":["Santa Fe Institute, NM 87501, USA. aw@santafe.edu","Santa Fe Institute, NM 87501, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Santa Fe Institute, NM 87501, USA. aw@santafe.edu","institution_ids":["https://openalex.org/I1308548392"]},{"raw_affiliation_string":"Santa Fe Institute, NM 87501, USA","institution_ids":["https://openalex.org/I1308548392"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5079730045"],"corresponding_institution_ids":["https://openalex.org/I1308548392"],"apc_list":null,"apc_paid":null,"fwci":2.4213,"has_fulltext":false,"cited_by_count":7,"citation_normalized_percentile":{"value":0.92020089,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":"264","last_page":"78"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.7509999871253967,"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":0.7509999871253967,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.08579999953508377,"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/T10497","display_name":"Fungal and yeast genetics research","score":0.07150000333786011,"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-binding-sites","display_name":"transcription factor binding sites","score":0.7699999809265137},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"transcriptional regulation","score":0.8550000190734863},{"id":"https://openalex.org/keywords/gene-regulatory-networks","display_name":"gene regulatory networks","score":0.5960000157356262},{"id":"https://openalex.org/keywords/transcription-factor-cooperativity","display_name":"transcription factor cooperativity","score":0.7820000052452087},{"id":"https://openalex.org/keywords/saccharomyces-cerevisiae","display_name":"Saccharomyces cerevisiae","score":0.906000018119812},{"id":"https://openalex.org/keywords/e2f-transcription-factors","display_name":"E2F transcription factors","score":0.9020000100135803},{"id":"https://openalex.org/keywords/uas","display_name":"UAS","score":0.46000000834465027},{"id":"https://openalex.org/keywords/gal1-promoter","display_name":"GAL1 promoter","score":0.8650000095367432},{"id":"https://openalex.org/keywords/candidate-gene-identification","display_name":"candidate gene identification","score":0.722000002861023}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7072122097015381},{"id":"https://openalex.org/C2777576037","wikidata":"https://www.wikidata.org/wiki/Q719725","display_name":"Saccharomyces cerevisiae","level":3,"score":0.6895649433135986},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.6834615468978882},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6362107396125793},{"id":"https://openalex.org/C166014724","wikidata":"https://www.wikidata.org/wiki/Q337217","display_name":"Cooperativity","level":2,"score":0.5772153735160828},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5733376145362854},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.56552654504776},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.565386176109314},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5429770946502686},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5331197381019592},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.5280417203903198},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.42939502000808716},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.41703057289123535},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.14197596907615662}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008322","descriptor_name":"Mammals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008957","descriptor_name":"Models, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012441","descriptor_name":"Saccharomyces cerevisiae","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014158","descriptor_name":"Transcription, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016384","descriptor_name":"Consensus Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016386","descriptor_name":"Chromosome Walking","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016681","descriptor_name":"Genome, Fungal","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D017124","descriptor_name":"Conserved Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020218","descriptor_name":"Response Elements","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":2,"locations":[{"id":"pmid:9697188","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/9697188","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing","raw_type":"Journal Article"},{"id":"mag:2398934016","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/9697188","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":"PubMed","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":3,"referenced_works":["https://openalex.org/W2120062331","https://openalex.org/W2611591252","https://openalex.org/W2623408274"],"related_works":["https://openalex.org/W2082334764","https://openalex.org/W1483120103","https://openalex.org/W2105315497","https://openalex.org/W7101234663","https://openalex.org/W2077885464","https://openalex.org/W2039286232","https://openalex.org/W7095381799","https://openalex.org/W1810873884","https://openalex.org/W1956090332","https://openalex.org/W7098548885"],"abstract_inverted_index":{"To":[0],"delineate":[1],"the":[2,51,58,61,96,100,124,167,180,193,196,206,209,237,246,254,285,297],"astronomical":[3],"number":[4],"of":[5,8,47,53,60,72,99,123,145,192,198,205,226,289],"possible":[6],"interactions":[7],"all":[9],"genes":[10,101,207,213,301],"in":[11,102,131,137,166,170,179,231,275,286],"a":[12,15,54,103,219,242,261,276],"genome":[13,59,104,168],"is":[14,50,239,291],"task":[16],"for":[17,34,302],"which":[18,98,134,161],"conventional":[19],"experimental":[20],"techniques":[21],"are":[22,26,105,148,162],"ill-suited.":[23],"Sorely":[24],"needed":[25],"rapid":[27],"and":[28,169,202,268],"inexpensive":[29],"methods":[30],"that":[31,38,75,83,126],"identify":[32,212],"candidates":[33,37],"interacting":[35],"genes,":[36],"can":[39,182],"be":[40,108,183,216],"further":[41],"investigated":[42],"by":[43,110,153,185,218,304],"experiment.":[44],"The":[45,65,93,293],"subject":[46],"this":[48],"paper":[49],"application":[52],"novel":[55],"method":[56,66,94,238],"to":[57,68,85,107,151,158,211,215,241,253,266],"yeast":[62,247],"Saccharomyces":[63,232],"cerevisiae.":[64],"applies":[67],"an":[69],"important":[70],"class":[71],"gene":[73],"interactions,":[74],"is,":[76],"transcriptional":[77,132],"regulation":[78,303],"via":[79],"transcription":[80,221,229,256],"factors":[81,230],"(TFs)":[82],"bind":[84],"specific":[86],"enhancer":[87],"or":[88,112],"silencer":[89],"sites":[90,147,225],"on":[91],"DNA.":[92],"addresses":[95],"question:":[97],"likely":[106,214],"regulated":[109,217],"one":[111],"more":[113],"TFs":[114,128],"with":[115],"known":[116,189],"DNA":[117,248,262],"binding":[118,141,146,176,200,224,249,263,270],"specificity?":[119],"It":[120],"takes":[121],"advantage":[122],"fact":[125],"many":[127],"show":[129],"cooperativity":[130],"activation":[133],"manifests":[135],"itself":[136],"closely":[138],"spaced":[139],"TF":[140],"sites.":[142],"Such":[143],"\"clusters\"":[144],"very":[149],"unlikely":[150],"occur":[152],"chance":[154],"alone,":[155],"as":[156],"opposed":[157],"individual":[159],"sites,":[160],"often":[163],"abundant":[164],"both":[165],"promoter":[171,278],"regions.":[172],"Statistical":[173],"information":[174,186],"about":[175,187],"site":[177,271],"clusters":[178],"genome,":[181],"complemented":[184],"(i)":[188],"biochemical":[190],"functions":[191],"TF,":[194],"(ii)":[195],"structure":[197],"its":[199,269,282],"site,":[201],"(iii)":[203],"function":[204,288],"near":[208],"cluster,":[210],"given":[220],"factor.":[222],"Previously,":[223],"well":[227],"characterized":[228],"cerevisiae":[233],"were":[234],"analyzed.":[235],"Here,":[236],"applied":[240],"somewhat":[243],"different":[244],"situation:":[245],"activity":[250,274],"yE2F,":[251],"similar":[252],"mammalian":[255],"factor":[257],"E2F.":[258],"yE2F":[259,290],"has":[260],"specificity":[264],"identical":[265],"E2F,":[267],"shows":[272],"UAS":[273],"GAL1-based":[277],"construct.":[279],"However,":[280],"despite":[281],"high":[283],"conservation,":[284],"vivo":[287],"unknown.":[292],"analysis":[294],"carried":[295],"out":[296],"here":[298],"suggests":[299],"candidate":[300],"yE2F.":[305]},"counts_by_year":[],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2016-06-24T00:00:00"}