{"id":"https://openalex.org/W2144980057","doi":"https://doi.org/10.1186/1471-2105-10-s9-s6","title":"Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia","display_name":"Mechanism-anchored profiling derived from epigenetic networks predicts outcome in acute lymphoblastic leukemia","publication_year":2009,"publication_date":"2009-09-01","ids":{"openalex":"https://openalex.org/W2144980057","doi":"https://doi.org/10.1186/1471-2105-10-s9-s6","mag":"2144980057","pmid":"https://pubmed.ncbi.nlm.nih.gov/19761576"},"language":"en","primary_location":{"id":"doi:10.1186/1471-2105-10-s9-s6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s9-s6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S9-S6","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/10.1186/1471-2105-10-S9-S6","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5079231875","display_name":"Xinan Yang","orcid":"https://orcid.org/0000-0001-8061-8692"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Xinan Yang","raw_affiliation_strings":["Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA. xyang2@uchicago.edu","Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL 60637, USA. xyang2@uchicago.edu","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5044514129","display_name":"Yong Huang","orcid":"https://orcid.org/0009-0001-1989-8223"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yong Huang","raw_affiliation_strings":["Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5037373285","display_name":"James L. Chen","orcid":"https://orcid.org/0000-0002-4095-5202"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"James L Chen","raw_affiliation_strings":["Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5102154833","display_name":"Jianming Xie","orcid":null},"institutions":[{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Jianming Xie","raw_affiliation_strings":["State Key Laboratory of Bioelectronics, Southeast University, 210096, Nanjing, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioelectronics, Southeast University, 210096, Nanjing, PR China","institution_ids":["https://openalex.org/I76569877"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082259816","display_name":"Xiao Sun","orcid":"https://orcid.org/0000-0003-1048-7775"},"institutions":[{"id":"https://openalex.org/I76569877","display_name":"Southeast University","ror":"https://ror.org/04ct4d772","country_code":"CN","type":"education","lineage":["https://openalex.org/I76569877"]}],"countries":["CN"],"is_corresponding":false,"raw_author_name":"Xiao Sun","raw_affiliation_strings":["State Key Laboratory of Bioelectronics, Southeast University, 210096, Nanjing, PR China"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"State Key Laboratory of Bioelectronics, Southeast University, 210096, Nanjing, PR China","institution_ids":["https://openalex.org/I76569877"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5074706648","display_name":"Yves A. Lussier","orcid":"https://orcid.org/0000-0001-9854-1005"},"institutions":[{"id":"https://openalex.org/I40347166","display_name":"University of Chicago","ror":"https://ror.org/024mw5h28","country_code":"US","type":"education","lineage":["https://openalex.org/I40347166"]},{"id":"https://openalex.org/I4210127473","display_name":"Cancer Research Center","ror":"https://ror.org/03fbwjm33","country_code":"US","type":"nonprofit","lineage":["https://openalex.org/I4210127473"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Yves A Lussier","raw_affiliation_strings":["Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA","The Institute for Genomics and Systems Biology, and the Computational Institute, The University of Chicago, Chicago, IL, 60637, USA","The University of Chicago Cancer Research Center, and The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, 60637, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Biomedical Informatics and Section of Genetic Medicine, Department of Medicine, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"The Institute for Genomics and Systems Biology, and the Computational Institute, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166"]},{"raw_affiliation_string":"The University of Chicago Cancer Research Center, and The Ludwig Center for Metastasis Research, The University of Chicago, Chicago, IL, 60637, USA","institution_ids":["https://openalex.org/I40347166","https://openalex.org/I4210127473"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5074706648"],"corresponding_institution_ids":["https://openalex.org/I40347166","https://openalex.org/I4210127473"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":1.0236,"has_fulltext":true,"cited_by_count":11,"citation_normalized_percentile":{"value":0.81397562,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"10","issue":"S9","first_page":"S6","last_page":"S6"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10950","display_name":"Acute