{"id":"https://openalex.org/W2777770350","doi":"https://doi.org/10.1186/s12859-017-1992-2","title":"Super-delta: a new differential gene expression analysis procedure with robust data normalization","display_name":"Super-delta: a new differential gene expression analysis procedure with robust data normalization","publication_year":2017,"publication_date":"2017-12-01","ids":{"openalex":"https://openalex.org/W2777770350","doi":"https://doi.org/10.1186/s12859-017-1992-2","mag":"2777770350","pmid":"https://pubmed.ncbi.nlm.nih.gov/29268715"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-017-1992-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1992-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1992-2","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/track/pdf/10.1186/s12859-017-1992-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5100739795","display_name":"Yuhang Liu","orcid":"https://orcid.org/0000-0002-5246-1330"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yuhang Liu","raw_affiliation_strings":["Department of Statistics, Florida State University, Tallahassee, 32306, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Florida State University, Tallahassee, 32306, FL, USA","institution_ids":["https://openalex.org/I103163165"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100407234","display_name":"Jinfeng Zhang","orcid":"https://orcid.org/0000-0002-7429-7615"},"institutions":[{"id":"https://openalex.org/I103163165","display_name":"Florida State University","ror":"https://ror.org/05g3dte14","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165"]},{"id":"https://openalex.org/I1323276237","display_name":"Florida A&M University - Florida State University College of Engineering","ror":"https://ror.org/01v4tq883","country_code":"US","type":"education","lineage":["https://openalex.org/I103163165","https://openalex.org/I1323276237","https://openalex.org/I8248082"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Jinfeng Zhang","raw_affiliation_strings":["Department of Statistics, Florida State University, Tallahassee, 32306, FL, USA. jinfeng@stat.fsu.edu","Department of Statistics, Florida State University, Tallahassee, 32306, FL, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Statistics, Florida State University, Tallahassee, 32306, FL, USA. jinfeng@stat.fsu.edu","institution_ids":["https://openalex.org/I103163165","https://openalex.org/I1323276237"]},{"raw_affiliation_string":"Department of Statistics, Florida State University, Tallahassee, 32306, FL, USA","institution_ids":["https://openalex.org/I103163165"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5100686073","display_name":"Xing Qiu","orcid":"https://orcid.org/0000-0002-2330-3544"},"institutions":[{"id":"https://openalex.org/I28792581","display_name":"University of Rochester Medicine","ror":"https://ror.org/00trqv719","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I28792581","https://openalex.org/I5388228"]},{"id":"https://openalex.org/I5388228","display_name":"University of Rochester","ror":"https://ror.org/022kthw22","country_code":"US","type":"education","lineage":["https://openalex.org/I5388228"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Xing Qiu","raw_affiliation_strings":["Department of Biostatistics and Computational Biology, University of Rochester, Rochester, 14624, NY, USA. Xing_Qiu@URMC.Rochester.edu","Department of Biostatistics and Computational Biology, University of Rochester, Rochester, 14624, NY, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics and Computational Biology, University of Rochester, Rochester, 14624, NY, USA. Xing_Qiu@URMC.Rochester.edu","institution_ids":["https://openalex.org/I28792581","https://openalex.org/I5388228"]},{"raw_affiliation_string":"Department of Biostatistics and Computational Biology, University of Rochester, Rochester, 14624, NY, USA","institution_ids":["https://openalex.org/I5388228"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5100407234","https://openalex.org/A5100686073"],"corresponding_institution_ids":["https://openalex.org/I103163165","https://openalex.org/I1323276237","https://openalex.org/I28792581","https://openalex.org/I5388228"],"apc_list":{"value":2790,"currency":"USD","value_usd":2790},"apc_paid":{"value":2790,"currency":"USD","value_usd":2790},"fwci":0.4056,"has_fulltext":true,"cited_by_count":12,"citation_normalized_percentile":{"value":0.61192047,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":98},"biblio":{"volume":"18","issue":"1","first_page":"582","last_page":"582"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.8309000134468079,"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":0.8309000134468079,"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/T10136","display_name":"Statistical