{"id":"https://openalex.org/W2131719528","doi":"https://doi.org/10.1093/bioinformatics/btt318","title":"Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data","display_name":"Whole-Genome rVISTA: a tool to determine enrichment of transcription factor binding sites in gene promoters from transcriptomic data","publication_year":2013,"publication_date":"2013-06-04","ids":{"openalex":"https://openalex.org/W2131719528","doi":"https://doi.org/10.1093/bioinformatics/btt318","mag":"2131719528","pmid":"https://pubmed.ncbi.nlm.nih.gov/23736530"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btt318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt318","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/16/2059/49077015/bioinformatics_29_16_2059.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","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/bioinformatics/article-pdf/29/16/2059/49077015/bioinformatics_29_16_2059.pdf","any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107834893","display_name":"Inna Dubchak","orcid":null},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I2801780550","display_name":"California Pacific Medical Center","ror":"https://ror.org/02bjh0167","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I114073160","https://openalex.org/I2801780550"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Inna Dubchak","raw_affiliation_strings":["1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I188891513","https://openalex.org/I196679689","https://openalex.org/I2801780550"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5053276382","display_name":"Matthew Munoz","orcid":null},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I2801780550","display_name":"California Pacific Medical Center","ror":"https://ror.org/02bjh0167","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I114073160","https://openalex.org/I2801780550"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Matthew Munoz","raw_affiliation_strings":["1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I188891513","https://openalex.org/I196679689","https://openalex.org/I2801780550"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066994679","display_name":"Alexandre Poliakov","orcid":null},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I2801780550","display_name":"California Pacific Medical Center","ror":"https://ror.org/02bjh0167","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I114073160","https://openalex.org/I2801780550"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Alexandre Poliakov","raw_affiliation_strings":["1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I188891513","https://openalex.org/I196679689","https://openalex.org/I2801780550"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058320928","display_name":"Nathan Salomonis","orcid":"https://orcid.org/0000-0001-9689-2469"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I2801780550","display_name":"California Pacific Medical Center","ror":"https://ror.org/02bjh0167","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I114073160","https://openalex.org/I2801780550"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nathan Salomonis","raw_affiliation_strings":["1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I188891513","https://openalex.org/I196679689","https://openalex.org/I2801780550"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5048467633","display_name":"Simon Minovitsky","orcid":null},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I2801780550","display_name":"California Pacific Medical Center","ror":"https://ror.org/02bjh0167","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I114073160","https://openalex.org/I2801780550"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Simon Minovitsky","raw_affiliation_strings":["1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I188891513","https://openalex.org/I196679689","https://openalex.org/I2801780550"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5106441010","display_name":"Rolf Bodmer","orcid":"https://orcid.org/0000-0001-9087-1210"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I2801780550","display_name":"California Pacific Medical Center","ror":"https://ror.org/02bjh0167","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I114073160","https://openalex.org/I2801780550"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Rolf Bodmer","raw_affiliation_strings":["1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I188891513","https://openalex.org/I196679689","https://openalex.org/I2801780550"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5013084636","display_name":"Alexander C. Zambon","orcid":"https://orcid.org/0000-0001-7874-4462"},"institutions":[{"id":"https://openalex.org/I148283060","display_name":"Lawrence Berkeley National Laboratory","ror":"https://ror.org/02jbv0t02","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I188891513","display_name":"Sanford Burnham Prebys Medical Discovery Institute","ror":"https://ror.org/03m1g2s55","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I188891513"]},{"id":"https://openalex.org/I196679689","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337","country_code":"US","type":"facility","lineage":["https://openalex.org/I1330989302","https://openalex.org/I148283060","https://openalex.org/I196679689","https://openalex.org/I39565521"]},{"id":"https://openalex.org/I2801780550","display_name":"California Pacific Medical Center","ror":"https://ror.org/02bjh0167","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I114073160","https://openalex.org/I2801780550"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Alexander C. Zambon","raw_affiliation_strings":["1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"1 Genomics Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA, 2DOE Joint Genome Institute, Walnut Creek, CA 94598, USA, 3Departments of Pharmacology and Medicine, University of California at San Diego, La Jolla, CA 92093, USA, 4California Pacific Medical Center Research Institute, San Francisco, CA 94107, USA and 5Development and Aging