{"id":"https://openalex.org/W2903944008","doi":"https://doi.org/10.3389/fgene.2018.00670","title":"The Importance of Biologic Knowledge and Gene Expression Context for Genomic Data Interpretation","display_name":"The Importance of Biologic Knowledge and Gene Expression Context for Genomic Data Interpretation","publication_year":2018,"publication_date":"2018-12-18","ids":{"openalex":"https://openalex.org/W2903944008","doi":"https://doi.org/10.3389/fgene.2018.00670","mag":"2903944008","pmid":"https://pubmed.ncbi.nlm.nih.gov/30619486","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/6305277"},"language":"en","primary_location":{"id":"doi:10.3389/fgene.2018.00670","doi":"https://doi.org/10.3389/fgene.2018.00670","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fgene.2018.00670","pdf_url":"https://www.frontiersin.org/articles/10.3389/fgene.2018.00670/pdf","source":{"id":"https://openalex.org/S2597340651","display_name":"Frontiers in Genetics","issn_l":"1664-8021","issn":["1664-8021"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Genetics","raw_type":"journal-article"},"volume":null,"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.frontiersin.org/articles/10.3389/fgene.2018.00670/pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5054127002","display_name":"Michael T. Zimmermann","orcid":"https://orcid.org/0000-0001-7073-0525","observed_orcids":["https://orcid.org/0000-0001-7073-0525"]},"institutions":[{"id":"https://openalex.org/I204308271","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244","country_code":"US","type":"education","lineage":["https://openalex.org/I204308271"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Michael T. Zimmermann","raw_affiliation_strings":["Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States","Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics Research and Development Laboratory, Genomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, United States","institution_ids":["https://openalex.org/I204308271"]},{"raw_affiliation_string":"Clinical and Translational Sciences Institute, Medical College of Wisconsin, Milwaukee, WI, United States","institution_ids":["https://openalex.org/I204308271"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":1,"corresponding_author_ids":["https://openalex.org/A5054127002"],"corresponding_institution_ids":["https://openalex.org/I204308271"],"apc_list":{"value":3150,"currency":"CHF","value_usd":3801},"apc_paid":{"value":3150,"currency":"CHF","value_usd":3801},"fwci":0.7548,"has_fulltext":true,"cited_by_count":9,"citation_normalized_percentile":{"value":0.7095419,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":88,"max":96},"biblio":{"volume":"9","issue":null,"first_page":"670","last_page":"670"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9970999956130981,"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"}},"topics":[{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.9970999956130981,"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"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.0017999999690800905,"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/T10015","display_name":"Genomics and Phylogenetic Studies","score":0.00019999999494757503,"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/whole-exome-sequencing","display_name":"exome sequencing","score":0.9129999876022339},{"id":"https://openalex.org/keywords/variant-interpretation","display_name":"variant interpretation","score":0.9200000166893005},{"id":"https://openalex.org/keywords/tissue-specific-expression","display_name":"tissue-specific gene expression","score":0.8790000081062317},{"id":"https://openalex.org/keywords/disease-genes","display_name":"disease-associated genes","score":0.6919999718666077},{"id":"https://openalex.org/keywords/variant-annotation","display_name":"variant annotation","score":0.5239999890327454}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.6355003714561462},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.6139569282531738},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.5883455276489258},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5472466945648193},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.5302581191062927},{"id":"https://openalex.org/C161078062","wikidata":"https://www.wikidata.org/wiki/Q1068690","display_name":"Functional genomics","level":5,"score":0.4904591739177704},{"id":"https://openalex.org/C16671776","wikidata":"https://www.wikidata.org/wiki/Q5420592","display_name":"Exome sequencing","level":4,"score":0.47649258375167847},{"id":"https://openalex.org/C10590036","wikidata":"https://www.wikidata.org/wiki/Q417664","display_name":"Exome","level":5,"score":0.46995165944099426},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.4346632957458496},{"id":"https://openalex.org/C197077220","wikidata":"https://www.wikidata.org/wiki/Q720988","display_name":"Human genome","level":4,"score":0.4125858545303345},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.3423825800418854},{"id":"https://openalex.org/C141231307","wikidata":"https://www.wikidata.org/wiki/Q7020","display_name":"Genome","level":3,"score":0.3374493718147278},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.25066569447517395},{"id":"https://openalex.org/C151730666","wikidata":"https://www.wikidata.org/wiki/Q7205","display_name":"Paleontology","level":1,"score":0.0}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.3389/fgene.2018.00670","doi":"https://doi.org/10.3389/fgene.2018.00670","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fgene.2018.00670","pdf_url":"https://www.frontiersin.org/articles/10.3389/fgene.2018.00670/pdf","source":{"id":"https://openalex.org/S2597340651","display_name":"Frontiers