Methods and Inference","score":0.048700001090765,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.033900000154972076,"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/normalization","display_name":"Normalization (sociology)","score":0.7874260544776917},{"id":"https://openalex.org/keywords/type-i-and-type-ii-errors","display_name":"Type I and type II errors","score":0.6974416971206665},{"id":"https://openalex.org/keywords/outlier","display_name":"Outlier","score":0.5752783417701721},{"id":"https://openalex.org/keywords/statistical-hypothesis-testing","display_name":"Statistical hypothesis testing","score":0.5347909331321716},{"id":"https://openalex.org/keywords/statistical-power","display_name":"Statistical power","score":0.4725741446018219},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.46788448095321655},{"id":"https://openalex.org/keywords/sample-size-determination","display_name":"Sample size determination","score":0.44522377848625183},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.43040359020233154},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.40148016810417175},{"id":"https://openalex.org/keywords/statistics","display_name":"Statistics","score":0.3900276720523834},{"id":"https://openalex.org/keywords/algorithm","display_name":"Algorithm","score":0.3471793234348297},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.3212657570838928},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.25792405009269714},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.2554176449775696},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.21633344888687134},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.2068333625793457},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.13396170735359192}],"concepts":[{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.7874260544776917},{"id":"https://openalex.org/C40696583","wikidata":"https://www.wikidata.org/wiki/Q989120","display_name":"Type I and type II errors","level":2,"score":0.6974416971206665},{"id":"https://openalex.org/C79337645","wikidata":"https://www.wikidata.org/wiki/Q779824","display_name":"Outlier","level":2,"score":0.5752783417701721},{"id":"https://openalex.org/C87007009","wikidata":"https://www.wikidata.org/wiki/Q210832","display_name":"Statistical hypothesis testing","level":2,"score":0.5347909331321716},{"id":"https://openalex.org/C96608239","wikidata":"https://www.wikidata.org/wiki/Q1199823","display_name":"Statistical power","level":2,"score":0.4725741446018219},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.46788448095321655},{"id":"https://openalex.org/C129848803","wikidata":"https://www.wikidata.org/wiki/Q2564360","display_name":"Sample size determination","level":2,"score":0.44522377848625183},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.43040359020233154},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.40148016810417175},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.3900276720523834},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3471793234348297},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3212657570838928},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.25792405009269714},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.2554176449775696},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.21633344888687134},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.2068333625793457},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.13396170735359192},{"id":"https://openalex.org/C144024400","wikidata":"https://www.wikidata.org/wiki/Q21201","display_name":"Sociology","level":0,"score":0.0},{"id":"https://openalex.org/C19165224","wikidata":"https://www.wikidata.org/wiki/Q23404","display_name":"Anthropology","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":"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":"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":"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":"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":"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":"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":"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":"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":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012015","descriptor_name":"Reference