{"id":"https://openalex.org/W2075602427","doi":"https://doi.org/10.1093/nar/gkt386","title":"Graphite Web: web tool for gene set analysis exploiting pathway topology","display_name":"Graphite Web: web tool for gene set analysis exploiting pathway topology","publication_year":2013,"publication_date":"2013-05-10","ids":{"openalex":"https://openalex.org/W2075602427","doi":"https://doi.org/10.1093/nar/gkt386","mag":"2075602427","pmid":"https://pubmed.ncbi.nlm.nih.gov/23666626"},"language":"en","primary_location":{"id":"doi:10.1093/nar/gkt386","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt386","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W89/3836897/gkt386.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/nar/article-pdf/41/W1/W89/3836897/gkt386.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5070887609","display_name":"Gabriele Sales","orcid":"https://orcid.org/0000-0003-2078-5661"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":true,"raw_author_name":"Gabriele Sales","raw_affiliation_strings":["Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy","Department of Biology, University of Padova, Via U, Bassi, 58/B, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Department of Biology, University of Padova, Via U, Bassi, 58/B, 35121 Padova, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5091476817","display_name":"Enrica Calura","orcid":"https://orcid.org/0000-0001-8463-2432"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Enrica Calura","raw_affiliation_strings":["Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy","Department of Biology, University of Padova, Via U, Bassi, 58/B, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Department of Biology, University of Padova, Via U, Bassi, 58/B, 35121 Padova, Italy","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5058895507","display_name":"Paolo Martini","orcid":"https://orcid.org/0000-0002-0146-1031"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Paolo Martini","raw_affiliation_strings":["Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy","Department of Biology, University of Padova, Via U, Bassi, 58/B, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Department of Biology, University of Padova, Via U, Bassi, 58/B, 35121 Padova, Italy","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5082717632","display_name":"Chiara Romualdi","orcid":"https://orcid.org/0000-0003-4792-9047"},"institutions":[{"id":"https://openalex.org/I138689650","display_name":"University of Padua","ror":"https://ror.org/00240q980","country_code":"IT","type":"education","lineage":["https://openalex.org/I138689650"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Chiara Romualdi","raw_affiliation_strings":["Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy","Department of Biology, University of Padova, Via U, Bassi, 58/B, 35121 Padova, Italy"],"affiliations":[{"raw_affiliation_string":"Department of Biology, University of Padova, Via U. Bassi 58/B, 35121 Padova, Italy","institution_ids":["https://openalex.org/I138689650"]},{"raw_affiliation_string":"Department of Biology, University of Padova, Via U, Bassi, 58/B, 35121 Padova, Italy","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5070887609"],"corresponding_institution_ids":["https://openalex.org/I138689650"],"apc_list":{"value":3630,"currency":"USD","value_usd":3630},"apc_paid":{"value":3630,"currency":"USD","value_usd":3630},"fwci":4.1928,"has_fulltext":true,"cited_by_count":53,"citation_normalized_percentile":{"value":0.94872881,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":89,"max":99},"biblio":{"volume":"41","issue":"W1","first_page":"W89","last_page":"W97"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":"Bioinformatics and Genomic Networks","score":0.9998000264167786,"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":"Gene expression and cancer classification","score":0.9966999888420105,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.9659000039100647,"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/topology","display_name":"Topology (electrical circuits)","score":0.5187273621559143},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5157220959663391},{"id":"https://openalex.org/keywords/univariate","display_name":"Univariate","score":0.5057878494262695},{"id":"https://openalex.org/keywords/visualization","display_name":"Visualization","score":0.48061221837997437},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4711543321609497},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46763256192207336},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.4545859098434448},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4376237690448761},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.437095046043396},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.4210556447505951},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.35069388151168823},{"id":"https://openalex.org/keywords/multivariate-statistics","display_name":"Multivariate statistics","score":0.3257668614387512},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.32482221722602844},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23794406652450562},{"id":"https://openalex.org/keywords/machine-learning","display_name":"Machine