{"id":"https://openalex.org/W2157250512","doi":"https://doi.org/10.1186/1756-0381-3-2","title":"Large scale analysis of positional effects of single-base mismatches on microarray gene expression data","display_name":"Large scale analysis of positional effects of single-base mismatches on microarray gene expression data","publication_year":2010,"publication_date":"2010-04-29","ids":{"openalex":"https://openalex.org/W2157250512","doi":"https://doi.org/10.1186/1756-0381-3-2","mag":"2157250512","pmid":"https://pubmed.ncbi.nlm.nih.gov/20429935"},"language":"en","primary_location":{"id":"doi:10.1186/1756-0381-3-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-3-2","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-3-2","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-3-2","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5048142039","display_name":"Fenghai Duan","orcid":"https://orcid.org/0000-0002-5084-0070"},"institutions":[{"id":"https://openalex.org/I27804330","display_name":"Brown University","ror":"https://ror.org/05gq02987","country_code":"US","type":"education","lineage":["https://openalex.org/I27804330"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fenghai Duan","raw_affiliation_strings":["Center for Statistical Sciences, Brown University, Providence, RI, USA. fduan@stat.brown.edu","Center for Statistical Sciences, Brown University, Providence, RI, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Center for Statistical Sciences, Brown University, Providence, RI, USA. fduan@stat.brown.edu","institution_ids":["https://openalex.org/I27804330"]},{"raw_affiliation_string":"Center for Statistical Sciences, Brown University, Providence, RI, USA","institution_ids":["https://openalex.org/I27804330"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5056721115","display_name":"Mark Pauley","orcid":"https://orcid.org/0000-0003-1308-0321"},"institutions":[{"id":"https://openalex.org/I122266389","display_name":"University of Nebraska at Omaha","ror":"https://ror.org/04yrkc140","country_code":"US","type":"education","lineage":["https://openalex.org/I122266389"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mark A Pauley","raw_affiliation_strings":["College of Information Science & Technology, University of Nebraska at Omaha, Omaha, NE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"College of Information Science & Technology, University of Nebraska at Omaha, Omaha, NE, USA","institution_ids":["https://openalex.org/I122266389"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017495974","display_name":"Eliot R. Spindel","orcid":null},"institutions":[{"id":"https://openalex.org/I102507086","display_name":"Oregon National Primate Research Center","ror":"https://ror.org/05fcfqq67","country_code":"US","type":"facility","lineage":["https://openalex.org/I102507086"]},{"id":"https://openalex.org/I165690674","display_name":"Oregon Health & Science University","ror":"https://ror.org/009avj582","country_code":"US","type":"education","lineage":["https://openalex.org/I165690674"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Eliot R Spindel","raw_affiliation_strings":["Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Division of Neuroscience, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR, USA","institution_ids":["https://openalex.org/I102507086","https://openalex.org/I165690674"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5100425554","display_name":"Li Zhang","orcid":"https://orcid.org/0000-0002-3617-2627"},"institutions":[{"id":"https://openalex.org/I1343551460","display_name":"The University of Texas MD Anderson Cancer Center","ror":"https://ror.org/04twxam07","country_code":"US","type":"funder","lineage":["https://openalex.org/I1343551460"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Li Zhang","raw_affiliation_strings":["Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Bioinformatics and Computational Biology, University of Texas MD Anderson Cancer Center, Houston, TX, USA","institution_ids":["https://openalex.org/I1343551460"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5052865810","display_name":"Robert B. Norgren","orcid":"https://orcid.org/0000-0002-0021-5875"},"institutions":[{"id":"https://openalex.org/I59130452","display_name":"University of Nebraska Medical Center","ror":"https://ror.org/00thqtb16","country_code":"US","type":"funder","lineage":["https://openalex.org/I59130452"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Robert B Norgren","raw_affiliation_strings":["Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA","institution_ids":["https://openalex.org/I59130452"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5048142039","https://openalex.org/A5052865810"],"corresponding_institution_ids":["https://openalex.org/I27804330","https://openalex.org/I59130452"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.6805,"has_fulltext":true,"cited_by_count":20,"citation_normalized_percentile":{"value":0.70194114,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":97},"biblio":{"volume":"3","issue":"1","first_page":"2","last_page":"2"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.8083000183105469,"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":0.8083000183105469,"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/T12867","display_name":"Advanced