Standards","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D015972","descriptor_name":"Gene Expression Regulation, Neoplastic","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":"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":"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":"D052138","descriptor_name":"Genes, Neoplasm","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D052138","descriptor_name":"Genes, Neoplasm","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D052138","descriptor_name":"Genes, Neoplasm","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D052138","descriptor_name":"Genes, Neoplasm","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D052138","descriptor_name":"Genes, Neoplasm","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D052138","descriptor_name":"Genes, Neoplasm","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D058977","descriptor_name":"Molecular Sequence Annotation","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"doi:10.1186/s12859-017-1992-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1992-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1992-2","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:29268715","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/29268715","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:diginole.lib.fsu.edu:fsu_690639","is_oa":false,"landing_page_url":null,"pdf_url":null,"source":{"id":"https://openalex.org/S4306401638","display_name":"DigiNole (Florida State University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I103163165","host_organization_name":"Florida State University","host_organization_lineage":["https://openalex.org/I103163165"],"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":"text"},{"id":"pmh:oai:doaj.org/article:e082c00da3644f8eab218b1c942cd774","is_oa":false,"landing_page_url":"https://doaj.org/article/e082c00da3644f8eab218b1c942cd774","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 18, Iss 1, Pp 1-13 (2017)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:4664619","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/5740711","pdf_url":null,"source":{"id":"https://openalex.org/S4306400806","display_name":"Europe PMC (PubMed Central)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1303153112","host_organization_name":"European Bioinformatics Institute","host_organization_lineage":["https://openalex.org/I1303153112"],"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":null,"raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-017-1992-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-017-1992-2","pdf_url":"https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-017-1992-2","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/G1153115407","display_name":null,"funder_award_id":"NIH 5 P30 AI078498-08","funder_id":"https://openalex.org/F4320337692","funder_display_name":"Center for AIDS Research, University of Rochester Medical Center"},{"id":"https://openalex.org/G166373266","display_name":null,"funder_award_id":"P30 AI 078498","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G2259180468","display_name":null,"funder_award_id":"R01-GM126558","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2556264823","display_name":null,"funder_award_id":"HHSN272201200005C","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2889313661","display_name":null,"funder_award_id":"NIH 5 P30 AI078498-08","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G3028857811","display_name":"Nuclease Profiling as an Integrative Resource for Maize Epigenomics","funder_award_id":"1444532","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G3497421373","display_name":null,"funder_award_id":"UL1 TR000042","funder_id":"https://openalex.org/F4320337472","funder_display_name":"National Center for Advancing Translational Sciences"},{"id":"https://openalex.org/G3871997942","display_name":null,"funder_award_id":"AI078498","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"},{"id":"https://openalex.org/G4085904496","display_name":null,"funder_award_id":"AI078498","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4533853474","display_name":null,"funder_award_id":"PGRP #1444532","funder_id":"https://openalex.org/F4320306076","funder_display_name":"National Science Foundation"},{"id":"https://openalex.org/G476718775","display_name":null,"funder_award_id":"TR000042","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G5840802216","display_name":null,"funder_award_id":"P30 