{"id":"https://openalex.org/W4401855723","doi":"https://doi.org/10.1093/gpbjnl/qzae059","title":"eRNA-IDO: A One-stop Platform for Identification, Interactome Discovery, and Functional Annotation of Enhancer RNAs","display_name":"eRNA-IDO: A One-stop Platform for Identification, Interactome Discovery, and Functional Annotation of Enhancer RNAs","publication_year":2024,"publication_date":"2024-08-01","ids":{"openalex":"https://openalex.org/W4401855723","doi":"https://doi.org/10.1093/gpbjnl/qzae059","pmid":"https://pubmed.ncbi.nlm.nih.gov/39178387"},"language":"en","primary_location":{"id":"doi:10.1093/gpbjnl/qzae059","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gpbjnl/qzae059","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://doi.org/10.1093/gpbjnl/qzae059","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100326584","display_name":"Yuwei Zhang","orcid":"https://orcid.org/0000-0002-8395-3020"},"institutions":[{"id":"https://openalex.org/I109935558","display_name":"Ningbo University","ror":"https://ror.org/03et85d35","country_code":"CN","type":"education","lineage":["https://openalex.org/I109935558"]},{"id":"https://openalex.org/I4210143588","display_name":"Ningbo College of Health Sciences","ror":"https://ror.org/041tqx430","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210143588"]},{"id":"https://openalex.org/I4210166576","display_name":"First Affiliated Hospital Zhejiang University","ror":"https://ror.org/05m1p5x56","country_code":"CN","type":"healthcare","lineage":["https://openalex.org/I4210166576"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Yuwei Zhang","raw_affiliation_strings":["Biomedical Big Data Center, the First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310003,","School of Public Health, Health Science Center, Ningbo University , Ningbo 315211,","Biomedical Big Data Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China","School of Public Health, Health Science Center, Ningbo University, Ningbo 315211, China"],"affiliations":[{"raw_affiliation_string":"Biomedical Big Data Center, the First Affiliated Hospital, Zhejiang University School of Medicine , Hangzhou 310003,","institution_ids":["https://openalex.org/I4210166576"]},{"raw_affiliation_string":"School of Public Health, Health Science Center, Ningbo University , Ningbo 315211,","institution_ids":["https://openalex.org/I109935558","https://openalex.org/I4210143588"]},{"raw_affiliation_string":"Biomedical Big Data Center, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310003, China","institution_ids":["https://openalex.org/I4210166576"]},{"raw_affiliation_string":"School of Public Health, Health Science Center, Ningbo University, Ningbo 315211, China","institution_ids":["https://openalex.org/I109935558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5086631219","display_name":"Lihai Gong","orcid":"https://orcid.org/0009-0007-0880-8177"},"institutions":[{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lihai Gong","raw_affiliation_strings":["Institute of Systems and Physical Biology, Shenzhen Bay Laboratory , Shenzhen 518107,","Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China"],"affiliations":[{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory , Shenzhen 518107,","institution_ids":["https://openalex.org/I4210102541"]},{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China","institution_ids":["https://openalex.org/I4210102541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024571968","display_name":"Ruofan Ding","orcid":"https://orcid.org/0000-0003-1667-9866"},"institutions":[{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Ruofan Ding","raw_affiliation_strings":["Institute of Systems and Physical Biology, Shenzhen Bay Laboratory , Shenzhen 518107,","Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China"],"affiliations":[{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory , Shenzhen 518107,","institution_ids":["https://openalex.org/I4210102541"]},{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China","institution_ids":["https://openalex.org/I4210102541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101511923","display_name":"Wenyan Chen","orcid":"https://orcid.org/0000-0002-4821-9306"},"institutions":[{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Wenyan Chen","raw_affiliation_strings":["Institute of Systems and Physical Biology, Shenzhen Bay Laboratory , Shenzhen 518107,","Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China"],"affiliations":[{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory , Shenzhen 