{"id":"https://openalex.org/W2075019355","doi":"https://doi.org/10.1093/bib/bbl013","title":"Circumventing the cut-off for enrichment analysis","display_name":"Circumventing the cut-off for enrichment analysis","publication_year":2006,"publication_date":"2006-03-07","ids":{"openalex":"https://openalex.org/W2075019355","doi":"https://doi.org/10.1093/bib/bbl013","mag":"2075019355","pmid":"https://pubmed.ncbi.nlm.nih.gov/17201027"},"language":"en","primary_location":{"id":"doi:10.1093/bib/bbl013","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbl013","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"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/A5013919234","display_name":"Eitan Rubin","orcid":"https://orcid.org/0000-0002-7807-4005"},"institutions":[{"id":"https://openalex.org/I124227911","display_name":"Ben-Gurion University of the Negev","ror":"https://ror.org/05tkyf982","country_code":"IL","type":"education","lineage":["https://openalex.org/I124227911"]},{"id":"https://openalex.org/I4210099114","display_name":"Czech Academy of Sciences, Institute of Biotechnology","ror":"https://ror.org/00wzqmx94","country_code":"CZ","type":"facility","lineage":["https://openalex.org/I202391551","https://openalex.org/I4210099114"]}],"countries":["CZ","IL"],"is_corresponding":true,"raw_author_name":"E. Rubin","raw_affiliation_strings":["National Institute of Biotechnology,#N#Negev Ben Gurion University"],"affiliations":[{"raw_affiliation_string":"National Institute of Biotechnology,#N#Negev Ben Gurion University","institution_ids":["https://openalex.org/I124227911","https://openalex.org/I4210099114"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5013919234"],"corresponding_institution_ids":["https://openalex.org/I124227911","https://openalex.org/I4210099114"],"apc_list":{"value":4011,"currency":"USD","value_usd":4011},"apc_paid":null,"fwci":0.7948,"has_fulltext":false,"cited_by_count":9,"citation_normalized_percentile":{"value":0.69851731,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":94},"biblio":{"volume":"7","issue":"2","first_page":"202","last_page":"203"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","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/T10885","display_name":"Gene expression and cancer classification","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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9993000030517578,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9975000023841858,"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/pipeline","display_name":"Pipeline (software)","score":0.7461057305335999},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6823253035545349},{"id":"https://openalex.org/keywords/raw-data","display_name":"Raw data","score":0.5425240993499756},{"id":"https://openalex.org/keywords/set","display_name":"Set (abstract data type)","score":0.5205943584442139},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.5108818411827087},{"id":"https://openalex.org/keywords/rank","display_name":"Rank (graph theory)","score":0.43250083923339844},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4277940094470978},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.41758018732070923},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.22954517602920532},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.1795850694179535},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.16347479820251465},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.13814806938171387},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.08417028188705444}],"concepts":[{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.7461057305335999},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6823253035545349},{"id":"https://openalex.org/C132964779","wikidata":"https://www.wikidata.org/wiki/Q2110223","display_name":"Raw data","level":2,"score":0.5425240993499756},{"id":"https://openalex.org/C177264268","wikidata":"https://www.wikidata.org/wiki/Q1514741","display_name":"Set (abstract data type)","level":2,"score":0.5205943584442139},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.5108818411827087},{"id":"https://openalex.org/C164226766","wikidata":"https://www.wikidata.org/wiki/Q7293202","display_name":"Rank (graph theory)","level":2,"score":0.43250083923339844},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4277940094470978},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.41758018732070923},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.22954517602920532},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.1795850694179535},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.16347479820251465},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.13814806938171387},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.08417028188705444},{"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/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"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":"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":"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":"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}],"locations_count":2,"locations":[{"id":"doi:10.1093/bib/bbl013","is_oa":false,"landing_page_url":"https://doi.org/10.1093/bib/bbl013","pdf_url":null,"source":{"id":"https://openalex.org/S91767247","display_name":"Briefings in Bioinformatics","issn_l":"1467-5463","issn":["1467-5463","1477-4054"],"is_oa":false,"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":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Briefings in Bioinformatics","raw_type":"journal-article"},{"id":"pmid:17201027","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/17201027","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":"Briefings in bioinformatics","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"score":0.4399999976158142,"id":"https://metadata.un.org/sdg/9","display_name":"Industry, innovation and infrastructure"}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":3,"referenced_works":["https://openalex.org/W1603763592","https://openalex.org/W2130410032","https://openalex.org/W2134889157"],"related_works":["https://openalex.org/W2152992791","https://openalex.org/W3037187668","https://openalex.org/W4252510819","https://openalex.org/W2380685755","https://openalex.org/W2112835755","https://openalex.org/W2252100032","https://openalex.org/W2963436428","https://openalex.org/W2349674371","https://openalex.org/W3083218341","https://openalex.org/W4241634354"],"abstract_inverted_index":{"Three":[0],"tools":[1,92],"for":[2,35,79],"threshold-free":[3],"enrichment":[4,14,38,65],"analysis":[5,102],"of":[6,46,60,71,82,103],"microarray":[7],"data":[8,99],"are":[9],"introduced:":[10],"GSEA":[11,23],"(gene":[12],"set":[13],"analysis),":[15],"ermineJ":[16,49],"and":[17,31,43,75],"DRIM":[18,67],"(discovering":[19],"rank":[20],"imbalanced":[21],"motifs).":[22],"offers":[24,50],"an":[25,69,94],"interface":[26],"to":[27,55],"a":[28,32,51,63,72],"specific":[29],"algorithm":[30,74],"well-defined":[33],"pipeline":[34],"the":[36,44,80],"identifying":[37],"in":[39,97],"diverse":[40],"gene":[41],"sets":[42],"creation":[45],"signature":[47],"profiles.":[48],"combined":[52],"front":[53],"end":[54],"three":[56],"different":[57],"algorithms,":[58],"two":[59],"which":[61],"perform":[62],"cut-off-free":[64],"analysis.":[66],"comprises":[68],"implementation":[70],"new":[73,83],"is":[76],"specifically":[77],"designed":[78],"search":[81],"transcription-factor-binding":[84],"sites":[85],"based":[86],"on":[87],"expression":[88],"patterns.":[89],"Together,":[90],"these":[91],"demonstrate":[93],"emerging":[95],"trend":[96],"high-throughput":[98],"analysis-the":[100],"joint":[101],"raw":[104],"results":[105],"with":[106],"external":[107],"knowledge.":[108]},"counts_by_year":[{"year":2020,"cited_by_count":1}],"updated_date":"2025-11-06T03:46:38.306776","created_date":"2025-10-10T00:00:00"}