{"id":"https://openalex.org/W2143009057","doi":"https://doi.org/10.2390/biecoll-jib-2010-114","title":"Using surveys of Affymetrix GeneChips to study antisense expression","display_name":"Using surveys of Affymetrix GeneChips to study antisense expression","publication_year":2010,"publication_date":"2010-01-01","ids":{"openalex":"https://openalex.org/W2143009057","doi":"https://doi.org/10.2390/biecoll-jib-2010-114","mag":"2143009057","pmid":"https://pubmed.ncbi.nlm.nih.gov/20167985"},"language":"en","primary_location":{"id":"pmid:20167985","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20167985","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":"Journal of integrative bioinformatics","raw_type":null},"type":"article","indexed_in":["datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.2390/biecoll-jib-2010-114","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5065966412","display_name":"Olivia Sanchez-Graillet","orcid":"https://orcid.org/0000-0003-3483-265X"},"institutions":[{"id":"https://openalex.org/I110002522","display_name":"University of Essex","ror":"https://ror.org/02nkf1q06","country_code":"GB","type":"education","lineage":["https://openalex.org/I110002522"]}],"countries":["GB"],"is_corresponding":true,"raw_author_name":"Sanchez-Graillet, Olivia","raw_affiliation_strings":["Departments of Mathematical and Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom"],"affiliations":[{"raw_affiliation_string":"Departments of Mathematical and Biological Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, United Kingdom","institution_ids":["https://openalex.org/I110002522"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025631830","display_name":"Maria A. Stalteri","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Stalteri, Maria A.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5111896371","display_name":"Joanna Rowsell","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rowsell, Joanna","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5010341342","display_name":"Graham Upton","orcid":"https://orcid.org/0000-0002-0526-8247"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Upton, Graham J. G.","raw_affiliation_strings":[],"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5102718909","display_name":"Andrew Harrison","orcid":"https://orcid.org/0000-0002-7849-4640"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Harrison, Andrew P.","raw_affiliation_strings":[],"affiliations":[]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5065966412"],"corresponding_institution_ids":["https://openalex.org/I110002522"],"apc_list":null,"apc_paid":null,"fwci":0.4066,"has_fulltext":false,"cited_by_count":3,"citation_normalized_percentile":{"value":0.6393306,"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":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9987999796867371,"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/T10222","display_name":"Genomics and Chromatin Dynamics","score":0.9987999796867371,"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/T10604","display_name":"RNA Research and Splicing","score":0.996399998664856,"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/T10521","display_name":"RNA and protein synthesis mechanisms","score":0.9937000274658203,"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/sense","display_name":"Sense (electronics)","score":0.869831383228302},{"id":"https://openalex.org/keywords/antisense-rna","display_name":"Antisense RNA","score":0.6254733800888062},{"id":"https://openalex.org/keywords/exon","display_name":"Exon","score":0.6080945730209351},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.46488046646118164},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.44670072197914124},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.40943455696105957},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.39870432019233704},{"id":"https://openalex.org/keywords/molecular-biology","display_name":"Molecular biology","score":0.394719660282135},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.3722139298915863},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.10627171397209167}],"concepts":[{"id":"https://openalex.org/C143141573","wikidata":"https://www.wikidata.org/wiki/Q7450971","display_name":"Sense (electronics)","level":2,"score":0.869831383228302},{"id":"https://openalex.org/C202416437","wikidata":"https://www.wikidata.org/wiki/Q423832","display_name":"Antisense