{"id":"https://openalex.org/W2128085074","doi":"https://doi.org/10.1186/1471-2105-9-s4-s9","title":"Reconstructing networks of pathways via significance analysis of their intersections","display_name":"Reconstructing networks of pathways via significance analysis of their intersections","publication_year":2008,"publication_date":"2008-04-01","ids":{"openalex":"https://openalex.org/W2128085074","doi":"https://doi.org/10.1186/1471-2105-9-s4-s9","mag":"2128085074","pmid":"https://pubmed.ncbi.nlm.nih.gov/18460182"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-9-s4-s9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-s4-s9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-S4-S9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-S4-S9","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5069842779","display_name":"Mirko Francesconi","orcid":"https://orcid.org/0000-0002-8702-0877"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Mirko Francesconi","raw_affiliation_strings":["Centro Interdipartimentale \"L, Galvani\", Universit\u00e0 di Bologna, Bologna 40127, Italy. mirko.francesconi@studio.unibo.it","Centro Interdipartimentale \"L. Galvani\", Universit\u00e0 di Bologna, Bologna, 40127, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Interdipartimentale \"L, Galvani\", Universit\u00e0 di Bologna, Bologna 40127, Italy. mirko.francesconi@studio.unibo.it","institution_ids":["https://openalex.org/I9360294"]},{"raw_affiliation_string":"Centro Interdipartimentale \"L. Galvani\", Universit\u00e0 di Bologna, Bologna, 40127, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025807854","display_name":"Daniel Remondini","orcid":"https://orcid.org/0000-0003-3185-7456"},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Daniel Remondini","raw_affiliation_strings":["Centro Interdipartimentale \u201cL. Galvani\u201d, Universit\u00e0 di Bologna, Bologna, 40127, Italy","Department of Physics, Universit\u00e0 di Bologna, Bologna, 40127, Italy","Centro Interdipartimentale \"L. Galvani\", Universit\u00e0 di Bologna, Bologna, 40127, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Interdipartimentale \u201cL. Galvani\u201d, Universit\u00e0 di Bologna, Bologna, 40127, Italy","institution_ids":["https://openalex.org/I9360294"]},{"raw_affiliation_string":"Department of Physics, Universit\u00e0 di Bologna, Bologna, 40127, Italy","institution_ids":["https://openalex.org/I9360294"]},{"raw_affiliation_string":"Centro Interdipartimentale \"L. Galvani\", Universit\u00e0 di Bologna, Bologna, 40127, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011198947","display_name":"Nicola Neretti","orcid":"https://orcid.org/0000-0002-9552-1663"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]},{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT","US"],"is_corresponding":false,"raw_author_name":"Nicola Neretti","raw_affiliation_strings":["Dipartimento di Morfofisiologia veterinaria e Produzioni Animali (DIMORFIPA), Universit\u00e0 di Bologna, Bologna, 40064, Italy","Institute for Brain and Neural Systems, Brown University, Providence, RI 02906, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Dipartimento di Morfofisiologia veterinaria e Produzioni Animali (DIMORFIPA), Universit\u00e0 di Bologna, Bologna, 40064, Italy","institution_ids":["https://openalex.org/I9360294"]},{"raw_affiliation_string":"Institute for Brain and Neural Systems, Brown University, Providence, RI 02906, USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081797261","display_name":"John M. Sedivy","orcid":"https://orcid.org/0000-0001-9363-4253"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John M Sedivy","raw_affiliation_strings":["Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, RI 02903, USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5109971261","display_name":"Leon N. Cooper","orcid":null},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Leon N Cooper","raw_affiliation_strings":["Department of Physics, Brown University, Providence, RI 02906, USA","Institute for Brain and Neural Systems, Brown University, Providence, RI 02906, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Physics, Brown University, Providence, RI 02906, USA","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Institute for Brain and Neural Systems, Brown University, Providence, RI 02906, USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5033949989","display_name":"E. Verondini","orcid":null},"institutions":[{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Ettore Verondini","raw_affiliation_strings":["Centro Interdipartimentale \u201cL. Galvani\u201d, Universit\u00e0 di Bologna, Bologna, 40127, Italy","Department of Physics, Universit\u00e0 di Bologna, Bologna, 40127, Italy","Centro Interdipartimentale \"L. Galvani\", Universit\u00e0 di Bologna, Bologna, 