Biosensing Techniques and Applications","score":0.1120000034570694,"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/T11213","display_name":"Genomic variations and chromosomal abnormalities","score":0.0142000000923872,"subfield":{"id":"https://openalex.org/subfields/1311","display_name":"Genetics"},"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/dna-microarray","display_name":"DNA microarray","score":0.7055923342704773},{"id":"https://openalex.org/keywords/gene-chip-analysis","display_name":"Gene chip analysis","score":0.6117265224456787},{"id":"https://openalex.org/keywords/microarray","display_name":"Microarray","score":0.573891818523407},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.484768807888031},{"id":"https://openalex.org/keywords/hybridization-probe","display_name":"Hybridization probe","score":0.46775010228157043},{"id":"https://openalex.org/keywords/oligonucleotide","display_name":"Oligonucleotide","score":0.46601229906082153},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.4518128037452698},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4462496042251587},{"id":"https://openalex.org/keywords/microarray-analysis-techniques","display_name":"Microarray analysis techniques","score":0.41449999809265137},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.405465304851532},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.37062638998031616},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.32592901587486267},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.32567575573921204},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2744520306587219},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.14958801865577698}],"concepts":[{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.7055923342704773},{"id":"https://openalex.org/C24361400","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Gene chip analysis","level":5,"score":0.6117265224456787},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.573891818523407},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.484768807888031},{"id":"https://openalex.org/C130197536","wikidata":"https://www.wikidata.org/wiki/Q418436","display_name":"Hybridization probe","level":3,"score":0.46775010228157043},{"id":"https://openalex.org/C129312508","wikidata":"https://www.wikidata.org/wiki/Q133686","display_name":"Oligonucleotide","level":3,"score":0.46601229906082153},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.4518128037452698},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4462496042251587},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.41449999809265137},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.405465304851532},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.37062638998031616},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.32592901587486267},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.32567575573921204},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2744520306587219},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.14958801865577698}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.1186/1756-0381-3-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-3-2","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-3-2","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},{"id":"pmid:20429935","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20429935","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":"BioData mining","raw_type":null},{"id":"pmh:oai:digitalcommons.unmc.edu:com_gcba_articles-1036","is_oa":true,"landing_page_url":"https://digitalcommons.unmc.edu/com_gcba_articles/41","pdf_url":null,"source":{"id":"https://openalex.org/S4210227318","display_name":"Graduate Medical Education Research Journal","issn_l":"2578-6091","issn":["2578-6091","2578-6105"],"is_oa":false,"is_in_doaj":true,"is_core":true,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Journal Articles: Genetics, Cell Biology &amp; Anatomy","raw_type":"text"},{"id":"pmh:oai:doaj.org/article:2165cc2312da4ddd84ad12b8a24a1e4a","is_oa":false,"landing_page_url":"https://doaj.org/article/2165cc2312da4ddd84ad12b8a24a1e4a","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":"BioData Mining, Vol 3, Iss 1, p 2 (2010)","raw_type":"article"},{"id":"pmh:oai:europepmc.org:1921593","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/2877042","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:10.1186/1756-0381-3-2","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1756-0381-3-2","pdf_url":"https://biodatamining.biomedcentral.com/counter/pdf/10.1186/1756-0381-3-2","source":{"id":"https://openalex.org/S84409260","display_name":"BioData Mining","issn_l":"1756-0381","issn":["1756-0381"],"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":"BioData