{"id":"https://openalex.org/W2152026276","doi":"https://doi.org/10.1093/bioinformatics/btt019","title":"CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data","display_name":"CluePedia Cytoscape plugin: pathway insights using integrated experimental and in silico data","publication_year":2013,"publication_date":"2013-01-16","ids":{"openalex":"https://openalex.org/W2152026276","doi":"https://doi.org/10.1093/bioinformatics/btt019","mag":"2152026276","pmid":"https://pubmed.ncbi.nlm.nih.gov/23325622","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/3582273"},"language":"en","primary_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt019","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/5/661/16918665/btt019.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4811","1367-4803"],"is_oa":true,"is_in_doaj":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":"cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"type":"article","type_crossref":"journal-article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://academic.oup.com/bioinformatics/article-pdf/29/5/661/16918665/btt019.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5062069569","display_name":"Gabriela Bindea","orcid":"https://orcid.org/0000-0001-6013-6645"},"institutions":[{"id":"https://openalex.org/I4210092322","display_name":"Centre de Recherche des Cordeliers","ror":"https://ror.org/00dmms154","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I39804081","https://openalex.org/I4210092322"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210133830","display_name":"Laboratoire d\u2019immunologie int\u00e9grative du cancer","ror":"https://ror.org/03cqwn895","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I39804081","https://openalex.org/I4210092322","https://openalex.org/I4210133830"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Gabriela Bindea","raw_affiliation_string":"1 INSERM, Laboratory of Integrative Cancer Immunology, 75006 Paris, 2Cordeliers Research Center, Universit\u00e9 Paris Descartes, 75006 Paris and 3Cordeliers Research Center, Universit\u00e9 Pierre et Marie Curie Paris 6, Cordeliers Research Center, 75005 Paris, France","raw_affiliation_strings":["1 INSERM, Laboratory of Integrative Cancer Immunology, 75006 Paris, 2Cordeliers Research Center, Universit\u00e9 Paris Descartes, 75006 Paris and 3Cordeliers Research Center, Universit\u00e9 Pierre et Marie Curie Paris 6, Cordeliers Research Center, 75005 Paris, France"]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070615133","display_name":"J\u00e9r\u00f4me Galon","orcid":"https://orcid.org/0000-0001-9635-1339"},"institutions":[{"id":"https://openalex.org/I4210092322","display_name":"Centre de Recherche des Cordeliers","ror":"https://ror.org/00dmms154","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I39804081","https://openalex.org/I4210092322"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210133830","display_name":"Laboratoire d\u2019immunologie int\u00e9grative du cancer","ror":"https://ror.org/03cqwn895","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I39804081","https://openalex.org/I4210092322","https://openalex.org/I4210133830"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"J\u00e9r\u00f4me Galon","raw_affiliation_string":"1 INSERM, Laboratory of Integrative Cancer Immunology, 75006 Paris, 2Cordeliers Research Center, Universit\u00e9 Paris Descartes, 75006 Paris and 3Cordeliers Research Center, Universit\u00e9 Pierre et Marie Curie Paris 6, Cordeliers Research Center, 75005 Paris, France","raw_affiliation_strings":["1 INSERM, Laboratory of Integrative Cancer Immunology, 75006 Paris, 2Cordeliers Research Center, Universit\u00e9 Paris Descartes, 75006 Paris and 3Cordeliers Research Center, Universit\u00e9 Pierre et Marie Curie Paris 6, Cordeliers Research Center, 75005 Paris, France"]},{"author_position":"last","author":{"id":"https://openalex.org/A5078219830","display_name":"Bernhard Mlecnik","orcid":"https://orcid.org/0000-0002-3345-1030"},"institutions":[{"id":"https://openalex.org/I4210092322","display_name":"Centre de Recherche des Cordeliers","ror":"https://ror.org/00dmms154","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I39804081","https://openalex.org/I4210092322"]},{"id":"https://openalex.org/I154526488","display_name":"Inserm","ror":"https://ror.org/02vjkv261","country_code":"FR","type":"government","lineage":["https://openalex.org/I154526488"]},{"id":"https://openalex.org/I4210133830","display_name":"Laboratoire