AI078498","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7211645137","display_name":null,"funder_award_id":"R01 GM126558","funder_id":"https://openalex.org/F4320337354","funder_display_name":"National Institute of General Medical Sciences"},{"id":"https://openalex.org/G7313541307","display_name":null,"funder_award_id":"UL1 TR000042","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G8152436913","display_name":null,"funder_award_id":"UL1TR000042","funder_id":"https://openalex.org/F4320310246","funder_display_name":"University of Rochester"},{"id":"https://openalex.org/G8241010853","display_name":null,"funder_award_id":"P30 AI078498-08","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G924720756","display_name":null,"funder_award_id":"HHSN272201200005C","funder_id":"https://openalex.org/F4320337355","funder_display_name":"National Institute of Allergy and Infectious Diseases"}],"funders":[{"id":"https://openalex.org/F4320306076","display_name":"National Science Foundation","ror":"https://ror.org/021nxhr62"},{"id":"https://openalex.org/F4320310246","display_name":"University of Rochester","ror":"https://ror.org/022kthw22"},{"id":"https://openalex.org/F4320316438","display_name":"Georgia Clinical and Translational Science Alliance","ror":null},{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332582","display_name":"Center for AIDS Research, University of Washington","ror":"https://ror.org/00cvxb145"},{"id":"https://openalex.org/F4320337354","display_name":"National Institute of General Medical Sciences","ror":"https://ror.org/04q48ey07"},{"id":"https://openalex.org/F4320337355","display_name":"National Institute of Allergy and Infectious Diseases","ror":"https://ror.org/043z4tv69"},{"id":"https://openalex.org/F4320337472","display_name":"National Center for Advancing Translational Sciences","ror":"https://ror.org/04pw6fb54"},{"id":"https://openalex.org/F4320337692","display_name":"Center for AIDS Research, University of Rochester Medical Center","ror":"https://ror.org/00trqv719"}],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2777770350.pdf","grobid_xml":"https://content.openalex.org/works/W2777770350.grobid-xml"},"referenced_works_count":62,"referenced_works":["https://openalex.org/W1508249425","https://openalex.org/W1533335653","https://openalex.org/W1546952499","https://openalex.org/W1577577364","https://openalex.org/W1953115585","https://openalex.org/W1966261743","https://openalex.org/W1966746701","https://openalex.org/W1971700088","https://openalex.org/W1973847338","https://openalex.org/W1980460692","https://openalex.org/W1981509058","https://openalex.org/W1999463736","https://openalex.org/W2013139454","https://openalex.org/W2020541351","https://openalex.org/W2038392925","https://openalex.org/W2042459594","https://openalex.org/W2048355349","https://openalex.org/W2051219652","https://openalex.org/W2055770801","https://openalex.org/W2062637797","https://openalex.org/W2062989416","https://openalex.org/W2065138557","https://openalex.org/W2069225806","https://openalex.org/W2070494252","https://openalex.org/W2072320830","https://openalex.org/W2075033533","https://openalex.org/W2096161760","https://openalex.org/W2096686828","https://openalex.org/W2098792464","https://openalex.org/W2099114361","https://openalex.org/W2100668965","https://openalex.org/W2104074461","https://openalex.org/W2104194763","https://openalex.org/W2109972881","https://openalex.org/W2110065044","https://openalex.org/W2111542614","https://openalex.org/W2113005940","https://openalex.org/W2114104545","https://openalex.org/W2118221532","https://openalex.org/W2119012012","https://openalex.org/W2119063085","https://openalex.org/W2120742047","https://openalex.org/W2120865735","https://openalex.org/W2128914123","https://openalex.org/W2137526110","https://openalex.org/W2146512944","https://openalex.org/W2152239989","https://openalex.org/W2153178365","https://openalex.org/W2154029199","https://openalex.org/W2156402312","https://openalex.org/W2157795344","https://openalex.org/W2158217645","https://openalex.org/W2158501247","https://openalex.org/W2159482845","https://openalex.org/W2164465994","https://openalex.org/W2170989872","https://openalex.org/W2394842099","https://openalex.org/W3103221158","https://openalex.org/W4251742697","https://openalex.org/W4285719527","https://openalex.org/W4294107304","https://openalex.org/W4294216483"],"related_works":["https://openalex.org/W3003558595","https://openalex.org/W4255580