40127, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Interdipartimentale \u201cL. Galvani\u201d, Universit\u00e0 di Bologna, Bologna, 40127, Italy","institution_ids":["https://openalex.org/I9360294"]},{"raw_affiliation_string":"Department of Physics, Universit\u00e0 di Bologna, Bologna, 40127, Italy","institution_ids":["https://openalex.org/I9360294"]},{"raw_affiliation_string":"Centro Interdipartimentale \"L. Galvani\", Universit\u00e0 di Bologna, Bologna, 40127, Italy","institution_ids":["https://openalex.org/I9360294"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088629765","display_name":"Luciano Milanesi","orcid":"https://orcid.org/0000-0002-1201-3939"},"institutions":[{"id":"https://openalex.org/I4210124735","display_name":"Istituto per le Tecnologie Didattiche","ror":"https://ror.org/02xz4xc25","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210124735","https://openalex.org/I4210155236"]},{"id":"https://openalex.org/I4210154278","display_name":"Institute of Biomedical Technologies","ror":"https://ror.org/04ehykb85","country_code":"IT","type":"facility","lineage":["https://openalex.org/I4210154278","https://openalex.org/I4210155236"]}],"countries":["IT"],"is_corresponding":false,"raw_author_name":"Luciano Milanesi","raw_affiliation_strings":["Istituto di Tecnologie Biomediche (ITB) CNR, Milano, 20090, Italy"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Istituto di Tecnologie Biomediche (ITB) CNR, Milano, 20090, Italy","institution_ids":["https://openalex.org/I4210124735","https://openalex.org/I4210154278"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5026341152","display_name":"Gastone Castellani","orcid":"https://orcid.org/0000-0003-4892-925X"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]},{"id":"https://openalex.org/I9360294","display_name":"University of Bologna","ror":"https://ror.org/01111rn36","country_code":"IT","type":"education","lineage":["https://openalex.org/I9360294"]}],"countries":["IT","US"],"is_corresponding":true,"raw_author_name":"Gastone Castellani","raw_affiliation_strings":["Centro Interdipartimentale \u201cL. Galvani\u201d, Universit\u00e0 di Bologna, Bologna, 40127, Italy","Dipartimento di Morfofisiologia veterinaria e Produzioni Animali (DIMORFIPA), Universit\u00e0 di Bologna, Bologna, 40064, Italy","Institute for Brain and Neural Systems, Brown University, Providence, RI 02906, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Centro Interdipartimentale \u201cL. Galvani\u201d, Universit\u00e0 di Bologna, Bologna, 40127, Italy","institution_ids":["https://openalex.org/I9360294"]},{"raw_affiliation_string":"Dipartimento di Morfofisiologia veterinaria e Produzioni Animali (DIMORFIPA), Universit\u00e0 di Bologna, Bologna, 40064, Italy","institution_ids":["https://openalex.org/I9360294"]},{"raw_affiliation_string":"Institute for Brain and Neural Systems, Brown University, Providence, RI 02906, USA","institution_ids":["https://openalex.org/I27804330"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5026341152"],"corresponding_institution_ids":["https://openalex.org/I27804330","https://openalex.org/I9360294"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":1.8196,"has_fulltext":true,"cited_by_count":48,"citation_normalized_percentile":{"value":0.84836164,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":94,"max":99},"biblio":{"volume":"9","issue":"S4","first_page":"S9","last_page":"S9"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9143000245094299,"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":0.9143000245094299,"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":0.03999999910593033,"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/T11303","display_name":"Bayesian Modeling and Causal Inference","score":0.008299999870359898,"subfield":{"id":"https://openalex.org/subfields/1702","display_name":"Artificial Intelligence"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5464502573013306},{"id":"https://openalex.org/keywords/significance-analysis-of-microarrays","display_name":"Significance analysis of microarrays","score":0.543437123298645},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5185837745666504},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.48688140511512756},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4793837070465088},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.4733429253101349},{"id":"https://openalex.org/keywords/statistical-hypothesis-testing","display_name":"Statistical hypothesis testing","score":0.47109895944595337},{"id":"https://openalex.org/keywords/intersection","display_name":"Intersection (aeronautics)","score":0.46803975105285645},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4622231721878052},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.427929162979126},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3330554664134979},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2481895387172699},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.24765074253082275},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.1781524419784546},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.09052318334579468}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5464502573013306},{"id":"https://openalex.org/C77360908","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Significance analysis of microarrays","level":5,"score":0.543437123298645},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5185837745666504},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.48688140511512756},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4793837070465088},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.4733429253101349},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.47109895944595337},{"id":"https://openalex.org/C64543145","wikidata":"https://www.wikidata.org/wiki/Q162942","display_name":"Intersection (aeronautics)","level":2,"score":0.46803975105285645},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4622231721878052},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.427929162979126},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3330554664134979},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2481895387172699},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.24765074253082275},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.1781524419784546},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.09052318334579468},{"id":"https://openalex.org/C146978453","wikidata":"https://www.wikidata.org/wiki/Q3798668","display_name":"Aerospace engineering","level":1,"score":0.0},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003198","descriptor_name":"Computer Simulation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D003627","descriptor_name":"Data Interpretation, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D008954","descriptor_name":"Models, Biological","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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015233","descriptor_name":"Models, Statistical","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D015398","descriptor_name":"Signal Transduction","qualifier_ui":"Q000502","qualifier_name":"physiology","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D020543","descriptor_name":"Proteome","qualifier_ui":"Q000378","qualifier_name":"metabolism","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":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D025941","descriptor_name":"Protein Interaction Mapping","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/1471-2105-9-s4-s9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-s4-s9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-S4-S9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},{"id":"pmid:18460182","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/18460182","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":"BMC bioinformatics","raw_type":null},{"id":"pmh:oai:cris.unibo.it:11585/63714","is_oa":false,"landing_page_url":"http://hdl.handle.net/11585/63714","pdf_url":null,"source":{"id":"https://openalex.org/S4306402579","display_name":"Archivio istituzionale della ricerca (Alma Mater Studiorum Universit\u00e0 di Bologna)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210117483","host_organization_name":"Istituto di Ematologia di Bologna","host_organization_lineage":["https://openalex.org/I4210117483"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:doaj.org/article:6f444d97d64346289f66757fe40f67eb","is_oa":false,"landing_page_url":"https://doaj.org/article/6f444d97d64346289f66757fe40f67eb","pdf_url":null,"source":{"id":"https://openalex.org/S4306401280","display_name":"DOAJ (DOAJ: Directory of Open Access Journals)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 9, Iss Suppl 4, p S9 (2008)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:2367636","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2367636","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,"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":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1471-2105-9-s4-s9","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-9-s4-s9","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-9-S4-S9","source":{"id":"https://openalex.org/S19032547","display_name":"BMC Bioinformatics","issn_l":"1471-2105","issn":["1471-2105"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310320256","host_organization_name":"BioMed Central","host_organization_lineage":["https://openalex.org/P4310320256","https://openalex.org/P4310319965"],"host_organization_lineage_names":["BioMed Central","Springer Nature"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"BMC Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G2443267934","display_name":null,"funder_award_id":"R01 