d\u2019immunologie int\u00e9grative du cancer","ror":"https://ror.org/03cqwn895","country_code":"FR","type":"facility","lineage":["https://openalex.org/I154526488","https://openalex.org/I204730241","https://openalex.org/I39804081","https://openalex.org/I4210092322","https://openalex.org/I4210133830"]},{"id":"https://openalex.org/I39804081","display_name":"Sorbonne Universit\u00e9","ror":"https://ror.org/02en5vm52","country_code":"FR","type":"education","lineage":["https://openalex.org/I39804081"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]}],"countries":["FR"],"is_corresponding":true,"raw_author_name":"Bernhard Mlecnik","raw_affiliation_string":"1 INSERM, Laboratory of Integrative Cancer Immunology, 75006 Paris, 2Cordeliers Research Center, Universit\u00e9 Paris Descartes, 75006 Paris and 3Cordeliers Research Center, Universit\u00e9 Pierre et Marie Curie Paris 6, Cordeliers Research Center, 75005 Paris, France","raw_affiliation_strings":["1 INSERM, Laboratory of Integrative Cancer Immunology, 75006 Paris, 2Cordeliers Research Center, Universit\u00e9 Paris Descartes, 75006 Paris and 3Cordeliers Research Center, Universit\u00e9 Pierre et Marie Curie Paris 6, Cordeliers Research Center, 75005 Paris, France"]}],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5070615133","https://openalex.org/A5078219830"],"corresponding_institution_ids":["https://openalex.org/I4210092322","https://openalex.org/I154526488","https://openalex.org/I4210133830","https://openalex.org/I39804081","https://openalex.org/I204730241","https://openalex.org/I4210092322","https://openalex.org/I154526488","https://openalex.org/I4210133830","https://openalex.org/I39804081","https://openalex.org/I204730241"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618,"provenance":"doaj"},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618,"provenance":"doaj"},"has_fulltext":true,"fulltext_origin":"ngrams","cited_by_count":879,"cited_by_percentile_year":{"min":99,"max":100},"biblio":{"volume":"29","issue":"5","first_page":"661","last_page":"663"},"is_retracted":false,"is_paratext":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Analysis of Gene Interaction Networks","score":0.9999,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Analysis of Gene Interaction Networks","score":0.9999,"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/T10885","display_name":"Microarray Data Analysis and Gene Expression Profiling","score":0.9985,"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":"Prediction of Protein Subcellular Localization","score":0.9983,"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":[{"keyword":"pathway insights","score":0.5986}],"concepts":[{"id":"https://openalex.org/C4924752","wikidata":"https://www.wikidata.org/wiki/Q184148","display_name":"Plug-in","level":2,"score":0.9591911},{"id":"https://openalex.org/C2775905019","wikidata":"https://www.wikidata.org/wiki/Q192572","display_name":"In silico","level":3,"score":0.80753136},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.6830574},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.61272657},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.488953},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37860695},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34989297},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.30944908},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2341066},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.12865722},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.10229418}],"mesh":[{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":"","qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D035683","descriptor_name":"MicroRNAs","qualifier_ui":"","qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"","qualifier_name":null,"is_major_topic":false}],"locations_count":4,"locations":[{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt019","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/5/661/16918665/btt019.