Lymphoblastic Leukemia research","score":0.2565000057220459,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10950","display_name":"Acute Lymphoblastic Leukemia research","score":0.2565000057220459,"subfield":{"id":"https://openalex.org/subfields/2739","display_name":"Public Health, Environmental and Occupational Health"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10309","display_name":"Acute Myeloid Leukemia Research","score":0.18410000205039978,"subfield":{"id":"https://openalex.org/subfields/2720","display_name":"Hematology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T11215","display_name":"Chronic Myeloid Leukemia Treatments","score":0.14560000598430634,"subfield":{"id":"https://openalex.org/subfields/2720","display_name":"Hematology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/epigenetics","display_name":"Epigenetics","score":0.6580675840377808},{"id":"https://openalex.org/keywords/lymphoblastic-leukemia","display_name":"Lymphoblastic Leukemia","score":0.6472102999687195},{"id":"https://openalex.org/keywords/mechanism","display_name":"Mechanism (biology)","score":0.5788585543632507},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5723838806152344},{"id":"https://openalex.org/keywords/profiling","display_name":"Profiling (computer programming)","score":0.5493670105934143},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5453994274139404},{"id":"https://openalex.org/keywords/gene-expression-profiling","display_name":"Gene expression profiling","score":0.4616253972053528},{"id":"https://openalex.org/keywords/outcome","display_name":"Outcome (game theory)","score":0.425731360912323},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.42499592900276184},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.39662104845046997},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.3729837238788605},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.365261435508728},{"id":"https://openalex.org/keywords/oncology","display_name":"Oncology","score":0.33819708228111267},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3149253726005554},{"id":"https://openalex.org/keywords/leukemia","display_name":"Leukemia","score":0.3125988841056824},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.1490316390991211},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1111595630645752},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10857442021369934},{"id":"https://openalex.org/keywords/physics","display_name":"Physics","score":0.07582885026931763}],"concepts":[{"id":"https://openalex.org/C41091548","wikidata":"https://www.wikidata.org/wiki/Q26939","display_name":"Epigenetics","level":3,"score":0.6580675840377808},{"id":"https://openalex.org/C2909962599","wikidata":"https://www.wikidata.org/wiki/Q180664","display_name":"Lymphoblastic Leukemia","level":3,"score":0.6472102999687195},{"id":"https://openalex.org/C89611455","wikidata":"https://www.wikidata.org/wiki/Q6804646","display_name":"Mechanism (biology)","level":2,"score":0.5788585543632507},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5723838806152344},{"id":"https://openalex.org/C187191949","wikidata":"https://www.wikidata.org/wiki/Q1138496","display_name":"Profiling (computer programming)","level":2,"score":0.5493670105934143},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5453994274139404},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4616253972053528},{"id":"https://openalex.org/C148220186","wikidata":"https://www.wikidata.org/wiki/Q7111912","display_name":"Outcome (game theory)","level":2,"score":0.425731360912323},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.42499592900276184},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.39662104845046997},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.3729837238788605},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.365261435508728},{"id":"https://openalex.org/C143998085","wikidata":"https://www.wikidata.org/wiki/Q162555","display_name":"Oncology","level":1,"score":0.33819708228111267},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3149253726005554},{"id":"https://openalex.org/C2778461978","wikidata":"https://www.wikidata.org/wiki/Q29496","display_name":"Leukemia","level":2,"score":0.3125988841056824},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.1490316390991211},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1111595630645752},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10857442021369934},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.07582885026931763},{"id":"https://openalex.org/C111919701","wikidata":"https://www.wikidata.org/wiki/Q9135","display_name":"Operating