RNA","level":4,"score":0.6254733800888062},{"id":"https://openalex.org/C36823959","wikidata":"https://www.wikidata.org/wiki/Q373027","display_name":"Exon","level":3,"score":0.6080945730209351},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.46488046646118164},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.44670072197914124},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.40943455696105957},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.39870432019233704},{"id":"https://openalex.org/C153911025","wikidata":"https://www.wikidata.org/wiki/Q7202","display_name":"Molecular biology","level":1,"score":0.394719660282135},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.3722139298915863},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.10627171397209167},{"id":"https://openalex.org/C147789679","wikidata":"https://www.wikidata.org/wiki/Q11372","display_name":"Physical chemistry","level":1,"score":0.0}],"mesh":[{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000465","descriptor_name":"Algorithms","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000818","descriptor_name":"Animals","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D001483","descriptor_name":"Base Sequence","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":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D008969","descriptor_name":"Molecular Sequence Data","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D012333","descriptor_name":"RNA, Messenger","qualifier_ui":"Q000235","qualifier_name":"genetics","is_major_topic":false},{"descriptor_ui":"D016375","descriptor_name":"Antisense Elements (Genetics)","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016375","descriptor_name":"Antisense Elements (Genetics)","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D016375","descriptor_name":"Antisense Elements (Genetics)","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020224","descriptor_name":"Expressed Sequence Tags","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":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030541","descriptor_name":"Databases, Genetic","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":5,"locations":[{"id":"pmid:20167985","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/20167985","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":"Journal of integrative bioinformatics","raw_type":null},{"id":"pmh:oai:CiteSeerX.psu:10.1.1.621.1681","is_oa":false,"landing_page_url":"http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.621.1681","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://www.imbio.de/journal/articles/pdf/jib-114.pdf","raw_type":"text"},{"id":"pmh:oai:biecoll.ub.uni-bielefeld.de:5012","is_oa":false,"landing_page_url":"http://biecoll.ub.uni-bielefeld.de/volltexte/2010/5012/","pdf_url":null,"source":null,"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"http://journal.imbio.de/article.php?aid=114","raw_type":"Journal Article"},{"id":"pmh:oai:pub.librecat.org:2920014","is_oa":false,"landing_page_url":"https://pub.uni-bielefeld.de/record/2920014","pdf_url":null,"source":{"id":"https://openalex.org/S4306401671","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Sanchez Graillet O, Stalteri MA, Rowsell J, Upton GJG, Harrison AP. Using surveys of Affymetrix GeneChips to study antisense expression. &lt;em&gt;Journal of integrative bioinformatics&lt;/em&gt;. 2010;7(2):27--48.","raw_type":"info:eu-repo/semantics/article"},{"id":"doi:10.2390/biecoll-jib-2010-114","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2010-114","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article-journal"}],"best_oa_location":{"id":"doi:10.2390/biecoll-jib-2010-114","is_oa":true,"landing_page_url":"https://doi.org/10.2390/biecoll-jib-2010-114","pdf_url":null,"source":{"id":"https://openalex.org/S4306401670","display_name":"PUB \u2013 Publications at Bielefeld University (Bielefeld University)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I20121455","host_organization_name":"Bielefeld University","host_organization_lineage":["https://openalex.org/I20121455"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article-journal"},"sustainable_development_goals":[],"awards":[{"id":"https://openalex.org/G3150312408","display_name":null,"funder_award_id":"BB/E001742/1","funder_id":"https://openalex.org/F4320334629","funder_display_name":"Biotechnology