518107,","institution_ids":["https://openalex.org/I4210102541"]},{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China","institution_ids":["https://openalex.org/I4210102541"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101510116","display_name":"Hao Rong","orcid":"https://orcid.org/0000-0002-1650-0670"},"institutions":[{"id":"https://openalex.org/I109935558","display_name":"Ningbo University","ror":"https://ror.org/03et85d35","country_code":"CN","type":"education","lineage":["https://openalex.org/I109935558"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hao Rong","raw_affiliation_strings":["School of Clinical Medicine, Health Science Center, Ningbo University , Ningbo 315211,","School of Clinical Medicine, Health Science Center, Ningbo University, Ningbo 315211, China"],"affiliations":[{"raw_affiliation_string":"School of Clinical Medicine, Health Science Center, Ningbo University , Ningbo 315211,","institution_ids":["https://openalex.org/I109935558"]},{"raw_affiliation_string":"School of Clinical Medicine, Health Science Center, Ningbo University, Ningbo 315211, China","institution_ids":["https://openalex.org/I109935558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100631613","display_name":"Yanguo Li","orcid":null},"institutions":[{"id":"https://openalex.org/I109935558","display_name":"Ningbo University","ror":"https://ror.org/03et85d35","country_code":"CN","type":"education","lineage":["https://openalex.org/I109935558"]},{"id":"https://openalex.org/I159389169","display_name":"Ningbo University of Technology","ror":"https://ror.org/037dym702","country_code":"CN","type":"education","lineage":["https://openalex.org/I159389169"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yanguo Li","raw_affiliation_strings":["Institute of Drug Discovery Technology, Ningbo University , Ningbo 315211,","Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China"],"affiliations":[{"raw_affiliation_string":"Institute of Drug Discovery Technology, Ningbo University , Ningbo 315211,","institution_ids":["https://openalex.org/I159389169"]},{"raw_affiliation_string":"Institute of Drug Discovery Technology, Ningbo University, Ningbo 315211, China","institution_ids":["https://openalex.org/I109935558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5093535677","display_name":"Fawziya Shameem","orcid":null},"institutions":[{"id":"https://openalex.org/I109935558","display_name":"Ningbo University","ror":"https://ror.org/03et85d35","country_code":"CN","type":"education","lineage":["https://openalex.org/I109935558"]},{"id":"https://openalex.org/I4210143588","display_name":"Ningbo College of Health Sciences","ror":"https://ror.org/041tqx430","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210143588"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Fawziya Shameem","raw_affiliation_strings":["School of Public Health, Health Science Center, Ningbo University , Ningbo 315211,","School of Public Health, Health Science Center, Ningbo University, Ningbo 315211, China"],"affiliations":[{"raw_affiliation_string":"School of Public Health, Health Science Center, Ningbo University , Ningbo 315211,","institution_ids":["https://openalex.org/I109935558","https://openalex.org/I4210143588"]},{"raw_affiliation_string":"School of Public Health, Health Science Center, Ningbo University, Ningbo 315211, China","institution_ids":["https://openalex.org/I109935558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102594733","display_name":"Korakkandan Arshad Ali","orcid":"https://orcid.org/0009-0001-5987-1367"},"institutions":[{"id":"https://openalex.org/I109935558","display_name":"Ningbo University","ror":"https://ror.org/03et85d35","country_code":"CN","type":"education","lineage":["https://openalex.org/I109935558"]},{"id":"https://openalex.org/I4210143588","display_name":"Ningbo College of Health Sciences","ror":"https://ror.org/041tqx430","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210143588"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Korakkandan Arshad Ali","raw_affiliation_strings":["School of Public Health, Health Science Center, Ningbo University , Ningbo 315211,","School of Public Health, Health Science Center, Ningbo University, Ningbo 315211, China"],"affiliations":[{"raw_affiliation_string":"School of Public Health, Health Science Center, Ningbo University , Ningbo 315211,","institution_ids":["https://openalex.org/I109935558","https://openalex.org/I4210143588"]},{"raw_affiliation_string":"School of Public Health, Health Science Center, Ningbo University, Ningbo 315211, China","institution_ids":["https://openalex.org/I109935558"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100440418","display_name":"Lei