322","https://openalex.org/W154531455","https://openalex.org/W2030905385","https://openalex.org/W4249473446","https://openalex.org/W2259063491","https://openalex.org/W3142061843","https://openalex.org/W4387105795","https://openalex.org/W1936869636","https://openalex.org/W1493128026"],"abstract_inverted_index":{"BACKGROUND:":[0],"Normalization":[1],"is":[2,20,32,42,110,126,190,228],"an":[3,195],"important":[4],"data":[5,341],"preparation":[6],"step":[7],"in":[8,76,119,161,198],"gene":[9,215,252,301],"expression":[10,87,216,302],"analyses,":[11],"designed":[12,111],"to":[13,34,112,167,192,211,243,281,296,336],"remove":[14],"various":[15],"systematic":[16],"noise.":[17],"Sample":[18],"variance":[19,40],"greatly":[21],"reduced":[22],"after":[23],"normalization,":[24],"hence":[25],"the":[26,37,100,114,120,139,186,233,268,297,332],"power":[27,75,171],"of":[28,95,99,175,188,194,214,232,238,299,334],"subsequent":[29],"statistical":[30,74,170],"analyses":[31],"likely":[33],"increase.":[35],"On":[36],"other":[38,285,340],"hand,":[39],"reduction":[41],"made":[43],"possible":[44],"by":[45,117,236,276],"borrowing":[46],"information":[47],"across":[48],"all":[49,209,237,258],"genes,":[50],"including":[51],"differentially":[52],"expressed":[53],"genes":[54],"(DEGs)":[55],"and":[56,71,103,157,311,318],"outliers,":[57],"which":[58,199],"will":[59],"inevitably":[60],"introduce":[61],"some":[62],"bias.":[63],"This":[64],"bias":[65,115],"typically":[66],"inflates":[67],"type":[68,176,342],"I":[69,177],"error;":[70],"can":[72],"reduce":[73],"certain":[77],"situations.":[78],"In":[79,183],"this":[80],"study":[81],"we":[82],"propose":[83],"a":[84,96,104,212,229,289],"new":[85,290,294],"differential":[86,300],"analysis":[88,255],"pipeline,":[89,291],"dubbed":[90],"as":[91],"super-delta,":[92],"that":[93,135,193,257,273],"consists":[94],"multivariate":[97],"extension":[98],"global":[101],"normalization":[102,121,152,160],"modified":[105,124],"t-test.":[106],"A":[107],"robust":[108,141],"procedure":[109],"minimize":[113],"introduced":[116],"DEGs":[118,234,247],"step.":[122],"The":[123],"t-test":[125],"derived":[127],"based":[128],"on":[129,218,267,316],"asymptotic":[130,309],"theory":[131],"for":[132],"hypothesis":[133],"testing":[134],"suitably":[136],"pairs":[137],"with":[138,148,172,326,339],"proposed":[140],"normalization.":[142],"RESULTS:":[143],"We":[144,206],"first":[145],"compared":[146,325],"super-delta":[147,189,240,277,292],"four":[149],"commonly":[150],"used":[151],"methods:":[153],"global,":[154],"median-IQR,":[155],"quantile,":[156],"cyclic":[158],"loess":[159],"simulation":[162],"studies.":[163],"Super-delta":[164],"was":[165],"shown":[166],"have":[168,278],"better":[169,279],"tighter":[173],"control":[174],"error":[178],"rate":[179],"than":[180,248,284],"its":[181,249,308,322],"competitors.":[182,250],"many":[184],"cases,":[185],"performance":[187,324],"close":[191],"oracle":[196],"test":[197],"datasets":[200,217,320],"without":[201],"technical":[202,312],"noise":[203],"were":[204,241],"used.":[205],"then":[207],"applied":[208],"methods":[210,260],"collection":[213],"breast":[219,282],"cancer":[220,283],"patients":[221],"who":[222],"received":[223],"neoadjuvant":[224],"chemotherapy.":[225],"While":[226],"there":[227],"substantial":[230],"overlap":[231],"identified":[235,275],"them,":[239],"able":[242],"identify":[244],"comparatively":[245],"more":[246,344],"Downstream":[251],"set":[253],"enrichment":[254],"confirmed":[256],"these":[259],"selected":[261],"largely":[262],"consistent":[263],"pathways.":[264],"Detailed":[265],"investigations":[266],"relatively":[269],"small":[270],"differences":[271],"showed":[272],"pathways":[274],"connections":[280],"methods.":[286],"CONCLUSIONS:":[287],"As":[288],"provides":[293],"insights":[295],"area":[298],"analysis.":[303],"Solid":[304],"theoretical":[305],"foundation":[306],"supports":[307],"unbiasedness":[310],"noise-free":[313],"properties.":[314],"Implementation":[315],"real":[317],"simulated":[319],"demonstrates":[321],"decent":[323],"state-of-art":[327],"procedures.":[328],"It":[329],"also":[330],"has":[331],"potential":[333],"expansion":[335],"be":[337],"incorporated":[338],"and/or":[343],"general":[345],"between-group":[346],"comparison":[347],"problems.":[348]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2024,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":5},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":3}],"updated_date":"2026-08-01T09:00:35.917206","created_date":"2025-10-10T00:00:00"}