and Biological Sciences Research Council"}],"funders":[{"id":"https://openalex.org/F4320334629","display_name":"Biotechnology and Biological Sciences Research Council","ror":"https://ror.org/00cwqg982"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":23,"referenced_works":["https://openalex.org/W1913179380","https://openalex.org/W1986354736","https://openalex.org/W1997551568","https://openalex.org/W2004143065","https://openalex.org/W2025794959","https://openalex.org/W2028010103","https://openalex.org/W2036625331","https://openalex.org/W2037064308","https://openalex.org/W2055328188","https://openalex.org/W2056385746","https://openalex.org/W2062213820","https://openalex.org/W2097033194","https://openalex.org/W2097957138","https://openalex.org/W2099908088","https://openalex.org/W2110697718","https://openalex.org/W2121304560","https://openalex.org/W2128016314","https://openalex.org/W2136145671","https://openalex.org/W2136725005","https://openalex.org/W2148512171","https://openalex.org/W2154362705","https://openalex.org/W2162825358","https://openalex.org/W2163301533"],"related_works":["https://openalex.org/W2072500269","https://openalex.org/W2290935422","https://openalex.org/W2136075631","https://openalex.org/W2139083326","https://openalex.org/W2170172259","https://openalex.org/W1986354736","https://openalex.org/W2162825358","https://openalex.org/W1589807153","https://openalex.org/W2025953099","https://openalex.org/W2142445831","https://openalex.org/W1913179380","https://openalex.org/W2100639130","https://openalex.org/W2030924551","https://openalex.org/W2187166548","https://openalex.org/W2110697718","https://openalex.org/W2125487242","https://openalex.org/W1876798299","https://openalex.org/W2160697089","https://openalex.org/W1989027782","https://openalex.org/W2098160160"],"abstract_inverted_index":{"We":[0,23,70,87,147],"have":[1],"used":[2],"large":[3],"surveys":[4],"of":[5,17,28,58,68,76,82,93,110,115,140,151,163,187,202,207,234],"Affymetrix":[6],"GeneChip":[7],"data":[8,209],"in":[9,37,50,102,231],"the":[10,34,38,51,59,99,113,120,124,138,149,178,185,205,232],"public":[11],"domain":[12],"to":[13,33,47,63,98,176,212,217,227],"conduct":[14],"a":[15,65,74,141,161,193,214],"study":[16],"antisense":[18,39,60,83,106,121,127,180,191,235],"expression":[19,84],"across":[20],"diverse":[21],"conditions.":[22],"derive":[24,89],"correlations":[25,90],"between":[26,91],"groups":[27,61,78,92],"probes":[29,45,94,117,189],"which":[30,95],"map":[31,96],"uniquely":[32,97],"same":[35,100],"exon":[36,49,101],"direction.":[40,107],"When":[41],"there":[42],"are":[43,130,158],"no":[44],"assigned":[46],"an":[48,164,169,172],"sense":[52,104,116,125,188],"direction":[53],"we":[54],"find":[55,71,148],"that":[56,72],"many":[57],"fail":[62],"detect":[64],"coherent":[66,80],"block":[67],"transcription.":[69,86],"only":[73],"minority":[75],"these":[77,111],"contain":[79],"blocks":[81],"suggesting":[85],"also":[88],"both":[103],"and":[105,123,126,167],"In":[108,174],"some":[109],"cases":[112],"locations":[114],"overlap":[118],"with":[119,132,190],"probes,":[122,192],"probe":[128],"intensities":[129],"correlated":[131],"each":[133],"other.":[134],"This":[135],"configuration":[136],"suggests":[137],"existence":[139],"Natural":[142],"Antisense":[143],"Transcript":[144],"(NAT)":[145],"pair.":[146],"majority":[150],"such":[152],"NAT":[153],"pairs":[154],"detected":[155],"by":[156,160,184],"GeneChips":[157],"formed":[159],"transcript":[162],"established":[165],"gene":[166],"either":[168],"EST":[170],"or":[171],"mRNA.":[173],"order":[175],"determine":[177],"exact":[179],"regulatory":[181],"mechanism":[182],"indicated":[183],"correlation":[186],"further":[194],"investigation":[195],"is":[196],"necessary":[197],"for":[198],"every":[199],"particular":[200],"case":[201],"interest.":[203],"However,":[204],"analysis":[206],"microarray":[208],"has":[210],"proved":[211],"be":[213],"good":[215],"method":[216],"reconfirm":[218],"known":[219],"NATs,":[220],"discover":[221],"new":[222],"ones,":[223],"as":[224,226],"well":[225],"notice":[228],"possible":[229],"problems":[230],"annotation":[233],"transcripts.":[236]},"counts_by_year":[{"year":2013,"cited_by_count":1},{"year":2012,"cited_by_count":1}],"updated_date":"2026-04-04T16:13:02.066488","created_date":"2025-10-10T00:00:00"}
