{"id":"https://openalex.org/W1986092267","doi":"https://doi.org/10.1093/nar/gkg112","title":"rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation","display_name":"rSNP_Guide, a database system for analysis of transcription factor binding to DNA with variations: application to genome annotation","publication_year":2003,"publication_date":"2003-01-01","ids":{"openalex":"https://openalex.org/W1986092267","doi":"https://doi.org/10.1093/nar/gkg112","mag":"1986092267","pmid":"https://pubmed.ncbi.nlm.nih.gov/12519962"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkg112","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg112","pdf_url":"https://academic.oup.com/nar/article-pdf/31/1/118/7128008/gkg112.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":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"bronze","oa_url":"https://academic.oup.com/nar/article-pdf/31/1/118/7128008/gkg112.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070141127","display_name":"Julia Ponomarenko","orcid":"https://orcid.org/0000-0002-1477-9444"},"institutions":[{"id":"https://openalex.org/I4210116466","display_name":"Institute of Cytology and Genetics","ror":"https://ror.org/0277xgb12","country_code":"RU","type":"facility","lineage":["https://openalex.org/I1313323035","https://openalex.org/I1313323035","https://openalex.org/I188973947","https://openalex.org/I4210116466","https://openalex.org/I4210127387","https://openalex.org/I4210129690"]}],"countries":["RU"],"is_corresponding":true,"raw_author_name":"J. V. Ponomarenko","raw_affiliation_strings":["Institute of Cytology and Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. jpon@bionet.nsc.ru","Institute of Cytology and Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia"],"affiliations":[{"raw_affiliation_string":"Institute of Cytology and Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia. jpon@bionet.nsc.ru","institution_ids":["https://openalex.org/I4210116466"]},{"raw_affiliation_string":"Institute of Cytology and Genetics, 10 Lavrentyev Avenue, Novosibirsk, 630090, Russia","institution_ids":["https://openalex.org/I4210116466"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5070141127"],"corresponding_institution_ids":["https://openalex.org/I4210116466"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":null,"fwci":1.1439,"has_fulltext":true,"cited_by_count":30,"citation_normalized_percentile":{"value":0.75597057,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"31","issue":"1","first_page":"118","last_page":"121"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","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"}},{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9955000281333923,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9947999715805054,"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":0.8164942264556885},{"id":"https://openalex.org/keywords/annotation","display_name":"Annotation","score":0.7172886729240417},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.6073263883590698},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.5738423466682434},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5581647157669067},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5503364205360413},{"id":"https://openalex.org/keywords/dna","display_name":"DNA","score":0.5494999289512634},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5339490175247192},{"id":"https://openalex.org/keywords/binding-site","display_name":"Binding site","score":0.517096757888794},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.5114477872848511},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.46705305576324463},{"id":"https://openalex.org/keywords/homologous-chromosome","display_name":"Homologous chromosome","score":0.4106457233428955},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.2699653208255768},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.0885145366191864},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.08192753791809082}],"concepts":[{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.8164942264556885},{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7172886729240417},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.6073263883590698},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5738423466682434},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5581647157669067},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5503364205360413},{"id":"https://openalex.org/C552990157","wikidata":"https://www.wikidata.org/wiki/Q7430","display_name":"DNA","level":2,"score":0.5494999289512634},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5339490175247192},{"id":"https://openalex.org/C107824862","wikidata":"https://www.wikidata.org/wiki/Q616005","display_name":"Binding site","level":2,"score":0.517096757888794},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5114477872848511},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.46705305576324463},{"id":"https://openalex.org/C64894306","wikidata":"https://www.wikidata.org/wiki/Q849622","display_name":"Homologous chromosome","level":3,"score":0.4106457233428955},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.2699653208255768},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.0885145366191864},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.08192753791809082}],"mesh":[{"descriptor_ui":"D001665","descriptor_name":"Binding