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4811","1367-4803"],"is_oa":true,"is_in_doaj":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":"cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://europepmc.org/articles/pmc3582273","pdf_url":"https://europepmc.org/articles/pmc3582273?pdf=render","source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":["European Bioinformatics Institute"],"type":"repository"},"license":"cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582273","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":["National Institutes of Health"],"type":"repository"},"license":null,"version":"publishedVersion","is_accepted":true,"is_published":true},{"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23325622","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":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":["National Institutes of Health"],"type":"repository"},"license":null,"version":null,"is_accepted":false,"is_published":false}],"best_oa_location":{"is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btt019","pdf_url":"https://academic.oup.com/bioinformatics/article-pdf/29/5/661/16918665/btt019.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4811","1367-4803"],"is_oa":true,"is_in_doaj":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311647","https://openalex.org/P4310311648"],"host_organization_lineage_names":["University of Oxford","Oxford University Press"],"type":"journal"},"license":"cc-by","version":"publishedVersion","is_accepted":true,"is_published":true},"sustainable_development_goals":[],"grants":[],"referenced_works_count":17,"referenced_works":["https://openalex.org/W1771155305","https://openalex.org/W2000860171","https://openalex.org/W2017426710","https://openalex.org/W2024858956","https://openalex.org/W2028133290","https://openalex.org/W2046182607","https://openalex.org/W2057545775","https://openalex.org/W2103017472","https://openalex.org/W2132034930","https://openalex.org/W2134118500","https://openalex.org/W2136482324","https://openalex.org/W2140000393","https://openalex.org/W2159675211","https://openalex.org/W2165253681","https://openalex.org/W2165700458","https://openalex.org/W2166542841","https://openalex.org/W2169589032"],"related_works":["https://openalex.org/W4287378204","https://openalex.org/W47352601","https://openalex.org/W2545422590","https://openalex.org/W4240705470","https://openalex.org/W2945311252","https://openalex.org/W2981957539","https://openalex.org/W2912862995","https://openalex.org/W3129816939","https://openalex.org/W631546281","https://openalex.org/W4213354039"],"ngrams_url":"https://api.openalex.org/works/W2152026276/ngrams","abstract_inverted_index":{"Abstract":[0],"Summary:":[1],"The":[2,92,113],"CluePedia":[3,17,93,120],"Cytoscape":[4,94,110],"plugin":[5,75,95,111],"is":[6,81,96,116],"a":[7,44],"search":[8],"tool":[9],"for":[10,83],"new":[11,57,90],"markers":[12],"potentially":[13],"associated":[14],"to":[15],"pathways.":[16],"calculates":[18],"linear":[19],"and":[20,29,41,56,86,98,102,107],"non-linear":[21],"statistical":[22],"dependencies":[23],"from":[24],"experimental":[25,39],"data.":[26],"Genes,":[27],"proteins":[28],"miRNAs":[30],"can":[31,53,69],"be":[32,54,61,70],"connected":[33],"based":[34],"on":[35],"in":[36],"silico":[37],"and/or":[38],"information":[40],"integrated":[42],"into":[43],"ClueGO":[45],"network":[46],"of":[47,89],"terms/pathways.":[48],"Interrelations":[49],"within":[50],"each":[51],"pathway":[52],"investigated,":[55],"potential":[58],"associations":[59],"may":[60],"revealed":[62],"through":[63],"gene/protein/miRNA":[64],"enrichments.":[65],"A":[66],"pathway-like":[67],"visualization":[68],"created":[71],"using":[72],"the":[73,87,109,119],"Cerebral":[74],"layout.":[76],"Combining":[77],"all":[78],"these":[79],"features":[80],"essential":[82],"data":[84,129],"interpretation":[85],"generation":[88],"hypotheses.":[91],"user-friendly":[97],"has":[99],"an":[100],"expressive":[101],"intuitive":[103],"visualization.":[104],"Availability:":[105],"http://www.ici.upmc.fr/cluepedia/":[106],"via":[108],"manager.":[112],"user":[114],"manual":[115],"available":[117,131],"at":[118,132],"website.":[121],"Contact:":[122],"bernhard.mlecnik@crc.jussieu.fr":[123],"or":[124],"jerome.galon@crc.jussieu.fr":[125],"Supplementary":[126,128],"information:":[127],"are":[130],"Bioinformatics":[133],"online.":[134]},"cited_by_api_url":"https://api.openalex.org/works?filter=cites:W2152026276","counts_by_year":[{"year":2024,"cited_by_count":6},{"year":2023,"cited_by_count":100},{"year":2022,"cited_by_count":129},{"year":2021,"cited_by_count":147},{"year":2020,"cited_by_count":117},{"year":2019,"cited_by_count":118},{"year":2018,"cited_by_count":84},{"year":2017,"cited_by_count":56},{"year":2016,"cited_by_count":52},{"year":2015,"cited_by_count":33},{"year":2014,"cited_by_count":23},{"year":2013,"cited_by_count":3}],"updated_date":"2024-03-27T06:35:29.620666","created_date":"2016-06-24"}