Program, Sanford-Burnham Medical Research Institute, La Jolla, CA 92037, USA","institution_ids":["https://openalex.org/I148283060","https://openalex.org/I188891513","https://openalex.org/I196679689","https://openalex.org/I2801780550"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5013084636","https://openalex.org/A5107834893"],"corresponding_institution_ids":["https://openalex.org/I148283060","https://openalex.org/I188891513","https://openalex.org/I196679689","https://openalex.org/I2801780550"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":null,"fwci":1.9268,"has_fulltext":true,"cited_by_count":23,"citation_normalized_percentile":{"value":0.86141669,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"29","issue":"16","first_page":"2059","last_page":"2061"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9269999861717224,"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":0.9269999861717224,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.025699999183416367,"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/T12254","display_name":"Machine Learning in Bioinformatics","score":0.006800000090152025,"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/genome","display_name":"Genome","score":0.7333256006240845},{"id":"https://openalex.org/keywords/genome-browser","display_name":"Genome browser","score":0.7137923836708069},{"id":"https://openalex.org/keywords/promoter","display_name":"Promoter","score":0.6649910807609558},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.6138712763786316},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.5803940892219543},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5665359497070312},{"id":"https://openalex.org/keywords/dna-binding-site","display_name":"DNA binding site","score":0.5267897248268127},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5264930129051208},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.4720797538757324},{"id":"https://openalex.org/keywords/cis-regulatory-module","display_name":"Cis-regulatory module","score":0.4626205265522003},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.3724982738494873},{"id":"https://openalex.org/keywords/genomics","display_name":"Genomics","score":0.34044450521469116},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.281150758266449},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.15029320120811462}],"concepts":[{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.7333256006240845},{"id":"https://openalex.org/C2781148417","wikidata":"https://www.wikidata.org/wiki/Q5533486","display_name":"Genome browser","level":5,"score":0.7137923836708069},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.6649910807609558},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.6138712763786316},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5803940892219543},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5665359497070312},{"id":"https://openalex.org/C3662595","wikidata":"https://www.wikidata.org/wiki/Q5205743","display_name":"DNA binding site","level":5,"score":0.5267897248268127},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5264930129051208},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4720797538757324},{"id":"https://openalex.org/C190796033","wikidata":"https://www.wikidata.org/wiki/Q1093165","display_name":"Cis-regulatory module","level":5,"score":0.4626205265522003},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.3724982738494873},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.34044450521469116},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.281150758266449},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.15029320120811462}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D011401","descriptor_name":"Promoter Regions, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","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":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","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":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btt318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt318","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/16/2059/49077015/bioinformatics_29_16_2059.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:23736530","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23736530","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":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:europepmc.org:3099814","is_oa":false,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3722517","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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btt318","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt318","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/16/2059/49077015/bioinformatics_29_16_2059.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"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":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","score":0.41999998688697815,"id":"https://metadata.un.org/sdg/17"}],"awards":[{"id":"https://openalex.org/G1286236842","display_name":null,"funder_award_id":"-AC02-05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1414775356","display_name":null,"funder_award_id":"No. DE-AC02- 05-CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G1754231898","display_name":null,"funder_award_id":"R01 HL54732","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G1816284028","display_name":null,"funder_award_id":"Contract No. DE-AC02-05-CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G1861845559","display_name":null,"funder_award_id":"P01 AG033561","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G2112935040","display_name":null,"funder_award_id":"10SDG2630130","funder_id":"https://openalex.org/F4320306230","funder_display_name":"American Heart Association"},{"id":"https://openalex.org/G2292626618","display_name":null,"funder_award_id":"8UL1TR000100","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G2306795758","display_name":null,"funder_award_id":"P01 