Sites","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":"D001665","descriptor_name":"Binding Sites","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":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004247","descriptor_name":"DNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D004268","descriptor_name":"DNA-Binding Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005786","descriptor_name":"Gene Expression Regulation","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":"D005786","descriptor_name":"Gene Expression Regulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D014157","descriptor_name":"Transcription Factors","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":4,"locations":[{"id":"doi:10.1093/nar/gkg112","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg112","pdf_url":"https://academic.oup.com/nar/article-pdf/31/1/118/7128008/gkg112.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":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:12519962","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/12519962","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,"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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:europepmc.org:158735","is_oa":false,"landing_page_url":"http://europepmc.org/pmc/articles/PMC165559","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:165559","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/165559","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"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/gkg112","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkg112","pdf_url":"https://academic.oup.com/nar/article-pdf/31/1/118/7128008/gkg112.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":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320321079","display_name":"Russian Foundation for Basic Research","ror":"https://ror.org/02mh1ke95"},{"id":"https://openalex.org/F4320332603","display_name":"University of California, San Diego","ror":"https://ror.org/0168r3w48"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W1986092267.pdf","grobid_xml":"https://content.openalex.org/works/W1986092267.grobid-xml"},"referenced_works_count":25,"referenced_works":["https://openalex.org/W180216550","https://openalex.org/W1480160846","https://openalex.org/W1518105100","https://openalex.org/W1582005136","https://openalex.org/W1973046634","https://openalex.org/W1974901186","https://openalex.org/W1989213989","https://openalex.org/W2008900336","https://openalex.org/W2009539999","https://openalex.org/W2018924988","https://openalex.org/W2025982750","https://openalex.org/W2056572328","https://openalex.org/W2064879068","https://openalex.org/W2065087403","https://openalex.org/W2068011423","https://openalex.org/W2073264424","https://openalex.org/W2084681487","https://openalex.org/W2100428244","https://openalex.org/W2112444654","https://openalex.org/W2124886024","https://openalex.org/W2130541747","https://openalex.org/W2168507922","https://openalex.org/W2628074563","https://openalex.org/W4239468544","https://openalex.org/W4252546523"],"related_works":["https://openalex.org/W2036927633","https://openalex.org/W2153561273","https://openalex.org/W2152664145","https://openalex.org/W2079197459","https://openalex.org/W2379997263","https://openalex.org/W2165899269","https://openalex.org/W2236968607","https://openalex.org/W4233525429","https://openalex.org/W2367493320","https://openalex.org/W2131580913"],"abstract_inverted_index":{"The":[0,46,67,145],"analysis":[1],"of":[2,9,14,31,84,94,147],"gene":[3],"regulatory":[4],"networks":[5],"has":[6],"become":[7],"one":[8],"the":[10,15,95,100],"most":[11],"challenging":[12],"problems":[13],"postgenomic":[16],"era.":[17],"Earlier":[18],"we":[19,119],"developed":[20],"rSNP_Guide":[21,68,133],"(http://util.bionet.nsc.ru/databases/rsnp.html),":[22],"a":[23,73],"computer":[24],"system":[25],"and":[26,58,81,98,143],"database":[27],"devoted":[28],"to":[29,90,117,138],"prediction":[30,47],"transcription":[32],"factor":[33],"(TF)":[34],"binding":[35,116],"sites":[36,57,87,93,110,124],"(TF":[37],"sites),":[38],"which":[39],"can":[40],"be":[41],"responsible":[42],"for":[43,75],"disease":[44],"phenotypes.":[45],"results":[48],"were":[49,88],"confirmed":[50],"by":[51,63],"70":[52],"known":[53,112],"relationships":[54],"between":[55],"TF":[56,76,86,109,115,123,131],"diseases,":[59],"as":[60,62,72],"well":[61],"site-directed":[64],"mutagenesis":[65],"data.":[66],"is":[69,150],"being":[70],"investigated":[71],"tool":[74],"site":[77],"annotation.":[78],"Previously":[79],"analyzed":[80],"characterized":[82],"cases":[83],"altered":[85],"used":[89],"annotate":[91],"potential":[92,122,130],"same":[96,101],"type":[97],"at":[99],"location":[102],"in":[103,114,125],"homologous":[104,126],"genes.":[105,127],"Based":[106],"on":[107],"20":[108],"with":[111],"alterations":[113],"DNA,":[118],"localized":[120],"245":[121],"For":[128],"these":[129],"sites,":[132],"estimates":[134],"TF-DNA":[135],"interaction":[136],"according":[137],"three":[139],"categories:":[140],"'present',":[141],"'weak',":[142],"'absent'.":[144],"significance":[146],"each":[148],"assignment":[149],"statistically":[151],"measured.":[152]},"counts_by_year":[{"year":2016,"cited_by_count":4},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":3}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}