{"id":"https://openalex.org/W3104970623","doi":null,"title":"Genome-Wide Survey of MicroRNA- Transcription Factor Feed-Forward Regulatory Circuits in Human","display_name":"Genome-Wide Survey of MicroRNA- Transcription Factor Feed-Forward Regulatory Circuits in Human","publication_year":2013,"publication_date":"2013-08-04","ids":{"openalex":"https://openalex.org/W3104970623","mag":"3104970623"},"language":"en","primary_location":{"id":"pmh:oai:CiteSeerX.psu:10.1.1.313.9340","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.313.9340","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://arxiv.org/pdf/0907.4115v1.pdf","raw_type":"text"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":[],"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/A5039627791","display_name":"Angela Re","orcid":"https://orcid.org/0000-0002-3179-6967","observed_orcids":["https://orcid.org/0000-0002-3179-6967"]},"institutions":[{"id":"https://openalex.org/I193223587","display_name":"University of Trento","ror":"https://ror.org/05trd4x28","country_code":"IT","type":"education","lineage":["https://openalex.org/I193223587"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Angela Re A","raw_affiliation_strings":["CIBIO-Centre for Integrative Biology, University of Trento, Via delle Regole 101, I-38100 Trento, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"CIBIO-Centre for Integrative Biology, University of Trento, Via delle Regole 101, I-38100 Trento, Italy","institution_ids":["https://openalex.org/I193223587"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069341441","display_name":"Davide Cor\u00e0","orcid":"https://orcid.org/0000-0003-4123-1705","observed_orcids":["https://orcid.org/0000-0003-4123-1705"]},"institutions":[{"id":"https://openalex.org/I160013858","display_name":"Istituto Nazionale di Fisica Nucleare","ror":"https://ror.org/005ta0471","country_code":"IT","type":"government","lineage":["https://openalex.org/I160013858"]},{"id":"https://openalex.org/I4210099850","display_name":"Istituto Nazionale di Fisica Nucleare, Sezione di Torino","ror":"https://ror.org/01vj6ck58","country_code":"IT","type":"facility","lineage":["https://openalex.org/I160013858","https://openalex.org/I4210099850"]},{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Davide Cor\u00e1 B","raw_affiliation_strings":["Center for Complex Systems in Molecular Biology and Medicine, University of Torino, Via Accademia Albertina 13, I-10100 Torino, Italy","Department of Theoretical Physics, University of Torino and INFN, Via Pietro Giuria 1, I-10125 Torino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Complex Systems in Molecular Biology and Medicine, University of Torino, Via Accademia Albertina 13, I-10100 Torino, Italy","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Department of Theoretical Physics, University of Torino and INFN, Via Pietro Giuria 1, I-10125 Torino, Italy","institution_ids":["https://openalex.org/I160013858","https://openalex.org/I4210099850","https://openalex.org/I55143463"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5012376450","display_name":"Daniela Taverna","orcid":"https://orcid.org/0000-0002-6365-527X","observed_orcids":["https://orcid.org/0000-0002-6365-527X"]},"institutions":[{"id":"https://openalex.org/I55143463","display_name":"University of Turin","ror":"https://ror.org/048tbm396","country_code":"IT","type":"education","lineage":["https://openalex.org/I55143463"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Daniela Taverna C","raw_affiliation_strings":["Center for Complex Systems in Molecular Biology and Medicine, University of Torino, Via Accademia Albertina 13, I-10100 Torino, Italy","Department of Oncological Sciences, University of Torino and Molecular Biotechnology Center, Via Nizza 52, I-10126 Torino, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Complex Systems in Molecular Biology and Medicine, University of Torino, Via Accademia Albertina 13, I-10100 Torino, Italy","institution_ids":["https://openalex.org/I55143463"]},{"raw_affiliation_string":"Department of Oncological Sciences, University of Torino and Molecular Biotechnology Center, Via Nizza 52, I-10126 Torino, Italy","institution_ids":["https://openalex.org/I55143463"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":104,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10621","display_name":"Gene Regulatory Network Analysis","score":0.6406000256538391,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.6406000256538391,"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/T10062","display_name":"MicroRNA in disease regulation","score":0.24220000207424164,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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":0.04270000010728836,"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/feedforward-loop","display_name":"feed-forward loop","score":0.8989999890327454},{"id":"https://openalex.org/keywords/microrna","display_name":"microRNA","score":0.9649999737739563},{"id":"https://openalex.org/keywords/transcription-factors","display_name":"transcription factors","score":0.9810000061988831},{"id":"https://openalex.org/keywords/post-transcriptional-regulation","display_name":"post-transcriptional regulation","score":0.8769999742507935},{"id":"https://openalex.org/keywords/transcriptional-regulation","display_name":"transcriptional regulation","score":0.8199999928474426},{"id":"https://openalex.org/keywords/promoter-elements","display_name":"promoter elements","score":0.8029999732971191},{"id":"https://openalex.org/keywords/gene-regulatory-circuits","display_name":"gene regulatory circuits","score":0.4959999918937683},{"id":"https://openalex.org/keywords/cancer","display_name":"cancer","score":0.5580000281333923},{"id":"https://openalex.org/keywords/gene-ontology-enrichment","display_name":"gene ontology enrichment","score":0.671999990940094}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6725627183914185},{"id":"https://openalex.org/C86339819","wikidata":"https://www.wikidata.org/wiki/Q407384","display_name":"Transcription