{"id":"https://openalex.org/W2330617406","doi":"https://doi.org/10.4018/ijkdb.2014070104","title":"Gene Set- and Pathway- Centered Knowledge Discovery Assigns Transcriptional Activation Patterns in Brain, Blood, and Colon Cancer","display_name":"Gene Set- and Pathway- Centered Knowledge Discovery Assigns Transcriptional Activation Patterns in Brain, Blood, and Colon Cancer","publication_year":2014,"publication_date":"2014-07-01","ids":{"openalex":"https://openalex.org/W2330617406","doi":"https://doi.org/10.4018/ijkdb.2014070104","mag":"2330617406"},"language":"en","primary_location":{"id":"doi:10.4018/ijkdb.2014070104","is_oa":false,"landing_page_url":"https://doi.org/10.4018/ijkdb.2014070104","pdf_url":null,"source":{"id":"https://openalex.org/S113982356","display_name":"International Journal of Knowledge Discovery in Bioinformatics","issn_l":"1947-9115","issn":["1947-9115","1947-9123"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320424","host_organization_name":"IGI Global","host_organization_lineage":["https://openalex.org/P4310320424"],"host_organization_lineage_names":["IGI Global"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Knowledge Discovery in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5027476361","display_name":"Lilit Nersisyan","orcid":"https://orcid.org/0000-0001-8525-420X"},"institutions":[{"id":"https://openalex.org/I187562900","display_name":"American University of Armenia","ror":"https://ror.org/04dngzj56","country_code":"AM","type":"education","lineage":["https://openalex.org/I187562900"]},{"id":"https://openalex.org/I4210133976","display_name":"Institute of Molecular Biology","ror":"https://ror.org/03t8mqd25","country_code":"AM","type":"facility","lineage":["https://openalex.org/I4210133976","https://openalex.org/I99064381"]},{"id":"https://openalex.org/I99064381","display_name":"National Academy of Sciences of Armenia","ror":"https://ror.org/04mczx267","country_code":"AM","type":"government","lineage":["https://openalex.org/I99064381"]}],"countries":["AM"],"is_corresponding":false,"raw_author_name":"Lilit Nersisyan","raw_affiliation_strings":["Institute of Molecular Biology, National Academy of Sciences and College of Science and Engineering, American University of Armenia, Yerevan, Armenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Molecular Biology, National Academy of Sciences and College of Science and Engineering, American University of Armenia, Yerevan, Armenia","institution_ids":["https://openalex.org/I187562900","https://openalex.org/I4210133976","https://openalex.org/I99064381"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065981953","display_name":"Henry Loeffler\u2010Wirth","orcid":"https://orcid.org/0000-0001-8239-440X"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Henry L\u00f6ffler-Wirth","raw_affiliation_strings":["Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5052114174","display_name":"Arsen Arakelyan","orcid":"https://orcid.org/0000-0002-6851-1056"},"institutions":[{"id":"https://openalex.org/I187562900","display_name":"American University of Armenia","ror":"https://ror.org/04dngzj56","country_code":"AM","type":"education","lineage":["https://openalex.org/I187562900"]},{"id":"https://openalex.org/I4210133976","display_name":"Institute of Molecular Biology","ror":"https://ror.org/03t8mqd25","country_code":"AM","type":"facility","lineage":["https://openalex.org/I4210133976","https://openalex.org/I99064381"]},{"id":"https://openalex.org/I99064381","display_name":"National Academy of Sciences of Armenia","ror":"https://ror.org/04mczx267","country_code":"AM","type":"government","lineage":["https://openalex.org/I99064381"]}],"countries":["AM"],"is_corresponding":false,"raw_author_name":"Arsen Arakelyan","raw_affiliation_strings":["Institute of Molecular Biology, National Academy of Sciences and College of Science and Engineering, American University of Armenia, Yerevan, Armenia"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Institute of Molecular Biology, National Academy of Sciences and College of Science and Engineering, American University of Armenia, Yerevan, Armenia","institution_ids":["https://openalex.org/I187562900","https://openalex.org/I4210133976","https://openalex.org/I99064381"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045754538","display_name":"Hans Binder","orcid":"https://orcid.org/0000-0002-2242-4678"},"institutions":[{"id":"https://openalex.org/I926574661","display_name":"Leipzig University","ror":"https://ror.org/03s7gtk40","country_code":"DE","type":"education","lineage":["https://openalex.org/I926574661"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Hans Binder","raw_affiliation_strings":["Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Leipzig, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Interdisciplinary Centre for Bioinformatics (IZBI), Leipzig University, Leipzig, Germany","institution_ids":["https://openalex.org/I926574661"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":0.3899,"has_fulltext":false,"cited_by_count":14,"citation_normalized_percentile":{"value":0.62129892,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"4","issue":"2","first_page":"46","last_page":"69"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9995999932289124,"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":0.9995999932289124,"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":0.9980000257492065,"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":0.9979000091552734,"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/computational-biology","display_name":"Computational biology","score":0.661940336227417},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.6064499616622925},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5160812735557556},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4869872033596039},{"id":"https://openalex.org/keywords/gene-regulatory-network","display_name":"Gene regulatory network","score":0.458809494972229},{"id":"https://openalex.org/keywords/biological-pathway","display_name":"Biological