system","level":1,"score":0.0},{"id":"https://openalex.org/C144237770","wikidata":"https://www.wikidata.org/wiki/Q747534","display_name":"Mathematical economics","level":1,"score":0.0},{"id":"https://openalex.org/C62520636","wikidata":"https://www.wikidata.org/wiki/Q944","display_name":"Quantum mechanics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020869","descriptor_name":"Gene Expression Profiling","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D044127","descriptor_name":"Epigenesis, Genetic","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D053263","descriptor_name":"Gene Regulatory Networks","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054198","descriptor_name":"Precursor Cell Lymphoblastic Leukemia-Lymphoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054198","descriptor_name":"Precursor Cell Lymphoblastic Leukemia-Lymphoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054198","descriptor_name":"Precursor Cell Lymphoblastic Leukemia-Lymphoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D054198","descriptor_name":"Precursor Cell Lymphoblastic Leukemia-Lymphoma","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1186/1471-2105-10-s9-s6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s9-s6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S9-S6","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:19761576","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/19761576","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:pubmedcentral.nih.gov:2745693","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2745693","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:10.1186/1471-2105-10-s9-s6","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1471-2105-10-s9-s6","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/1471-2105-10-S9-S6","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/G2708175070","display_name":null,"funder_award_id":"U54 CA121852","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G4004976805","display_name":null,"funder_award_id":"60121101","funder_id":"https://openalex.org/F4320321001","funder_display_name":"National Natural Science Foundation of China"},{"id":"https://openalex.org/G7583224788","display_name":null,"funder_award_id":"1U54CA121852","funder_id":"https://openalex.org/F4320337351","funder_display_name":"National Cancer Institute"},{"id":"https://openalex.org/G7972181056","display_name":null,"funder_award_id":"K22 LM008308","funder_id":"https://openalex.org/F4320337372","funder_display_name":"U.S. National Library of Medicine"}],"funders":[{"id":"https://openalex.org/F4320321001","display_name":"National Natural Science Foundation of China","ror":"https://ror.org/01h0zpd94"},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337351","display_name":"National Cancer Institute","ror":"https://ror.org/040gcmg81"},{"id":"https://openalex.org/F4320337372","display_name":"U.S. National Library of Medicine","ror":"https://ror.org/0060t0j89"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2144980057.pdf","grobid_xml":"https://content.openalex.org/works/W2144980057.grobid-xml"},"referenced_works_count":54,"referenced_works":["https://openalex.org/W1706564076","https://openalex.org/W1887579480","https://openalex.org/W1967291882","https://openalex.org/W1977873692","https://openalex.org/W1988392802","https://openalex.org/W1988553741","https://openalex.org/W2001400919","https://openalex.org/W2004159986","https://openalex.org/W2016782531","https://openalex.org/W2019339067","https://openalex.org/W2028604413","https://openalex.org/W2029694543","https://openalex.org/W2034403778","https://openalex.org/W2034595398","https://openalex.org/W2039365544","https://openalex.org/W2041236924","https://openalex.org/W2043033879","https://openalex.org/W2048674295","https://openalex.org/W2057626690","https://openalex.org/W2059526410","https://openalex.org/W2074557360","https://openalex.org/W2076723282","https://openalex.org/W2091947792","https://openalex.org/W2096081005","https://openalex.org/W2100025044","https://openalex.org/W2101859647","https://openalex.org/W2105381419","https://openalex.org/W2106285921","https://openalex.org/W2119943416","https://openalex.org/W2120413242","https://openalex.org/W2122598723","https://openalex.org/W2124970707","https://openalex.org/W2125905177","https://openalex.org/W2126124351","https://openalex.org/W2138550913","https://openalex.org/W2140000393","https://openalex.org/W2141410747","https://openalex.org/W2144266296","https://