learning","score":0.20693376660346985},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1870109736919403},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.12961506843566895}],"concepts":[{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.5187273621559143},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5157220959663391},{"id":"https://openalex.org/C199163554","wikidata":"https://www.wikidata.org/wiki/Q1681619","display_name":"Univariate","level":3,"score":0.5057878494262695},{"id":"https://openalex.org/C36464697","wikidata":"https://www.wikidata.org/wiki/Q451553","display_name":"Visualization","level":2,"score":0.48061221837997437},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4711543321609497},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46763256192207336},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.4545859098434448},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4376237690448761},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.437095046043396},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.4210556447505951},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.35069388151168823},{"id":"https://openalex.org/C161584116","wikidata":"https://www.wikidata.org/wiki/Q1952580","display_name":"Multivariate statistics","level":2,"score":0.3257668614387512},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32482221722602844},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23794406652450562},{"id":"https://openalex.org/C119857082","wikidata":"https://www.wikidata.org/wiki/Q2539","display_name":"Machine learning","level":1,"score":0.20693376660346985},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1870109736919403},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.12961506843566895},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","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},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015179","descriptor_name":"Colorectal Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D017423","descriptor_name":"Sequence Analysis, RNA","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D051379","descriptor_name":"Mice","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1093/nar/gkt386","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt386","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W89/3836897/gkt386.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},{"id":"pmid:23666626","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23666626","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":"Nucleic acids research","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.890.6221","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.890.6221","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://europepmc.org/backend/ptpmcrender.fcgi?accid%3DPMC3977659%26blobtype%3Dpdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.890.9344","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.890.9344","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/early/2013/05/10/nar.gkt386.full.pdf","raw_type":"text"},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.898.6060","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.898.6060","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://nar.oxfordjournals.org/content/41/W1/W89.full.pdf","raw_type":"text"},{"id":"pmh:oai:europepmc.org:2960006","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3977659","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Text"},{"id":"pmh:oai:iris.unibs.it:11379/533934","is_oa":false,"landing_page_url":"http://hdl.handle.net/11379/533934","pdf_url":null,"source":{"id":"https://openalex.org/S4306400804","display_name":"Institutional Research Information System (Universit\u00e0 degli Studi di Brescia)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I66752286","host_organization_name":"University of Milano-Bicocca","host_organization_lineage":["https://openalex.org/I66752286"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:www.research.unipd.it:11577/2802287","is_oa":false,"landing_page_url":"http://hdl.handle.net/11577/2802287","pdf_url":null,"source":{"id":"https://openalex.org/S4306402547","display_name":"Padua Research Archive (University of Padova)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I138689650","host_organization_name":"University of Padua","host_organization_lineage":["https://openalex.org/I138689650"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"info:eu-repo/semantics/article"}],"best_oa_location":{"id":"doi:10.1093/nar/gkt386","is_oa":true,"landing_page_url":"https://doi.org/10.1093/nar/gkt386","pdf_url":"https://academic.oup.com/nar/article-pdf/41/W1/W89/3836897/gkt386.pdf","source":{"id":"https://openalex.org/S134668137","display_name":"Nucleic Acids Research","issn_l":"0305-1048","issn":["0305-1048","1362-4954","1362-4962"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Nucleic Acids Research","raw_type":"journal-article"},"sustainable_development_goals":[{"score":0.4300000071525574,"display_name":"Quality Education","id":"https://metadata.un.org/sdg/4"}],"awards":[{"id":"https://openalex.org/G2489103016","display_name":null,"funder_award_id":"RISIB","funder_id":"https://openalex.org/F4320326074","funder_display_name":"Regione del Veneto"}],"funders":[{"id":"https://openalex.org/F4320321966","display_name":"Universit\u00e0 degli Studi di Padova","ror":"https://ror.org/00240q980"},{"id":"https://openalex.org/F4320326074","display_name":"Regione del Veneto","ror":"https://ror.org/03mm67z69"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2075602427.pdf","grobid_xml":"https://content.openalex.org/works/W2075602427.