HL098053","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3083819904","display_name":null,"funder_award_id":"05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G365575497","display_name":null,"funder_award_id":"No. DE-AC02-05-CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G3823137783","display_name":null,"funder_award_id":"1U54HL08460","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G382641700","display_name":null,"funder_award_id":"DE-AC02\u201305CH11231","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3953114765","display_name":null,"funder_award_id":"P01AG033561","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G419881185","display_name":null,"funder_award_id":"DEAC02\u201305CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G42916606","display_name":null,"funder_award_id":"DE AC02 05CH11231","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"},{"id":"https://openalex.org/G4501827968","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G498139845","display_name":null,"funder_award_id":"DE-AC02","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G5053987926","display_name":null,"funder_award_id":"R01 HL54732","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G5878053389","display_name":null,"funder_award_id":"P01 HL0980539","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G610060463","display_name":null,"funder_award_id":"P01-HL-098053","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G7205239661","display_name":null,"funder_award_id":"AC02-05CH11231","funder_id":"https://openalex.org/F4320316170","funder_display_name":"Joint Genome Institute"},{"id":"https://openalex.org/G7523504524","display_name":null,"funder_award_id":"R01 HL091495","funder_id":"https://openalex.org/F4320337338","funder_display_name":"National Heart, Lung, and Blood Institute"},{"id":"https://openalex.org/G7630368773","display_name":null,"funder_award_id":"HL54732","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G805243471","display_name":null,"funder_award_id":"Contract No. DE-AC02-05CH11231","funder_id":"https://openalex.org/F4320332359","funder_display_name":"Office of Science"},{"id":"https://openalex.org/G834277795","display_name":null,"funder_award_id":"DE\u2013AC02\u201305CH11231","funder_id":"https://openalex.org/F4320316170","funder_display_name":"Joint Genome Institute"},{"id":"https://openalex.org/G969889393","display_name":null,"funder_award_id":"DE-AC02-","funder_id":"https://openalex.org/F4320306084","funder_display_name":"U.S. Department of Energy"}],"funders":[{"id":"https://openalex.org/F4320306084","display_name":"U.S. Department of Energy","ror":"https://ror.org/01bj3aw27"},{"id":"https://openalex.org/F4320306230","display_name":"American Heart Association","ror":"https://ror.org/013kjyp64"},{"id":"https://openalex.org/F4320316170","display_name":"Joint Genome Institute","ror":"https://ror.org/04xm1d337"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332359","display_name":"Office of Science","ror":"https://ror.org/00mmn6b08"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"},{"id":"https://openalex.org/F4320337338","display_name":"National Heart, Lung, and Blood Institute","ror":"https://ror.org/012pb6c26"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2131719528.pdf","grobid_xml":"https://content.openalex.org/works/W2131719528.grobid-xml"},"referenced_works_count":12,"referenced_works":["https://openalex.org/W2030500606","https://openalex.org/W2065579185","https://openalex.org/W2078845557","https://openalex.org/W2079670268","https://openalex.org/W2098816661","https://openalex.org/W2113117122","https://openalex.org/W2129943843","https://openalex.org/W2135030836","https://openalex.org/W2145748421","https://openalex.org/W2146368849","https://openalex.org/W2170677539","https://openalex.org/W2172121366"],"related_works":["https://openalex.org/W1971216836","https://openalex.org/W2146517458","https://openalex.org/W1984003821","https://openalex.org/W2117549173","https://openalex.org/W2166221896","https://openalex.org/W1759033142","https://openalex.org/W2042252096","https://openalex.org/W2334377329","https://openalex.org/W2130750927","https://openalex.org/W2789707457"],"abstract_inverted_index":{"SUMMARY:":[0],"We":[1],"have":[2],"developed":[3],"a":[4,75,101,127],"web-based":[5],"query":[6,31,107,120],"tool,":[7],"Whole-Genome":[8],"rVISTA":[9],"(WGRV),":[10],"that":[11],"determines":[12],"enrichment":[13],"of":[14,24,37,55,78,103,140],"transcription":[15,40],"factors":[16],"(TFs)":[17],"and":[18,58,85,115,144],"associated":[19],"target":[20],"genes":[21,104],"in":[22,44,118,126,133],"sets":[23],"co-regulated":[25,79],"genes.":[26],"WGRV":[27,81],"enables":[28],"users":[29],"to":[30,51],"databases":[32],"containing":[33,109],"pre-computed":[34],"genome":[35,136],"coordinates":[36,147],"evolutionarily":[38,86],"conserved":[39,87,142],"factor":[41],"binding":[42,62,88,113],"sites":[43,63,114,143],"the":[45,70,92,106,110,119,134],"proximal":[46],"promoters":[47],"(from":[48],"100":[49],"bp":[50],"5":[52],"kb":[53],"upstream)":[54],"human,":[56],"mouse":[57],"Drosophila":[59],"genomes.":[60],"TF":[61,112],"are":[64,124,148],"based":[65],"on":[66],"position-weight":[67],"matrices":[68],"from":[69,105],"TRANSFAC":[71],"Professional":[72],"database.":[73],"For":[74],"given":[76],"set":[77,108,121],"genes,":[80],"returns":[82],"statistically":[83],"enriched":[84,111],"sites,":[89],"mapped":[90,141],"by":[91],"regulatory":[93],"VISTA":[94],"(rVISTA)":[95],"algorithm.":[96],"Users":[97],"can":[98],"then":[99],"retrieve":[100],"list":[102],"their":[116,145],"location":[117],"promoters.":[122],"Results":[123],"exported":[125],"BED":[128],"format":[129],"for":[130,151],"rapid":[131],"visualization":[132],"UCSC":[135],"browser.":[137],"Flat":[138],"files":[139],"genomic":[146],"also":[149],"available":[150],"analysis":[152],"with":[153],"stand-alone":[154],"software.":[155],"AVAILABILITY:":[156],"http://genome.lbl.gov/cgi-bin/WGRVistaInputCommon.pl.":[157]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":1},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":3},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}