openalex.org/W2148059192","https://openalex.org/W2149052195","https://openalex.org/W2151445954","https://openalex.org/W2155592900","https://openalex.org/W2155699197","https://openalex.org/W2160697532","https://openalex.org/W2161409973","https://openalex.org/W2163296115","https://openalex.org/W2163480486","https://openalex.org/W2164141804","https://openalex.org/W2166667584","https://openalex.org/W2168301815","https://openalex.org/W2914577469","https://openalex.org/W3099289621","https://openalex.org/W4254209065","https://openalex.org/W4285719527"],"related_works":["https://openalex.org/W2069695727","https://openalex.org/W1996185163","https://openalex.org/W2084813257","https://openalex.org/W2045929470","https://openalex.org/W2081127504","https://openalex.org/W2122223946","https://openalex.org/W4233500668","https://openalex.org/W1974145978","https://openalex.org/W1977867163","https://openalex.org/W2393426762"],"abstract_inverted_index":{"BACKGROUND:":[0],"Current":[1],"outcome":[2,43,211,227],"predictors":[3],"based":[4],"on":[5,9,138],"\"molecular":[6],"profiling\"":[7],"rely":[8],"gene":[10],"lists":[11],"selected":[12],"without":[13],"consideration":[14],"for":[15],"their":[16],"molecular":[17,294],"mechanisms.":[18,75],"This":[19,133,274],"study":[20],"was":[21,141,199,213,231],"designed":[22],"to":[23,32,41,67,96,115,164,174,225,265,270,280,291],"demonstrate":[24,266],"that":[25,180,296],"we":[26],"could":[27],"learn":[28],"about":[29],"genes":[30,73,94,123,259],"related":[31],"a":[33,47,56,62,121,144,205],"specific":[34],"mechanism":[35,102,128],"and":[36,74,118,129,159,170,185,204,241,264],"further":[37],"use":[38],"this":[39,81,250],"knowledge":[40],"predict":[42,226,271],"in":[44,80,99,143,289,304],"patients":[45],"-":[46],"paradigm":[48],"shift":[49],"towards":[50],"accurate":[51],"\"mechanism-anchored":[52],"profiling\".":[53],"We":[54,166],"propose":[55],"novel":[57],"algorithm,":[58],"PGnet,":[59],"which":[60,136],"predicts":[61],"tripartite":[63,178],"mechanism-anchored":[64],"network":[65,82,179,224],"associated":[66,260],"epigenetic":[68,139,262],"regulation":[69,288],"consisting":[70],"of":[71,85,103,147,162,182,189,197,221,229,258,302],"phenotypes,":[72],"Genes":[76],"termed":[77],"as":[78,120],"GEMs":[79,190],"meet":[83],"all":[84],"the":[86,100,116,127,130,176,242,252],"following":[87],"criteria:":[88],"(i)":[89],"they":[90,106],"are":[91,107,297],"co-expressed":[92],"with":[93,125,155,261],"known":[95],"be":[97,278],"involved":[98],"biological":[101],"interest,":[104],"(ii)":[105],"also":[108],"differentially":[109],"expressed":[110],"between":[111],"distinct":[112,157,193],"phenotypes":[113,158,184],"relevant":[114],"study,":[117,135],"(iii)":[119],"biomodule,":[122],"correlate":[124],"both":[126],"phenotype.":[131],"RESULTS:":[132],"proof-of-concept":[134],"focuses":[137],"mechanisms,":[140],"conducted":[142],"well-studied":[145],"set":[146],"132":[148],"acute":[149],"lymphoblastic":[150],"leukemia":[151],"(ALL)":[152],"microarrays":[153],"annotated":[154],"nine":[156],"three":[160],"measures":[161],"response":[163],"therapy.":[165],"used":[167],"established":[168],"parametric":[169,172],"non":[171],"statistics":[173],"derive":[175,292],"PGnet":[177,198,275,303],"consisted":[181],"10":[183],"33":[186],"significant":[187,232],"clusters":[188],"comprising":[191],"535":[192],"genes.":[194],"The":[195,219,300],"significance":[196],"estimated":[200],"from":[201,209],"empirical":[202],"p-values,":[203],"robust":[206,223],"subnetwork":[207],"derived":[208,222],"ALL":[210],"data":[212],"produced":[214],"by":[215],"repeated":[216],"random":[217],"sampling.":[218],"evaluation":[220],"(relapse":[228],"ALL)":[230],"(p":[233],"=":[234],"3%),":[235],"using":[236],"one":[237],"hundred":[238],"three-fold":[239],"cross-validations":[240],"shrunken":[243],"centroids":[244],"classifier.":[245],"CONCLUSION:":[246],"To":[247],"our":[248],"knowledge,":[249],"is":[251,306],"first":[253],"method":[254],"predicting":[255],"co-expression":[256],"networks":[257],"mechanisms":[263,283],"its":[267],"inherent":[268],"capability":[269],"therapeutic":[272],"outcome.":[273],"approach":[276],"can":[277],"applied":[279],"any":[281],"regulatory":[282],"including":[284],"transcriptional":[285],"or":[286],"microRNA":[287],"order":[290],"predictive":[293],"profiles":[295],"mechanistically":[298],"anchored.":[299],"implementation":[301],"R":[305],"freely":[307],"available":[308],"at":[309],"http://Lussierlab.org/publication/PGnet.":[310]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2020,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":2},{"year":2013,"cited_by_count":1}],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
