{"id":"https://openalex.org/W1981710287","doi":"https://doi.org/10.1109/isb.2012.6314122","title":"cGRNexp: a web platform for building combinatorial gene regulation networks based on user-uploaded gene expression datasets","display_name":"cGRNexp: a web platform for building combinatorial gene regulation networks based on user-uploaded gene expression datasets","publication_year":2012,"publication_date":"2012-08-01","ids":{"openalex":"https://openalex.org/W1981710287","doi":"https://doi.org/10.1109/isb.2012.6314122","mag":"1981710287"},"language":"en","primary_location":{"id":"doi:10.1109/isb.2012.6314122","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isb.2012.6314122","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 6th International Conference on Systems Biology (ISB)","raw_type":"proceedings-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079900267","display_name":"Huayong Xu","orcid":null},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":true,"raw_author_name":"Huayong Xu","raw_affiliation_strings":["School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shangai, China"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shangai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5024895838","display_name":"Hui Yu","orcid":"https://orcid.org/0000-0002-4491-8855"},"institutions":[{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Hui Yu","raw_affiliation_strings":["Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China","Shanghai Center for Bioinformation Technology, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]},{"raw_affiliation_string":"Shanghai Center for Bioinformation Technology, Shanghai, China","institution_ids":["https://openalex.org/I4210162648"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082656015","display_name":"Kang Tu","orcid":"https://orcid.org/0000-0003-4314-2896"},"institutions":[{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Kang Tu","raw_affiliation_strings":["Shanghai Center for Bioinformation Technology, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Shanghai Center for Bioinformation Technology, Shanghai, China","institution_ids":["https://openalex.org/I4210162648"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058311447","display_name":"Qianqian Shi","orcid":"https://orcid.org/0000-0002-5266-6731"},"institutions":[{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Qianqian Shi","raw_affiliation_strings":["Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010368404","display_name":"Chaochun Wei","orcid":"https://orcid.org/0000-0002-1031-034X"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Chaochun Wei","raw_affiliation_strings":["School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shangai, China"],"affiliations":[{"raw_affiliation_string":"School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shangai, China","institution_ids":["https://openalex.org/I183067930"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100384402","display_name":"Yuanyuan Li","orcid":"https://orcid.org/0000-0001-8755-4695"},"institutions":[{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yuanyuan Li","raw_affiliation_strings":["Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China","School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shangai, China","Shanghai Center for Bioinformation Technology, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]},{"raw_affiliation_string":"School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shangai, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Shanghai Center for Bioinformation Technology, Shanghai, China","institution_ids":["https://openalex.org/I4210162648"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5008280608","display_name":"Yixue Li","orcid":"https://orcid.org/0000-0002-1198-7176"},"institutions":[{"id":"https://openalex.org/I4210162648","display_name":"Shanghai Center For Bioinformation Technology","ror":"https://ror.org/04nyf1f54","country_code":"CN","type":"facility","lineage":["https://openalex.org/I4210162648"]},{"id":"https://openalex.org/I19820366","display_name":"Chinese Academy of Sciences","ror":"https://ror.org/034t30j35","country_code":"CN","type":"funder","lineage":["https://openalex.org/I19820366"]},{"id":"https://openalex.org/I4210106477","display_name":"Shanghai Institutes for Biological Sciences","ror":"https://ror.org/011rf9d86","country_code":"CN","type":"facility","lineage":["https://openalex.org/I19820366","https://openalex.org/I4210106477"]},{"id":"https://openalex.org/I183067930","display_name":"Shanghai Jiao Tong University","ror":"https://ror.org/0220qvk04","country_code":"CN","type":"education","lineage":["https://openalex.org/I183067930"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Yixue Li","raw_affiliation_strings":["Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China","School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shangai, China","Shanghai Center for Bioinformation Technology, Shanghai, China"],"affiliations":[{"raw_affiliation_string":"Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China","institution_ids":["https://openalex.org/I4210106477","https://openalex.org/I19820366"]},{"raw_affiliation_string":"School of Life Sciences and Biotechnology, Shanghai Jiaotong University, Shangai, China","institution_ids":["https://openalex.org/I183067930"]},{"raw_affiliation_string":"Shanghai Center for Bioinformation Technology, Shanghai, China","institution_ids":["https://openalex.org/I4210162648"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":7,"corresponding_author_ids":["https://openalex.org/A5079900267"],"corresponding_institution_ids":["https://openalex.org/I183067930"],"apc_list":null,"apc_paid":null,"fwci":0.1313,"has_fulltext":false,"cited_by_count":1,"citation_normalized_percentile":{"value":0.49889529,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"1","issue":null,"first_page":"113","last_page":"117"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10604","display_name":"RNA Research and Splicing","score":0.9983000159263611,"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/T10604","display_name":"RNA Research and Splicing","score":0.9983000159263611,"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/T10207","display_name":"Advanced