Li","orcid":"https://orcid.org/0000-0003-3924-2544"},"institutions":[{"id":"https://openalex.org/I4210102541","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210102541"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Lei Li","raw_affiliation_strings":["Institute of Systems and Physical Biology, Shenzhen Bay Laboratory , Shenzhen 518107,","Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China"],"affiliations":[{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory , Shenzhen 518107,","institution_ids":["https://openalex.org/I4210102541"]},{"raw_affiliation_string":"Institute of Systems and Physical Biology, Shenzhen Bay Laboratory, Shenzhen 518107, China","institution_ids":["https://openalex.org/I4210102541"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5102004889","display_name":"Qi Liao","orcid":"https://orcid.org/0000-0001-6796-104X"},"institutions":[{"id":"https://openalex.org/I109935558","display_name":"Ningbo University","ror":"https://ror.org/03et85d35","country_code":"CN","type":"education","lineage":["https://openalex.org/I109935558"]},{"id":"https://openalex.org/I4210143588","display_name":"Ningbo College of Health Sciences","ror":"https://ror.org/041tqx430","country_code":"CN","type":"education","lineage":["https://openalex.org/I4210143588"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qi Liao","raw_affiliation_strings":["School of Public Health, Health Science Center, Ningbo University , Ningbo 315211,","School of Public Health, Health Science Center, Ningbo University, Ningbo 315211, China"],"affiliations":[{"raw_affiliation_string":"School of Public Health, Health Science Center, Ningbo University , Ningbo 315211,","institution_ids":["https://openalex.org/I109935558","https://openalex.org/I4210143588"]},{"raw_affiliation_string":"School of Public Health, Health Science Center, Ningbo University, Ningbo 315211, China","institution_ids":["https://openalex.org/I109935558"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":10,"corresponding_author_ids":["https://openalex.org/A5100326584"],"corresponding_institution_ids":["https://openalex.org/I109935558","https://openalex.org/I4210143588","https://openalex.org/I4210166576"],"apc_list":{"value":3500,"currency":"USD","value_usd":3500},"apc_paid":{"value":3500,"currency":"USD","value_usd":3500},"fwci":1.3686,"has_fulltext":true,"cited_by_count":6,"citation_normalized_percentile":{"value":0.80748419,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":96,"max":98},"biblio":{"volume":"22","issue":"4","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9998999834060669,"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":0.9998999834060669,"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":0.9995999932289124,"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/T11482","display_name":"RNA modifications and cancer","score":0.9993000030517578,"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/interactome","display_name":"Interactome","score":0.8726983070373535},{"id":"https://openalex.org/keywords/enhancer","display_name":"Enhancer","score":0.6905949115753174},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.6598417162895203},{"id":"https://openalex.org/keywords/identification","display_name":"Identification (biology)","score":0.46236422657966614},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.43134838342666626},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.3831096887588501},{"id":"https://openalex.org/keywords/transcription-factor","display_name":"Transcription factor","score":0.37018492817878723},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3422788679599762},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.26301687955856323}],"concepts":[{"id":"https://openalex.org/C9760119","wikidata":"https://www.wikidata.org/wiki/Q841382","display_name":"Interactome","level":3,"score":0.8726983070373535},{"id":"https://openalex.org/C111936080","wikidata":"https://www.wikidata.org/wiki/Q913367","display_name":"Enhancer","level":4,"score":0.6905949115753174},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6598417162895203},{"id":"https://openalex.org/C116834253","wikidata":"https://www.wikidata.org/wiki/Q2039217","display_name":"Identification (biology)","level":2,"score":0.46236422657966614},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43134838342666626},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3831096887588501},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.37018492817878723},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3422788679599762},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.26301687955856323},{"id":"https://openalex.org/C59822182","wikidata":"https://www.wikidata.org/wiki/Q441","display_name":"Botany","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000095499","descriptor_name":"Enhancer