{"id":"https://openalex.org/W3089928188","doi":"https://doi.org/10.1371/journal.pcbi.1008295","title":"Increased comparability between RNA-Seq and microarray data by utilization of gene sets","display_name":"Increased comparability between RNA-Seq and microarray data by utilization of gene sets","publication_year":2020,"publication_date":"2020-09-30","ids":{"openalex":"https://openalex.org/W3089928188","doi":"https://doi.org/10.1371/journal.pcbi.1008295","mag":"3089928188","pmid":"https://pubmed.ncbi.nlm.nih.gov/32997685"},"language":"en","primary_location":{"id":"doi:10.1371/journal.pcbi.1008295","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008295","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008295&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008295&type=printable","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5005697336","display_name":"Frans van der Kloet","orcid":"https://orcid.org/0000-0002-8573-2651"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Frans M. van der Kloet","raw_affiliation_strings":["Swammerdam Institute for Life Sciences, University of Amsterdam"],"raw_orcid":"https://orcid.org/0000-0002-8573-2651","affiliations":[{"raw_affiliation_string":"Swammerdam Institute for Life Sciences, University of Amsterdam","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078081460","display_name":"Jeroen Buurmans","orcid":"https://orcid.org/0000-0002-6436-4706"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Jeroen Buurmans","raw_affiliation_strings":["Swammerdam Institute for Life Sciences, University of Amsterdam"],"raw_orcid":"https://orcid.org/0000-0002-6436-4706","affiliations":[{"raw_affiliation_string":"Swammerdam Institute for Life Sciences, University of Amsterdam","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112104130","display_name":"Martijs J. Jonker","orcid":"https://orcid.org/0000-0003-4304-0486"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Martijs J. Jonker","raw_affiliation_strings":["Swammerdam Institute for Life Sciences, University of Amsterdam"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Swammerdam Institute for Life Sciences, University of Amsterdam","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5083251527","display_name":"Age K. Smilde","orcid":"https://orcid.org/0000-0002-3052-4644"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":false,"raw_author_name":"Age K. Smilde","raw_affiliation_strings":["Swammerdam Institute for Life Sciences, University of Amsterdam"],"raw_orcid":"https://orcid.org/0000-0002-3052-4644","affiliations":[{"raw_affiliation_string":"Swammerdam Institute for Life Sciences, University of Amsterdam","institution_ids":["https://openalex.org/I887064364"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5017155895","display_name":"Johan A. Westerhuis","orcid":"https://orcid.org/0000-0002-6747-9779"},"institutions":[{"id":"https://openalex.org/I887064364","display_name":"University of Amsterdam","ror":"https://ror.org/04dkp9463","country_code":"NL","type":"education","lineage":["https://openalex.org/I887064364"]}],"countries":["NL"],"is_corresponding":true,"raw_author_name":"Johan A. Westerhuis","raw_affiliation_strings":["Swammerdam Institute for Life Sciences, University of Amsterdam"],"raw_orcid":"https://orcid.org/0000-0002-6747-9779","affiliations":[{"raw_affiliation_string":"Swammerdam Institute for Life Sciences, University of Amsterdam","institution_ids":["https://openalex.org/I887064364"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5017155895"],"corresponding_institution_ids":["https://openalex.org/I887064364"],"apc_list":{"value":2655,"currency":"USD","value_usd":2655},"apc_paid":{"value":2655,"currency":"USD","value_usd":2655},"fwci":2.9259,"has_fulltext":true,"cited_by_count":56,"citation_normalized_percentile":{"value":0.92116138,"is_in_top_1_percent":false,"is_in_top_10_percent":true},"cited_by_percentile_year":{"min":98,"max":100},"biblio":{"volume":"16","issue":"9","first_page":"e1008295","last_page":"e1008295"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.9998000264167786,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9970999956130981,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.9915000200271606,"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":0.5659142732620239},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.4994940757751465},{"id":"https://openalex.org/keywords/transcriptome","display_name":"Transcriptome","score":0.49558794498443604},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-Seq","score":0.48578599095344543},{"id":"https://openalex.org/keywords/comparability","display_name":"Comparability","score":0.46583643555641174},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4611663222312927},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.4530401825904846},{"id":"https://openalex.org/keywords/concordance","display_name":"Concordance","score":0.4318183958530426},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.42466267943382263},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.4243115782737732},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.4232676029205322},{"id":"https://openalex.org/keywords/data-set","display_name":"Data