{"id":"https://openalex.org/W4230406063","doi":"https://doi.org/10.1093/nar/gki486","title":"CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes","display_name":"CisMols Analyzer: identification of compositionally similar cis-element clusters in ortholog conserved regions of coordinately expressed genes","publication_year":2005,"publication_date":"2005-06-26","ids":{"openalex":"https://openalex.org/W4230406063","doi":"https://doi.org/10.1093/nar/gki486"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gki486","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki486","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W408/7623659/gki486.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W408/7623659/gki486.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5061689835","display_name":"Anil G. Jegga","orcid":"https://orcid.org/0000-0002-4881-7752"},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]},{"id":"https://openalex.org/I2802872610","display_name":"Hospital Research Foundation","ror":"https://ror.org/043ae3f44","country_code":"AU","type":"nonprofit","lineage":["https://openalex.org/I2802872610"]}],"countries":["AU","US"],"is_corresponding":true,"raw_author_name":"A. G. Jegga","raw_affiliation_strings":["Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC, 3333 Burnet Avenue, Cincinnati, OH-45229, USA","Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA"],"affiliations":[{"raw_affiliation_string":"Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC, 3333 Burnet Avenue, Cincinnati, OH-45229, USA","institution_ids":["https://openalex.org/I2802872610"]},{"raw_affiliation_string":"Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA","institution_ids":["https://openalex.org/I1285204247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5085406883","display_name":"Apoorva Gupta","orcid":"https://orcid.org/0000-0001-6534-2835"},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"A. Gupta","raw_affiliation_strings":["Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA"],"affiliations":[{"raw_affiliation_string":"Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA","institution_ids":["https://openalex.org/I1285204247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111221988","display_name":"Siva Gowrisankar","orcid":null},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Gowrisankar","raw_affiliation_strings":["Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA"],"affiliations":[{"raw_affiliation_string":"Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA","institution_ids":["https://openalex.org/I1285204247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082656829","display_name":"Mrunal Deshmukh","orcid":null},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"M. A. Deshmukh","raw_affiliation_strings":["Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA"],"affiliations":[{"raw_affiliation_string":"Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA","institution_ids":["https://openalex.org/I1285204247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069976028","display_name":"Shane T. Connolly","orcid":"https://orcid.org/0009-0000-7483-6263"},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Connolly","raw_affiliation_strings":["Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA"],"affiliations":[{"raw_affiliation_string":"Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA","institution_ids":["https://openalex.org/I1285204247"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5019127145","display_name":"K. Finley","orcid":null},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"K. Finley","raw_affiliation_strings":["Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA"],"affiliations":[{"raw_affiliation_string":"Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA","institution_ids":["https://openalex.org/I1285204247"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5064856328","display_name":"Bruce J. Aronow","orcid":"https://orcid.org/0000-0001-5109-6514"},"institutions":[{"id":"https://openalex.org/I1285204247","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I1285204247"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"B. J. Aronow","raw_affiliation_strings":["Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA"],"affiliations":[{"raw_affiliation_string":"Division of Biomedical Informatics, Children's Hospital Research Foundation, CCHMC  3333 Burnet Avenue, Cincinnati, OH-45229, USA","institution_ids":["https://openalex.org/I1285204247"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5061689835"],"corresponding_institution_ids":["https://openalex.org/I1285204247","https://openalex.org/I2802872610"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.5654,"has_fulltext":true,"cited_by_count":15,"citation_normalized_percentile":{"value":0.94492887,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"33","issue":"Web Server","first_page":"W408","last_page":"W411"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10184","display_name":"Plant Molecular Biology Research","score":0.9289000034332275,"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"}},"topics":[{"id":"https://openalex.org/T10184","display_name":"Plant Molecular Biology Research","score":0.9289000034332275,"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":0.9110000133514404,"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/T10268","display_name":"Developmental Biology and Gene Regulation","score":0.9025999903678894,"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/biology","display_name":"Biology","score":0.8453141450881958},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.695189356803894},{"id":"https://openalex.org/keywords/conserved-sequence","display_name":"Conserved sequence","score":0.6748365759849548},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.6048870086669922},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5339953303337097},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5203453898429871},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.49930644035339355},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.46148481965065},{"id":"https://openalex.org/keywords/phylogenetic-tree","display_name":"Phylogenetic tree","score":0.4489735960960388},{"id":"https://openalex.org/keywords/regulatory-sequence","display_name":"Regulatory sequence","score":0.4207090735435486},{"id":"https://openalex.org/keywords/regulation-of-gene-expression","display_name":"Regulation of gene expression","score":0.3388437330722809},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3303290009498596},{"id":"https://openalex.org/keywords/peptide-sequence","display_name":"Peptide sequence","score":0.1595352590084076}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8453141450881958},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.695189356803894},{"id":"https://openalex.org/C199216141","wikidata":"https://www.wikidata.org/wiki/Q4995178","display_name":"Conserved