factor","level":3,"score":0.5885050892829895},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5862661004066467},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5737850069999695},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.5683243274688721},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.49257975816726685},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.48975706100463867},{"id":"https://openalex.org/C101762097","wikidata":"https://www.wikidata.org/wiki/Q224093","display_name":"Promoter","level":4,"score":0.4882374107837677},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4510091245174408},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4442431330680847},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1495739221572876}],"mesh":[],"locations_count":1,"locations":[{"id":"pmh:oai:CiteSeerX.psu:10.1.1.313.9340","doi":null,"is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.313.9340","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://arxiv.org/pdf/0907.4115v1.pdf","raw_type":"text"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4043000042438507,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":51,"referenced_works":["https://openalex.org/W1596515083","https://openalex.org/W1599498186","https://openalex.org/W1648301895","https://openalex.org/W1975437957","https://openalex.org/W1977372263","https://openalex.org/W1979268646","https://openalex.org/W1980389572","https://openalex.org/W1994955065","https://openalex.org/W2009764755","https://openalex.org/W2011920499","https://openalex.org/W2017270642","https://openalex.org/W2017718158","https://openalex.org/W2026472364","https://openalex.org/W2030955818","https://openalex.org/W2032231928","https://openalex.org/W2040191060","https://openalex.org/W2040851473","https://openalex.org/W2042504292","https://openalex.org/W2049446122","https://openalex.org/W2050869737","https://openalex.org/W2060283905","https://openalex.org/W2060515857","https://openalex.org/W2083381199","https://openalex.org/W2085442947","https://openalex.org/W2085951776","https://openalex.org/W2087966784","https://openalex.org/W2098212444","https://openalex.org/W2102243804","https://openalex.org/W2110699703","https://openalex.org/W2112717966","https://openalex.org/W2117391818","https://openalex.org/W2117465894","https://openalex.org/W2125818518","https://openalex.org/W2129071328","https://openalex.org/W2131253190","https://openalex.org/W2135030836","https://openalex.org/W2137144878","https://openalex.org/W2139393817","https://openalex.org/W2149146453","https://openalex.org/W2150597604","https://openalex.org/W2152091242","https://openalex.org/W2153624566","https://openalex.org/W2158107632","https://openalex.org/W2158174582","https://openalex.org/W2163199119","https://openalex.org/W2164194749","https://openalex.org/W2171682260","https://openalex.org/W2409075727","https://openalex.org/W4210241463","https://openalex.org/W4237473415","https://openalex.org/W7075726979"],"related_works":["https://openalex.org/W7216788220","https://openalex.org/W2126305708","https://openalex.org/W2999456717","https://openalex.org/W3216177247","https://openalex.org/W2330554275","https://openalex.org/W2005885406","https://openalex.org/W2588588160","https://openalex.org/W7100731216","https://openalex.org/W1633748206","https://openalex.org/W2000406884"],"abstract_inverted_index":{"In":[0,108],"this":[1],"work":[2],"we":[3,89,115],"describe":[4],"a":[5,33,38,44,57,101,175],"computational":[6,135],"framework":[7],"for":[8,77,95,137],"the":[9,65,71,91,127,131,138,142,151,157,178],"genomewide":[10],"identification":[11],"and":[12,40,67,83,86,170],"characterization":[13],"of":[14,46,70,103,130,141,150,156,167,177],"mixed":[15,96],"transcriptional":[16,66],"/":[17],"posttranscriptional":[18],"regulatory":[19,73,98,139],"circuits":[20,53,118],"in":[21,25,31,81,153,164,182],"human.":[22],"We":[23,61,172],"concentrated":[24],"particular":[26],"on":[27],"Feed-Forward":[28],"Loops":[29],"(FFL)":[30],"which":[32],"master":[34],"transcription":[35],"factor":[36],"regulates":[37],"microRNA":[39],"together":[41],"with":[42,56],"it":[43],"set":[45],"joint":[47,128],"target":[48],"protein":[49],"coding":[50],"genes.":[51],"The":[52],"were":[54],"assembled":[55],"two":[58,92],"step":[59],"procedure.":[60],"first":[62],"constructed":[63],"separately":[64],"post-transcriptional":[68],"components":[69],"human":[72,82],"network":[74],"by":[75],"looking":[76,94],"conserved":[78],"overrepresented":[79],"motifs":[80],"mouse":[84],"promoters":[85],"3\u2019-UTRs.":[87],"Then":[88],"combined":[90],"subnetworks":[93],"feed-forward":[97],"interactions,":[99],"finding":[100],"total":[102],"638":[104],"putative":[105],"(merged)":[106],"FFLs.":[107],"order":[109],"to":[110,161],"investigate":[111],"their":[112],"biological":[113],"relevance":[114],"filtered":[116],"these":[117],"using":[119],"three":[120],"selection":[121],"criteria:":[122],"(I)":[123],"GeneOntology":[124],"enrichment":[125],"among":[126],"targets":[129],"FFL":[132,152],"(II)":[133],"Independent":[134],"evidence":[136],"interactions":[140],"FFL,":[143],"extracted":[144],"from":[145],"external":[146],"databases":[147],"(III)":[148],"Relevance":[149],"cancer.":[154],"Most":[155],"selected":[158],"FFLs":[159],"seem":[160],"be":[162],"involved":[163],"various":[165],"aspects":[166],"organism":[168],"development":[169],"differentiation.":[171],"finally":[173],"discuss":[174],"few":[176],"most":[179],"interesting":[180],"cases":[181],"detail.":[183]},"counts_by_year":[{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":8},{"year":2017,"cited_by_count":2},{"year":2016,"cited_by_count":10},{"year":2015,"cited_by_count":8},{"year":2014,"cited_by_count":16},{"year":2013,"cited_by_count":13},{"year":2012,"cited_by_count":16}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2020-11-23T00:00:00"}