pathway","score":0.45001545548439026},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4377390146255493},{"id":"https://openalex.org/keywords/genome","display_name":"Genome","score":0.43074730038642883},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3515821397304535},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.2956615090370178},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.23562020063400269}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.661940336227417},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.6064499616622925},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5160812735557556},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4869872033596039},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.458809494972229},{"id":"https://openalex.org/C9927688","wikidata":"https://www.wikidata.org/wiki/Q4915012","display_name":"Biological pathway","level":4,"score":0.45001545548439026},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4377390146255493},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.43074730038642883},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3515821397304535},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.2956615090370178},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.23562020063400269},{"id":"https://openalex.org/C199360897","wikidata":"https://www.wikidata.org/wiki/Q9143","display_name":"Programming language","level":1,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"doi:10.4018/ijkdb.2014070104","is_oa":false,"landing_page_url":"https://doi.org/10.4018/ijkdb.2014070104","pdf_url":null,"source":{"id":"https://openalex.org/S113982356","display_name":"International Journal of Knowledge Discovery in Bioinformatics","issn_l":"1947-9115","issn":["1947-9115","1947-9123"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310320424","host_organization_name":"IGI Global","host_organization_lineage":["https://openalex.org/P4310320424"],"host_organization_lineage_names":["IGI Global"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"International Journal of Knowledge Discovery in Bioinformatics","raw_type":"journal-article"},{"id":"pmh:oai:RePEc:igg:jkdb00:v:4:y:2014:i:2:p:46-69","is_oa":false,"landing_page_url":"http://services.igi-global.com/resolvedoi/resolve.aspx?doi=10.4018/IJKDB.2014070104","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4699999988079071,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":27,"referenced_works":["https://openalex.org/W65738273","https://openalex.org/W1488442803","https://openalex.org/W1505191356","https://openalex.org/W1519855763","https://openalex.org/W1862015311","https://openalex.org/W1983463159","https://openalex.org/W1984365472","https://openalex.org/W1989619485","https://openalex.org/W2022397091","https://openalex.org/W2027670219","https://openalex.org/W2031980017","https://openalex.org/W2034269086","https://openalex.org/W2052581434","https://openalex.org/W2058451329","https://openalex.org/W2073902642","https://openalex.org/W2076889248","https://openalex.org/W2077350268","https://openalex.org/W2130410032","https://openalex.org/W2133131759","https://openalex.org/W2139696807","https://openalex.org/W2151485201","https://openalex.org/W2151937508","https://openalex.org/W2157031069","https://openalex.org/W2159482845","https://openalex.org/W2161289668","https://openalex.org/W2495191183","https://openalex.org/W2506219372"],"related_works":["https://openalex.org/W2009966535","https://openalex.org/W1603543036","https://openalex.org/W2014988381","https://openalex.org/W2810320185","https://openalex.org/W1994539334","https://openalex.org/W4241525120","https://openalex.org/W2113203134","https://openalex.org/W2909382709","https://openalex.org/W2580080859","https://openalex.org/W2156615630"],"abstract_inverted_index":{"Genome-wide":[0],"\u2018omics'-assays":[1],"provide":[2,106],"a":[3,18,71,107],"comprehensive":[4],"view":[5,20],"on":[6,174],"the":[7,82,85,143,151,154],"molecular":[8,133],"landscapes":[9],"of":[10,24,48,73,76,84,145,153,165,171],"healthy":[11,31],"and":[12,32,79,128,141,157,170,178],"diseased":[13,33],"cells.":[14],"Bioinformatics":[15],"traditionally":[16],"pursues":[17],"\u2018gene-centered'":[19],"by":[21,41,70],"extracting":[22],"lists":[23],"genes":[25,78,100],"differentially":[26],"expressed":[27],"or":[28],"methylated":[29],"between":[30],"states.":[34],"Biological":[35],"knowledge":[36,108],"mining":[37],"is":[38],"then":[39],"performed":[40],"applying":[42],"gene":[43,50,155],"set":[44,101,156],"techniques":[45],"using":[46,119,162],"libraries":[47],"functional":[49,74],"sets":[51],"obtained":[52],"from":[53,132],"independent":[54],"studies.":[55],"This":[56],"analysis":[57,96],"strategy":[58],"neglects":[59],"two":[60],"facts:":[61],"(i)":[62],"that":[63,81,94,111],"different":[64],"disease":[65],"states":[66],"can":[67,89],"be":[68],"characterized":[69],"series":[72],"modules":[75],"co-regulated":[77],"(ii)":[80],"topology":[83],"underlying":[86],"regulatory":[87,130],"networks":[88],"induce":[90],"complex":[91],"expression":[92,163],"patterns":[93],"require":[95],"methods":[97,161],"beyond":[98],"traditional":[99],"techniques.":[102],"The":[103,148],"authors":[104,149],"here":[105],"discovery":[109],"method":[110],"overcomes":[112],"these":[113],"shortcomings.":[114],"It":[115,126],"combines":[116],"machine":[117],"learning":[118],"self-organizing":[120],"maps":[121,136],"with":[122],"pathway":[123,158,167],"flow":[124,160],"analysis.":[125],"extracts":[127],"visualizes":[129],"modes":[131],"omics":[134],"data,":[135],"them":[137],"onto":[138],"selected":[139],"pathways":[140],"estimates":[142],"impact":[144],"pathway-activity":[146],"changes.":[147],"illustrate":[150],"performance":[152],"signal":[159],"data":[164,173],"oncogenic":[166],"activation":[168],"experiments":[169],"patient":[172],"glioma,":[175],"B-cell":[176],"lymphoma":[177],"colorectal":[179],"cancer.":[180]},"counts_by_year":[{"year":2024,"cited_by_count":1},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":2},{"year":2019,"cited_by_count":4},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":3}],"updated_date":"2026-07-22T07:51:19.307946","created_date":"2025-10-10T00:00:00"}