RNAs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095499","descriptor_name":"Enhancer RNAs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095499","descriptor_name":"Enhancer RNAs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095499","descriptor_name":"Enhancer RNAs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095499","descriptor_name":"Enhancer RNAs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000095499","descriptor_name":"Enhancer RNAs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D004742","descriptor_name":"Enhancer Elements, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"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":"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":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D012313","descriptor_name":"RNA","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"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":"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":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/gpbjnl/qzae059","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gpbjnl/qzae059","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},{"id":"pmid:39178387","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/39178387","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":"Genomics, proteomics & bioinformatics","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:11514848","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/11514848","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC11514848/pdf/qzae059.pdf","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":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Genomics Proteomics Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/gpbjnl/qzae059","is_oa":true,"landing_page_url":"https://doi.org/10.1093/gpbjnl/qzae059","pdf_url":null,"source":{"id":"https://openalex.org/S155547894","display_name":"Genomics Proteomics & Bioinformatics","issn_l":"1672-0229","issn":["1672-0229","2210-3244"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320990","host_organization_name":"Elsevier BV","host_organization_lineage":["https://openalex.org/P4310320990"],"host_organization_lineage_names":["Elsevier BV"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Genomics, Proteomics &amp; Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G163923174","display_name":null,"funder_award_id":"SZBL2021080601001","funder_id":"https://openalex.org/F4320331248","funder_display_name":"Shenzhen Bay Laboratory"},{"id":"https://openalex.org/G2087396116","display_name":null,"funder_award_id":"China","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G2981938667","display_name":null,"funder_award_id":"Shenzhen","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3085993365","display_name":null,"funder_award_id":"(Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3317480652","display_name":null,"funder_award_id":"Science","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G3420414886","display_name":null,"funder_award_id":"601001","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G391238517","display_name":null,"funder_award_id":", and","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G4227595719","display_name":null,"funder_award_id":"32300430","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5493769407","display_name":null,"funder_award_id":"32100533","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5762773393","display_name":null,"funder_award_id":"202108","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5904485574","display_name":null,"funder_award_id":"31970630","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G5994120800","display_name":null,"funder_award_id":"Natural","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7336270407","display_name":null,"funder_award_id":"LY21C060002","funder_id":"https://openalex.org/F4320338464","funder_display_name":"Natural Science Foundation of Zhejiang Province"},{"id":"https://openalex.org/G7726157001","display_name":null,"funder_award_id":"Grant No.","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G8955107213","display_name":null,"funder_award_id":"Major","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320331248","display_name":"Shenzhen Bay Laboratory","ror":"https://ror.org/00sdcjz77"},{"id":"https://openalex.org/F4320338464","display_name":"Natural Science Foundation of Zhejiang