Mining","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G1040343330","display_name":null,"funder_award_id":"RR016469","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"},{"id":"https://openalex.org/G629313854","display_name":null,"funder_award_id":"P20 RR016469","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G7652910328","display_name":null,"funder_award_id":"P20 RR016469","funder_id":"https://openalex.org/F4320337375","funder_display_name":"National Center for Research Resources"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320332635","display_name":"Oregon National Primate Research Center","ror":"https://ror.org/05fcfqq67"},{"id":"https://openalex.org/F4320337375","display_name":"National Center for Research Resources","ror":"https://ror.org/04pw6fb54"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W2157250512.pdf"},"referenced_works_count":21,"referenced_works":["https://openalex.org/W3984577","https://openalex.org/W1599912094","https://openalex.org/W1945375853","https://openalex.org/W1973614663","https://openalex.org/W1978673080","https://openalex.org/W2036193631","https://openalex.org/W2070491426","https://openalex.org/W2074642610","https://openalex.org/W2097255127","https://openalex.org/W2097957146","https://openalex.org/W2100008799","https://openalex.org/W2100904733","https://openalex.org/W2111178756","https://openalex.org/W2130494035","https://openalex.org/W2132354121","https://openalex.org/W2135995702","https://openalex.org/W2138121233","https://openalex.org/W2161952084","https://openalex.org/W2162266792","https://openalex.org/W2167980479","https://openalex.org/W4247420482"],"related_works":["https://openalex.org/W2767847608","https://openalex.org/W2361788533","https://openalex.org/W2051808073","https://openalex.org/W2015700328","https://openalex.org/W2138580185","https://openalex.org/W2911678823","https://openalex.org/W170658859","https://openalex.org/W4310366902","https://openalex.org/W3023720143","https://openalex.org/W2490137852"],"abstract_inverted_index":{"BACKGROUND:":[0],"Affymetrix":[1,81],"GeneChips":[2],"utilize":[3],"25-mer":[4,90],"oligonucleotides":[5],"probes":[6,29,39,78,91],"linked":[7],"to":[8,12,19,122,200],"a":[9,119,123,130,145,152,162],"silica":[10],"surface":[11],"detect":[13],"targets":[14,41],"in":[15,56,107,126,187,224],"solution.":[16],"Mismatches":[17],"due":[18],"single":[20],"nucleotide":[21],"polymorphisms":[22],"(SNPs)":[23],"can":[24,227],"affect":[25],"the":[26,45,57,80,88,99,103,116,133,136,140,149,158,169,177,195,216,239],"hybridization":[27],"between":[28,38,72,148],"and":[30,40,76,238],"targets.":[31],"Previous":[32],"research":[33],"has":[34,52],"indicated":[35],"that":[36,183],"binding":[37],"strongly":[42],"depends":[43],"on":[44,102,221],"positions":[46,101],"of":[47,59,68,98,110,118,135,139,151,155,161,176,179,215,218,234],"these":[48],"mismatches.":[49],"However,":[50,193],"there":[51],"been":[53],"substantial":[54],"variability":[55],"effect":[58,178],"mismatch":[60,114,131,141,180,196],"type":[61,109],"across":[62],"studies.":[63],"METHODS:":[64],"By":[65],"taking":[66],"advantage":[67],"naturally":[69],"occurring":[70],"mismatches":[71,95,156,220],"rhesus":[73],"macaque":[74],"transcripts":[75],"human":[77],"from":[79],"U133":[82],"Plus":[83],"2":[84],"GeneChip,":[85],"we":[86],"collected":[87],"largest":[89],"dataset":[92],"with":[93],"single-base":[94,219],"at":[96,115,132,157,168],"each":[97],"25":[100],"probe":[104,120,163],"ever":[105],"used":[106],"this":[108,225],"analysis.":[111],"RESULTS:":[112],"A":[113,172],"center":[117],"led":[121],"greater":[124,165],"loss":[125],"signal":[127],"intensity":[128],"than":[129,166],"ends":[134,150],"probe,":[137],"regardless":[138],"type.":[142],"There":[143],"was":[144],"slight":[146],"asymmetry":[147],"probe:":[153],"effects":[154,217],"3'":[159],"end":[160],"were":[164,185,198],"those":[167],"5'":[170],"end.":[171],"cross":[173,205],"study":[174,206],"comparison":[175],"types":[181,197],"revealed":[182],"results":[184],"not":[186],"good":[188],"agreement":[189],"among":[190],"different":[191],"reports.":[192],"if":[194],"consolidated":[199],"purine":[201],"or":[202],"pyrimidine":[203],"mismatches,":[204],"conclusions":[207],"could":[208],"be":[209,228],"generated.":[210],"CONCLUSION:":[211],"The":[212],"comprehensive":[213],"assessment":[214],"microarrays":[222],"provided":[223],"report":[226],"useful":[229],"for":[230],"improving":[231],"future":[232],"versions":[233],"microarray":[235],"platform":[236],"design":[237],"corresponding":[240],"data":[241],"analysis":[242],"algorithms.":[243]},"counts_by_year":[{"year":2025,"cited_by_count":2},{"year":2023,"cited_by_count":1},{"year":2022,"cited_by_count":1},{"year":2021,"cited_by_count":1},{"year":2019,"cited_by_count":2},{"year":2018,"cited_by_count":2},{"year":2017,"cited_by_count":1},{"year":2016,"cited_by_count":1},{"year":2015,"cited_by_count":3},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":3}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}