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W89255747","https://openalex.org/W95074246","https://openalex.org/W191383808","https://openalex.org/W1528905581","https://openalex.org/W1596515083","https://openalex.org/W1966505629","https://openalex.org/W1982503072","https://openalex.org/W1983463159","https://openalex.org/W2013318867","https://openalex.org/W2024227785","https://openalex.org/W2027895157","https://openalex.org/W2037580272","https://openalex.org/W2042794886","https://openalex.org/W2052523188","https://openalex.org/W2060913247","https://openalex.org/W2069058535","https://openalex.org/W2070407539","https://openalex.org/W2078284062","https://openalex.org/W2081098333","https://openalex.org/W2082081674","https://openalex.org/W2083089709","https://openalex.org/W2090969569","https://openalex.org/W2098647860","https://openalex.org/W2106248311","https://openalex.org/W2107060225","https://openalex.org/W2107249189","https://openalex.org/W2108819945","https://openalex.org/W2110687686","https://openalex.org/W2111862142","https://openalex.org/W2113342764","https://openalex.org/W2114104545","https://openalex.org/W2118069309","https://openalex.org/W2122683221","https://openalex.org/W2123106337","https://openalex.org/W2130410032","https://openalex.org/W2130666470","https://openalex.org/W2132992030","https://openalex.org/W2133074013","https://openalex.org/W2134736660","https://openalex.org/W2139036189","https://openalex.org/W2141703917","https://openalex.org/W2154458783","https://openalex.org/W2155142785","https://openalex.org/W2157646380","https://openalex.org/W2159835316","https://openalex.org/W2165040702","https://openalex.org/W2166373524","https://openalex.org/W2167119716","https://openalex.org/W2171427413","https://openalex.org/W2171437346","https://openalex.org/W2962821542","https://openalex.org/W4301861531","https://openalex.org/W6663687618","https://openalex.org/W6665464122"],"related_works":["https://openalex.org/W1828158523","https://openalex.org/W2049578243","https://openalex.org/W2122079181","https://openalex.org/W2000145235","https://openalex.org/W3122045730","https://openalex.org/W2889939530","https://openalex.org/W2074324799","https://openalex.org/W2354804553","https://openalex.org/W4297813473","https://openalex.org/W2909382709"],"abstract_inverted_index":{"Graphite":[0,137,171,187],"web":[1,5,142,172],"is":[2,189],"a":[3,85],"novel":[4],"tool":[6],"for":[7,13,144,166],"pathway":[8,24,69,145,156,185],"analyses":[9,25,157,178],"and":[10,20,37,44,58,89,94,105,118,154,183],"network":[11,86,164],"visualization":[12],"gene":[14,78,148,176],"expression":[15,48,149],"data":[16,150],"of":[17,47,162],"both":[18],"microarray":[19],"RNA-seq":[21],"experiments.":[22],"Several":[23],"have":[26],"been":[27],"proposed":[28],"either":[29],"in":[30,34,74],"the":[31,35,42,45,99,110,115,139],"univariate":[32,106],"or":[33],"global":[36],"multivariate":[38,119,155],"context":[39],"to":[40,62,65,126],"tackle":[41],"complexity":[43],"interpretation":[46],"results.":[49],"These":[50],"methods":[51,60],"can":[52,81],"be":[53,82,127],"further":[54],"divided":[55],"into":[56],"'topological'":[57],"'non-topological'":[59],"according":[61],"their":[63],"ability":[64],"gain":[66],"power":[67],"from":[68],"topology.":[70],"Biological":[71],"pathways":[72],"are,":[73,91],"fact,":[75],"not":[76],"only":[77],"lists":[79],"but":[80,124],"represented":[83],"through":[84],"where":[87],"genes":[88],"connections":[90],"respectively,":[92],"nodes":[93],"edges.":[95],"To":[96],"this":[97],"day,":[98],"most":[100],"used":[101,128],"approaches":[102,120],"are":[103,121],"non-topological":[104],"although":[107],"they":[108],"miss":[109],"relationship":[111],"among":[112],"genes.":[113],"On":[114],"contrary,":[116],"topological":[117,153],"more":[122],"powerful,":[123],"difficult":[125],"by":[129],"researchers":[130],"without":[131],"bioinformatic":[132],"skills.":[133],"Here":[134],"we":[135],"present":[136],"web,":[138],"first":[140],"public":[141],"server":[143],"analysis":[146],"on":[147,179],"that":[151],"combines":[152],"with":[158],"an":[159],"efficient":[160],"system":[161],"interactive":[163],"visualizations":[165],"easy":[167],"results":[168],"interpretation.":[169],"Specifically,":[170],"implements":[173],"five":[174],"different":[175],"set":[177],"three":[180],"model":[181],"organisms":[182],"two":[184],"databases.":[186],"Web":[188],"freely":[190],"available":[191],"at":[192],"http://graphiteweb.bio.unipd.it/.":[193]},"counts_by_year":[{"year":2024,"cited_by_count":2},{"year":2023,"cited_by_count":5},{"year":2022,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":6},{"year":2019,"cited_by_count":3},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3},{"year":2016,"cited_by_count":8},{"year":2015,"cited_by_count":9},{"year":2014,"cited_by_count":10},{"year":2013,"cited_by_count":1}],"updated_date":"2026-04-21T08:09:41.155169","created_date":"2025-10-10T00:00:00"}