Province","ror":"https://ror.org/01h0zpd94"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":56,"referenced_works":["https://openalex.org/W978145915","https://openalex.org/W1834862890","https://openalex.org/W1981974167","https://openalex.org/W2027347575","https://openalex.org/W2053293102","https://openalex.org/W2111099379","https://openalex.org/W2138207763","https://openalex.org/W2160313295","https://openalex.org/W2179977976","https://openalex.org/W2214074259","https://openalex.org/W2235841654","https://openalex.org/W2527824902","https://openalex.org/W2578822114","https://openalex.org/W2610159395","https://openalex.org/W2615786037","https://openalex.org/W2762129112","https://openalex.org/W2767904963","https://openalex.org/W2770026599","https://openalex.org/W2779442968","https://openalex.org/W2789609639","https://openalex.org/W2789794079","https://openalex.org/W2792264137","https://openalex.org/W2792595343","https://openalex.org/W2797262602","https://openalex.org/W2898789672","https://openalex.org/W2901027836","https://openalex.org/W2944310291","https://openalex.org/W2979624544","https://openalex.org/W2989837622","https://openalex.org/W3000068022","https://openalex.org/W3010299821","https://openalex.org/W3024997712","https://openalex.org/W3045910546","https://openalex.org/W3091019271","https://openalex.org/W3097471811","https://openalex.org/W3105910321","https://openalex.org/W3111061871","https://openalex.org/W3130001625","https://openalex.org/W3133859624","https://openalex.org/W3159940140","https://openalex.org/W3165793769","https://openalex.org/W3189237835","https://openalex.org/W3192868352","https://openalex.org/W3195654716","https://openalex.org/W3200887597","https://openalex.org/W4200260682","https://openalex.org/W4206027885","https://openalex.org/W4213151014","https://openalex.org/W4220800475","https://openalex.org/W4293577203","https://openalex.org/W4294675785","https://openalex.org/W4297147390","https://openalex.org/W4307845770","https://openalex.org/W4366224338","https://openalex.org/W4387966116","https://openalex.org/W6770304583"],"related_works":["https://openalex.org/W4292634579","https://openalex.org/W2022326234","https://openalex.org/W1531941329","https://openalex.org/W4388694323","https://openalex.org/W3215098729","https://openalex.org/W4243081378","https://openalex.org/W1979330259","https://openalex.org/W2622356054","https://openalex.org/W2804670115","https://openalex.org/W4303699336"],"abstract_inverted_index":{"Growing":[0],"evidence":[1],"supports":[2],"the":[3,40,46,104,121,150],"transcription":[4],"of":[5,53,77,154],"enhancer":[6,78,84],"RNAs":[7],"(eRNAs)":[8],"and":[9,22,50,61,87,99,114,140,152],"their":[10,17,23],"important":[11],"roles":[12],"in":[13,127,137],"gene":[14],"regulation.":[15],"However,":[16],"interactions":[18],"with":[19],"other":[20],"biomolecules":[21],"corresponding":[24],"functionality":[25],"remain":[26],"poorly":[27],"understood.":[28],"In":[29,89],"an":[30],"attempt":[31],"to":[32,82],"facilitate":[33,147],"mechanistic":[34],"research,":[35],"this":[36],"study":[37],"presents":[38],"eRNA-IDO,":[39],"first":[41],"integrative":[42],"computational":[43],"platform":[44],"for":[45,96],"identification,":[47],"interactome":[48,106],"discovery,":[49],"functional":[51,94],"annotation":[52,95],"human":[54],"eRNAs.":[55,155],"eRNA-IDO":[56,145,157],"comprises":[57],"two":[58],"modules:":[59],"eRNA-ID":[60,64,73],"eRNA-Anno.":[62],"Functionally,":[63],"can":[65,146],"identify":[66],"eRNAs":[67,101,113],"from":[68,107],"de":[69],"novo":[70],"assembled":[71],"transcriptomes.":[72],"includes":[74],"eight":[75],"kinds":[76],"makers,":[79],"enabling":[80],"users":[81],"customize":[83],"regions":[85],"flexibly":[86],"conveniently.":[88],"addition,":[90],"eRNA-Anno":[91],"provides":[92],"cell-/tissue-specific":[93],"both":[97],"new":[98],"known":[100],"by":[102],"analyzing":[103],"eRNA":[105],"prebuilt":[108,118],"or":[109],"user-defined":[110],"networks":[111,119,126,136],"between":[112],"protein-coding":[115],"genes.":[116],"The":[117,130,156],"include":[120],"Genotype-Tissue":[122],"Expression":[123],"(GTEx)-based":[124],"co-expression":[125,135],"normal":[128],"tissues,":[129,139],"Cancer":[131],"Genome":[132],"Atlas":[133],"(TCGA)-based":[134],"cancer":[138],"omics-based":[141],"eRNA-centric":[142],"regulatory":[143],"networks.":[144],"research":[148],"on":[149],"biogenesis":[151],"functions":[153],"server":[158],"is":[159],"freely":[160],"available":[161],"at":[162],"http://bioinfo.szbl.ac.cn/eRNA_IDO/.":[163]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":5}],"updated_date":"2026-04-13T07:58:08.660418","created_date":"2025-10-10T00:00:00"}