sequence","level":4,"score":0.6748365759849548},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.6048870086669922},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5339953303337097},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5203453898429871},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.49930644035339355},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.46148481965065},{"id":"https://openalex.org/C193252679","wikidata":"https://www.wikidata.org/wiki/Q242125","display_name":"Phylogenetic tree","level":3,"score":0.4489735960960388},{"id":"https://openalex.org/C21592294","wikidata":"https://www.wikidata.org/wiki/Q3238407","display_name":"Regulatory sequence","level":4,"score":0.4207090735435486},{"id":"https://openalex.org/C165864922","wikidata":"https://www.wikidata.org/wiki/Q411391","display_name":"Regulation of gene expression","level":3,"score":0.3388437330722809},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3303290009498596},{"id":"https://openalex.org/C167625842","wikidata":"https://www.wikidata.org/wiki/Q899763","display_name":"Peptide sequence","level":3,"score":0.1595352590084076},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.1093/nar/gki486","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki486","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W408/7623659/gki486.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmh:oai:pubmedcentral.nih.gov:1160246","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/1160246","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"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":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Nucleic Acids Res","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/nar/gki486","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gki486","pdf_url":"https://academic.oup.com/nar/article-pdf/33/suppl_2/W408/7623659/gki486.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.699999988079071,"display_name":"Life in Land","id":"https://metadata.un.org/sdg/15"}],"awards":[{"id":"https://openalex.org/G2498467786","display_name":null,"funder_award_id":"P30-ES06096","funder_id":"https://openalex.org/F4320337361","funder_display_name":"National Institute of Environmental Health Sciences"},{"id":"https://openalex.org/G2579644219","display_name":null,"funder_award_id":"NIEHS","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3324792662","display_name":null,"funder_award_id":"P30-ES06096","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8611459891","display_name":null,"funder_award_id":"R24 DK 064403","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320309575","display_name":"Cincinnati Children's Hospital Medical Center","ror":"https://ror.org/01hcyya48"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337361","display_name":"National Institute of Environmental Health Sciences","ror":"https://ror.org/00j4k1h63"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W4230406063.pdf","grobid_xml":"https://content.openalex.org/works/W4230406063.grobid-xml"},"referenced_works_count":13,"referenced_works":["https://openalex.org/W1669012339","https://openalex.org/W1799635531","https://openalex.org/W1821582542","https://openalex.org/W1965280193","https://openalex.org/W1998300401","https://openalex.org/W1999909705","https://openalex.org/W2008546628","https://openalex.org/W2008900336","https://openalex.org/W2046017372","https://openalex.org/W2057998009","https://openalex.org/W2124025352","https://openalex.org/W2157523980","https://openalex.org/W4298215144"],"related_works":["https://openalex.org/W3108101741","https://openalex.org/W2977893617","https://openalex.org/W4254703907","https://openalex.org/W2096761497","https://openalex.org/W1995867836","https://openalex.org/W2053053668","https://openalex.org/W2157344326","https://openalex.org/W1581778452","https://openalex.org/W2408793279","https://openalex.org/W1979755982"],"abstract_inverted_index":{"Combinatorial":[0],"interactions":[1,86],"of":[2,25,28,34,41,48,55,65,72,142,145,157,169,178],"sequence-specific":[3],"trans-acting":[4],"factors":[5],"with":[6,131,166],"localized":[7],"genomic":[8],"ciselement":[9,74],"clusters":[10,92,153],"are":[11,59],"the":[12,23,32,35,53,66,78,138,193],"principal":[13],"mechanism":[14],"for":[15,38,52,99,137],"regulating":[16],"tissue-specific":[17],"and":[18,69,77,110,140,148,172,180,189,195],"developmental":[19],"gene":[20,103],"expression.":[21],"With":[22],"emergence":[24],"expanding":[26],"numbers":[27,144],"genome-wide":[29],"expression":[30,112],"analyses,":[31],"identification":[33,54,141],"cis-elements":[36],"responsible":[37],"specific":[39],"patterns":[40],"transcriptional":[42],"regulation":[43],"represents":[44],"a":[45,117,155,167,206],"critical":[46],"area":[47],"investigation.":[49],"Computational":[50],"methods":[51],"functional":[56],"cis-regulatory":[57,151],"modules":[58],"difficult":[60,119],"to":[61,135],"devise,":[62],"principally":[63],"because":[64],"short":[67],"length":[68],"degenerate":[70],"nature":[71],"individual":[73,101],"binding":[75],"sites":[76],"inherent":[79],"complexity":[80],"that":[81],"is":[82,97,116,203],"generated":[83],"by":[84],"combinatorial":[85],"within":[87],"cis-clusters.":[88],"Filtering":[89],"candidate":[90],"cis-element":[91],"based":[93],"on":[94],"phylogenetic":[95],"conservation":[96],"helpful":[98],"an":[100,127],"ortholog":[102,128,176],"pair,":[104],"but":[105],"combining":[106],"data":[107],"from":[108,154],"cis-conservation":[109],"coordinate":[111],"across":[113],"multiple":[114],"genes":[115,181,191],"more":[118],"problem.":[120],"To":[121],"approach":[122],"this,":[123],"we":[124],"have":[125],"extended":[126],"genepair":[129],"database":[130],"additional":[132],"analytical":[133],"architecture":[134],"allow":[136],"analysis":[139],"maximal":[143],"compositionally":[146],"similar":[147],"phylogenetically":[149],"conserved":[150],"element":[152],"list":[156],"user-selected":[158],"genes.":[159],"The":[160],"system":[161],"has":[162],"been":[163],"successfully":[164],"tested":[165],"series":[168],"functionally":[170],"related":[171],"microarray":[173],"profile-based":[174],"co-expressed":[175,190],"pairs":[177],"promoters":[179],"using":[182],"known":[183],"regulatory":[184],"regions":[185],"as":[186,198],"training":[187],"sets":[188],"in":[192],"olfactory":[194],"immunohematologic":[196],"systems":[197],"test":[199],"sets.":[200],"CisMols":[201],"Analyzer":[202],"accessible":[204],"via":[205],"Web":[207],"interface":[208],"at":[209],"http://cismols.cchmc.org/.":[210]},"counts_by_year":[{"year":2018,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-10T15:06:20.359241","created_date":"2025-10-10T00:00:00"}