GM41690-17","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G6642348146","display_name":null,"funder_award_id":"R01 GM041690","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"}],"funders":[{"id":"https://openalex.org/F4320321873","display_name":"Ministero dell\u2019Istruzione, dell\u2019Universit\u00e0 e della Ricerca","ror":"https://ror.org/0166hxq48"},{"id":"https://openalex.org/F4320327843","display_name":"Istituto Nazionale di Fisica Nucleare","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2128085074.pdf","grobid_xml":"https://content.openalex.org/works/W2128085074.grobid-xml"},"referenced_works_count":28,"referenced_works":["https://openalex.org/W177818563","https://openalex.org/W1535641839","https://openalex.org/W1971937094","https://openalex.org/W1975511102","https://openalex.org/W1977978614","https://openalex.org/W2001627351","https://openalex.org/W2006333907","https://openalex.org/W2054777324","https://openalex.org/W2062348957","https://openalex.org/W2096441034","https://openalex.org/W2102992354","https://openalex.org/W2103017472","https://openalex.org/W2109044536","https://openalex.org/W2109363337","https://openalex.org/W2115226431","https://openalex.org/W2116525802","https://openalex.org/W2118069309","https://openalex.org/W2119739306","https://openalex.org/W2123106337","https://openalex.org/W2127299993","https://openalex.org/W2130029389","https://openalex.org/W2130410032","https://openalex.org/W2132032809","https://openalex.org/W2154947819","https://openalex.org/W2154972152","https://openalex.org/W2159482845","https://openalex.org/W2170989872","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W2066632517","https://openalex.org/W2384739783","https://openalex.org/W4294107304","https://openalex.org/W2049066753","https://openalex.org/W2350887638","https://openalex.org/W1986892844","https://openalex.org/W2062353821","https://openalex.org/W1991841244","https://openalex.org/W2918144038","https://openalex.org/W429198448"],"abstract_inverted_index":{"BACKGROUND:":[0],"Significance":[1],"analysis":[2,56,85,181],"at":[3,199],"single":[4,69,104],"gene":[5,54,127],"level":[6],"may":[7,72],"suffer":[8],"from":[9,134,151,163],"the":[10,22,25,41,64,89,101,109,119,130,147,152,179,200,212],"limited":[11],"number":[12],"of":[13,24,91,93,103,121,123,154,182,185,197],"samples":[14],"and":[15,71,108,158],"experimental":[16],"noise":[17],"that":[18,173,195],"can":[19,57,205],"severely":[20],"limit":[21],"power":[23],"chosen":[26],"statistical":[27,171],"test.":[28],"This":[29],"problem":[30],"is":[31],"typically":[32],"approached":[33],"by":[34,220],"applying":[35],"post":[36],"hoc":[37],"corrections":[38],"to":[39,62,68,74,125,187,216],"control":[40],"false":[42],"discovery":[43],"rate,":[44],"without":[45],"taking":[46],"into":[47],"account":[48],"prior":[49],"biological":[50,77],"knowledge.":[51],"Pathway":[52],"or":[53],"ontology":[55],"provide":[58],"an":[59],"alternative":[60],"way":[61],"relax":[63],"significance":[65,102,180],"threshold":[66],"applied":[67],"genes":[70,186,198],"lead":[73],"a":[75,83,135,142],"better":[76],"interpretation.":[78],"RESULTS:":[79],"Here":[80],"we":[81],"propose":[82],"new":[84],"method":[86,117,169],"based":[87],"on":[88],"study":[90],"networks":[92,96,122],"pathways.":[94],"These":[95],"are":[97,217],"reconstructed":[98],"considering":[99],"both":[100],"pathways":[105,124,204,213],"(network":[106],"nodes)":[107],"intersection":[110],"between":[111,190,202],"them":[112],"(links).":[113],"We":[114,193],"apply":[115],"this":[116],"for":[118,178],"reconstruction":[120],"two":[126],"expression":[128],"datasets:":[129],"first":[131],"one":[132,149],"obtained":[133,150],"c-Myc":[136],"rat":[137],"fibroblast":[138],"cell":[139],"line":[140],"expressing":[141],"conditional":[143],"Myc-estrogen":[144],"receptor":[145],"oncoprotein;":[146],"second":[148],"comparison":[153],"Acute":[155,159],"Myeloid":[156],"Leukemia":[157,161],"Lymphoblastic":[160],"derived":[162],"bone":[164],"marrow":[165],"samples.":[166],"CONCLUSION:":[167],"Our":[168],"extends":[170],"models":[172],"have":[174],"been":[175],"recently":[176],"adopted":[177],"functional":[183],"groups":[184,196],"infer":[188],"links":[189],"these":[191],"groups.":[192],"show":[194],"interface":[201],"different":[203],"be":[206],"considered":[207],"as":[208],"relevant":[209],"even":[210],"if":[211],"they":[214],"belong":[215],"not":[218],"significant":[219],"themselves.":[221]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2021,"cited_by_count":3},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":5},{"year":2016,"cited_by_count":3},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":4},{"year":2012,"cited_by_count":7}],"updated_date":"2026-07-23T08:03:31.855105","created_date":"2025-10-10T00:00:00"}