biosensing and bioanalysis techniques","score":0.9977999925613403,"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/T11970","display_name":"Molecular Biology Techniques and Applications","score":0.9968000054359436,"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/upload","display_name":"Upload","score":0.8656996488571167},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6391867995262146},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.570221483707428},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.4864811599254608},{"id":"https://openalex.org/keywords/web-server","display_name":"Web server","score":0.4848085939884186},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4416036307811737},{"id":"https://openalex.org/keywords/expression","display_name":"Expression (computer science)","score":0.42898616194725037},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.3852459192276001},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.335201233625412},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.32410502433776855},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.3128563463687897},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.26114505529403687},{"id":"https://openalex.org/keywords/the-internet","display_name":"The Internet","score":0.2489735186100006},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.24694475531578064},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.11856138706207275}],"concepts":[{"id":"https://openalex.org/C71901391","wikidata":"https://www.wikidata.org/wiki/Q7126699","display_name":"Upload","level":2,"score":0.8656996488571167},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6391867995262146},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.570221483707428},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.4864811599254608},{"id":"https://openalex.org/C11392498","wikidata":"https://www.wikidata.org/wiki/Q11288","display_name":"Web server","level":3,"score":0.4848085939884186},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4416036307811737},{"id":"https://openalex.org/C90559484","wikidata":"https://www.wikidata.org/wiki/Q778379","display_name":"Expression (computer science)","level":2,"score":0.42898616194725037},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3852459192276001},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.335201233625412},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32410502433776855},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3128563463687897},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.26114505529403687},{"id":"https://openalex.org/C110875604","wikidata":"https://www.wikidata.org/wiki/Q75","display_name":"The Internet","level":2,"score":0.2489735186100006},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.24694475531578064},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11856138706207275},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.1109/isb.2012.6314122","is_oa":false,"landing_page_url":"https://doi.org/10.1109/isb.2012.6314122","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"2012 IEEE 6th International Conference on Systems Biology (ISB)","raw_type":"proceedings-article"}],"best_oa_location":null,"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":16,"referenced_works":["https://openalex.org/W130589596","https://openalex.org/W1980389572","https://openalex.org/W1987067655","https://openalex.org/W1992696908","https://openalex.org/W2006348395","https://openalex.org/W2016903963","https://openalex.org/W2030371558","https://openalex.org/W2092501057","https://openalex.org/W2106085645","https://openalex.org/W2121796038","https://openalex.org/W2125321800","https://openalex.org/W2153234291","https://openalex.org/W2155142785","https://openalex.org/W2168251502","https://openalex.org/W2517751726","https://openalex.org/W3104970623"],"related_works":["https://openalex.org/W2944823289","https://openalex.org/W3037018281","https://openalex.org/W2003209439","https://openalex.org/W4321854979","https://openalex.org/W2358319515","https://openalex.org/W2972592048","https://openalex.org/W4312214821","https://openalex.org/W2497626292","https://openalex.org/W4234342421","https://openalex.org/W2909040123"],"abstract_inverted_index":{"While":[0],"we":[1,25,66,86],"witness":[2],"rapid":[3],"progresses":[4],"in":[5,132],"development":[6],"of":[7,29,90,123],"methodologies/algorithms":[8],"for":[9,34,72,99,146],"constructing":[10],"and":[11,22,53,94,105,113,136],"analyzing":[12],"the":[13,55,61,111,133,150],"combinatorial":[14,56,74,152],"regulation":[15,76],"network":[16],"which":[17],"includes":[18],"both":[19],"TF":[20],"regulators":[21],"miRNA":[23,124],"regulators,":[24],"find":[26],"a":[27,69,120],"lack":[28],"tools":[30],"or":[31,125],"servers":[32],"available":[33],"facilitating":[35],"related":[36],"works.":[37],"A":[38],"web":[39,70,139],"service":[40],"is":[41,161],"especially":[42],"needed":[43],"that":[44],"allows":[45],"user":[46],"to":[47],"upload":[48],"their":[49,156],"own":[50,157],"expression":[51,82,103,108,127,158],"datasets":[52,104,128],"mine":[54,149],"gene":[57,75,81,102],"reglatory":[58],"networks":[59,77,154],"regarding":[60],"particular":[62],"experimental":[63],"context.":[64],"Herein":[65],"report":[67],"cGRNexp,":[68,85],"platform":[71,140],"building":[73],"based":[78],"on":[79],"user-uploaded":[80],"datasets.":[83,109,159],"In":[84],"deposit":[87],"three":[88],"types":[89],"sequence-matching-based":[91],"regulatory":[92,153],"relationships":[93],"implement":[95],"two":[96],"functional":[97],"modules":[98],"processing":[100],"microRNA-perturbed":[101],"parallel":[106],"miRNA/mRNA":[107],"With":[110],"microarrays":[112],"next-generation":[114],"sequencing":[115],"platforms":[116],"being":[117],"increasingly":[118],"accessible,":[119],"large":[121],"amount":[122],"mRNA":[126],"will":[129,142],"be":[130,143],"attainable":[131],"near":[134],"future,":[135],"thus,":[137],"our":[138],"cGRNexp":[141,160],"very":[144],"useful":[145],"helping":[147],"people":[148],"conditional":[151],"from":[155],"accessible":[162],"at":[163],"http://www.scbit.org/cgrnexp/.":[164]},"counts_by_year":[{"year":2013,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}