set","score":0.4201778471469879},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41574573516845703},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3948465585708618},{"id":"https://openalex.org/keywords/bioinformatics","display_name":"Bioinformatics","score":0.3179122805595398},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.19652393460273743},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.18135011196136475},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.13636445999145508}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5659142732620239},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.4994940757751465},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.49558794498443604},{"id":"https://openalex.org/C107397762","wikidata":"https://www.wikidata.org/wiki/Q2542347","display_name":"RNA-Seq","level":5,"score":0.48578599095344543},{"id":"https://openalex.org/C197947376","wikidata":"https://www.wikidata.org/wiki/Q5155608","display_name":"Comparability","level":2,"score":0.46583643555641174},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4611663222312927},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.4530401825904846},{"id":"https://openalex.org/C160798450","wikidata":"https://www.wikidata.org/wiki/Q4230870","display_name":"Concordance","level":2,"score":0.4318183958530426},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.42466267943382263},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.4243115782737732},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.4232676029205322},{"id":"https://openalex.org/C58489278","wikidata":"https://www.wikidata.org/wiki/Q1172284","display_name":"Data set","level":2,"score":0.4201778471469879},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41574573516845703},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3948465585708618},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3179122805595398},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.19652393460273743},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.18135011196136475},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.13636445999145508},{"id":"https://openalex.org/C114614502","wikidata":"https://www.wikidata.org/wiki/Q76592","display_name":"Combinatorics","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D000081246","descriptor_name":"RNA-Seq","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D001943","descriptor_name":"Breast Neoplasms","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D005260","descriptor_name":"Female","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D006801","descriptor_name":"Humans","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015203","descriptor_name":"Reproducibility of Results","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020411","descriptor_name":"Oligonucleotide Array Sequence Analysis","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D059467","descriptor_name":"Transcriptome","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false}],"locations_count":8,"locations":[{"id":"doi:10.1371/journal.pcbi.1008295","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008295","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008295&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},{"id":"pmid:32997685","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/32997685","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":"PLoS computational biology","raw_type":null},{"id":"pmh:oai:dare.uva.nl:openaire/0ff3b2f2-80ac-4186-888a-8515496a5456","is_oa":true,"landing_page_url":"https://handle.uba.uva.nl/personal/pure/en/publications/increased-comparability-between-rnaseq-and-microarray-data-by-utilization-of-gene-sets(0ff3b2f2-80ac-4186-888a-8515496a5456).html","pdf_url":"https://pure.uva.nl/ws/files/51469254/journal.pcbi.1008295.pdf","source":{"id":"https://openalex.org/S4306400088","display_name":"UvA-DARE (University of Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887064364","host_organization_name":"University of Amsterdam","host_organization_lineage":["https://openalex.org/I887064364"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"van der Kloet, F M, Buurmans, J, Jonker, M J, Smilde, A K & Westerhuis, J A 2020, 'Increased comparability between RNA-Seq and microarray data by utilization of gene sets', PLoS Computational Biology, vol. 16, no. 9, e1008295. https://doi.org/10.1371/journal.pcbi.1008295","raw_type":"info:eu-repo/semantics/publishedVersion"},{"id":"pmh:uvapub:oai:dare.uva.nl:publications/0ff3b2f2-80ac-4186-888a-8515496a5456","is_oa":true,"landing_page_url":"https://dare.uva.nl/personal/pure/en/publications/increased-comparability-between-rnaseq-and-microarray-data-by-utilization-of-gene-sets(0ff3b2f2-80ac-4186-888a-8515496a5456).html","pdf_url":"https://dare.uva.nl/personal/pure/en/publications/increased-comparability-between-rnaseq-and-microarray-data-by-utilization-of-gene-sets(0ff3b2f2-80ac-4186-888a-8515496a5456).html","source":{"id":"https://openalex.org/S4306401843","display_name":"Data Archiving and Networked Services (DANS)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1322597698","host_organization_name":"Royal Netherlands Academy of Arts and Sciences","host_organization_lineage":["https://openalex.org/I1322597698"],"host_organization_lineage_names":[],"type":"repository"},"license":"other-oa","license_id":"https://openalex.org/licenses/other-oa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, 16(9):e1008295. Public Library of Science","raw_type":"info:eu-repo/semantics/article"},{"id":"pmh:oai:RePEc:plo:pcbi00:1008295","is_oa":false,"landing_page_url":"https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1008295","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"},{"id":"pmh:oai:dare.uva.nl:publications/0ff3b2f2-80ac-4186-888a-8515496a5456","is_oa":false,"landing_page_url":"http://hdl.handle.net/11245.1/0ff3b2f2-80ac-4186-888a-8515496a5456","pdf_url":null,"source":{"id":"https://openalex.org/S4306400088","display_name":"UvA-DARE (University of Amsterdam)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I887064364","host_organization_name":"University of Amsterdam","host_organization_lineage":["https://openalex.org/I887064364"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"","raw_type":""},{"id":"pmh:oai:doaj.org/article:a1d388711bf847178003c0123966834d","is_oa":true,"landing_page_url":"https://doaj.org/article/a1d388711bf847178003c0123966834d","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"PLoS Computational Biology, Vol 16, Iss 9, p e1008295 (2020)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:7549825","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/7549825","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":"PLoS Comput Biol","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1371/journal.pcbi.1008295","is_oa":true,"landing_page_url":"https://doi.org/10.1371/journal.pcbi.1008295","pdf_url":"https://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1008295&type=printable","source":{"id":"https://openalex.org/S86033158","display_name":"PLoS Computational Biology","issn_l":"1553-734X","issn":["1553-734X","1553-7358"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310315706","host_organization_name":"Public Library of Science","host_organization_lineage":["https://openalex.org/P4310315706"],"host_organization_lineage_names":["Public Library of Science"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"PLOS Computational Biology","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.44999998807907104}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3089928188.pdf","grobid_xml":"https://content.openalex.org/works/W3089928188.grobid-xml"},"referenced_works_count":17,"referenced_works":["https://openalex.org/W1915087491","https://openalex.org/W1970156673","https://openalex.org/W1981509058","https://openalex.org/W2032618685","https://openalex.org/W2043398720","https://openalex.org/W2045949302","https://openalex.org/W2064641822","https://openalex.org/W2077836479","https://openalex.org/W2082516237","https://openalex.org/W2123879591","https://openalex.org/W2145825942","https://openalex.org/W2154431984","https://openalex.org/W2159707944","https://openalex.org/W2164222385","https://openalex.org/W2214074259","https://openalex.org/W2674752536","https://openalex.org/W2909239315"],"related_works":["https://openalex.org/W2041540252","https://openalex.org/W2796636403","https://openalex.org/W2415545834","https://openalex.org/W1547158732","https://openalex.org/W3203113381","https://openalex.org/W2366558827","https://openalex.org/W170658859","https://openalex.org/W1483316219","https://openalex.org/W4310366902","https://openalex.org/W3023720143"],"abstract_inverted_index":{"The":[0,198],"field":[1],"of":[2,11,53,59,154,194,216,222],"transcriptomics":[3,69],"uses":[4],"and":[5,26,79,109,128,166,220],"measures":[6],"mRNA":[7],"as":[8],"a":[9,47,76,124,188],"proxy":[10],"gene":[12,89,178,199,208,223],"expression.":[13],"There":[14],"are":[15,36,226],"currently":[16],"two":[17,72,196],"major":[18],"platforms":[19,55,74,103],"in":[20,123,191],"use":[21],"for":[22,92,228,233],"quantifying":[23],"mRNA,":[24],"microarray":[25,147,165],"RNA-Seq.":[27],"Many":[28],"comparative":[29],"studies":[30],"have":[31],"shown":[32,203],"that":[33,116,225],"their":[34,184],"results":[35],"not":[37],"always":[38],"consistent.":[39],"In":[40],"this":[41],"study":[42],"we":[43],"aim":[44],"to":[45,50,134,151,204],"find":[46],"robust":[48],"method":[49],"increase":[51],"comparability":[52],"both":[54,63,102],"enabling":[56],"data":[57,61,70,100,108,119,122,192],"analysis":[58],"merged":[60],"from":[62,71,101],"platforms.":[64,197],"We":[65,95,114,138],"transformed":[66],"high":[67],"dimensional":[68],"different":[73],"into":[75,175],"lower":[77],"dimensional,":[78],"biologically":[80,125,176,206],"relevant":[81,126,177,207],"dataset":[82],"by":[83],"calculating":[84],"enrichment":[85,112,149,158,180],"scores":[86,150,159,181],"based":[87,104,148,160],"on":[88,105,110,161,213],"set":[90,179,200],"collections":[91,201],"all":[93],"samples.":[94],"compared":[96],"the":[97,106,111,117,121,140,195,214,217,229],"similarity":[98],"between":[99],"raw":[107],"scores.":[113],"show":[115],"performed":[118],"transforms":[120],"way":[127],"filters":[129],"out":[130],"noise":[131],"which":[132,186],"leads":[133],"increased":[135],"platform":[136],"concordance.":[137],"validate":[139],"procedure":[141],"using":[142,157],"predictive":[143],"models":[144],"built":[145],"with":[146],"predict":[152],"subtypes":[153],"breast":[155],"cancer":[156],"sequenced":[162],"data.":[163],"Although":[164],"RNA-Seq":[167],"expression":[168],"levels":[169],"might":[170],"appear":[171],"different,":[172],"transforming":[173],"them":[174],"significantly":[182],"increases":[183],"correlation,":[185],"is":[187,231],"step":[189],"forward":[190],"integration":[193],"were":[202],"contain":[205],"sets.":[209],"More":[210],"in-depth":[211],"investigation":[212],"effect":[215],"composition,":[218],"size,":[219],"number":[221],"sets":[224],"used":[227],"transformation":[230],"suggested":[232],"future":[234],"research.":[235]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":5},{"year":2024,"cited_by_count":16},{"year":2023,"cited_by_count":19},{"year":2022,"cited_by_count":7},{"year":2021,"cited_by_count":7}],"updated_date":"2026-01-13T01:12:25.745995","created_date":"2025-10-10T00:00:00"}