in Genetics","issn_l":"1664-8021","issn":["1664-8021"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Genetics","raw_type":"journal-article"},{"id":"pmh:oai:europepmc.org:5293818","doi":null,"is_oa":true,"landing_page_url":"http://europepmc.org/pmc/articles/PMC6305277","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:6305277","doi":null,"is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/6305277","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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Front Genet","raw_type":"Text"},{"id":"pmid:30619486","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/30619486","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,"listed_in":[],"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":"Frontiers in genetics","raw_type":"Journal Article"},{"id":"pmh:oai:doaj.org/article:f634f84523f94513917584f78935c4cf","doi":null,"is_oa":true,"landing_page_url":"https://doaj.org/article/f634f84523f94513917584f78935c4cf","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,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Frontiers in Genetics, Vol 9 (2018)","raw_type":"article"}],"best_oa_location":{"id":"doi:10.3389/fgene.2018.00670","doi":"https://doi.org/10.3389/fgene.2018.00670","is_oa":true,"landing_page_url":"https://doi.org/10.3389/fgene.2018.00670","pdf_url":"https://www.frontiersin.org/articles/10.3389/fgene.2018.00670/pdf","source":{"id":"https://openalex.org/S2597340651","display_name":"Frontiers in Genetics","issn_l":"1664-8021","issn":["1664-8021"],"is_oa":true,"is_in_doaj":true,"is_core":true,"listed_in":["anvur-scientific","cwts-core","doaj","jufo-1","ki-jl-1","norway-1","poland-100","russia-white-list-2","vabb-shw"],"host_organization":"https://openalex.org/P4310320527","host_organization_name":"Frontiers Media","host_organization_lineage":["https://openalex.org/P4310320527"],"host_organization_lineage_names":["Frontiers Media"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Frontiers in Genetics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Good health and well-being","score":0.504800021648407,"id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320310914","display_name":"Medical College of Wisconsin","ror":"https://ror.org/00qqv6244"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2903944008.pdf","grobid_xml":"https://content.openalex.org/works/W2903944008.grobid-xml"},"referenced_works_count":33,"referenced_works":["https://openalex.org/W229097380","https://openalex.org/W1533942137","https://openalex.org/W1611787727","https://openalex.org/W1975669536","https://openalex.org/W1998767819","https://openalex.org/W2012034410","https://openalex.org/W2012609840","https://openalex.org/W2021349213","https://openalex.org/W2028133290","https://openalex.org/W2081375228","https://openalex.org/W2106578986","https://openalex.org/W2130410032","https://openalex.org/W2131086009","https://openalex.org/W2144086069","https://openalex.org/W2145809383","https://openalex.org/W2148853260","https://openalex.org/W2154866190","https://openalex.org/W2170792029","https://openalex.org/W2340179598","https://openalex.org/W2344561059","https://openalex.org/W2558643140","https://openalex.org/W2587567366","https://openalex.org/W2593747486","https://openalex.org/W2594573607","https://openalex.org/W2601986670","https://openalex.org/W2604183875","https://openalex.org/W2766498398","https://openalex.org/W2768157269","https://openalex.org/W2790295707","https://openalex.org/W2804947682","https://openalex.org/W2854827211","https://openalex.org/W2963424525","https://openalex.org/W4252232449"],"related_works":["https://openalex.org/W4283015054","https://openalex.org/W2786602521","https://openalex.org/W2562330244","https://openalex.org/W4234384124","https://openalex.org/W2951842647","https://openalex.org/W3085774086","https://openalex.org/W3123589318","https://openalex.org/W2996633770","https://openalex.org/W4295353219","https://openalex.org/W3184650986"],"abstract_inverted_index":{"Background:":[0],"Genomic":[1],"sequencing,":[2],"including":[3,226],"whole":[4],"exome":[5],"sequencing":[6],"(WES),":[7],"is":[8,51,80,91],"enabling":[9],"research":[10],"and":[11,26,58,116,121,125,139,145,159,175,183,188,229],"the":[12,17,39,45,110,162,178,191,202,239],"medical":[13],"practice":[14,27],"to":[15,68,76,129,142,200],"increase":[16],"resolution":[18],"with":[19],"which":[20,38,78],"we":[21,72,98],"define":[22],"diseases,":[23],"understand":[24,77],"mechanisms,":[25],"clinical":[28],"care.":[29],"However,":[30],"WES":[31,48,70,106,195],"routinely":[32],"identifies":[33,196],"many":[34,53],"genomic":[35,86,131,197],"variants":[36,207],"for":[37,83,244],"functional":[40,203],"associations":[41],"are":[42],"unknown.":[43],"Furthering":[44],"uncertainty":[46],"in":[47,168,208],"data":[49,107,132,246],"interpretation":[50,108],"that":[52,218],"genes":[54,163,192],"express":[55],"multiple":[56,123,223],"transcripts":[57],"this":[59,96],"pattern":[60],"may":[61],"differ":[62],"by":[63,153],"body":[64],"tissue.":[65],"In":[66,95],"order":[67],"interpret":[69,201],"data,":[71],"not":[73],"only":[74],"need":[75],"transcript":[79,154,227],"most":[81,92],"relevant":[82],"a":[84,148,212],"novel":[85],"variant,":[87],"but":[88,199],"what":[89],"tissue":[90,170],"relevant.":[93],"Methods:":[94],"work,":[97],"quantify":[99],"how":[100],"frequently":[101],"these":[102],"two":[103],"features":[104],"impact":[105],"at":[109],"level":[111],"of":[112,161,177,181,190,205,215,241],"gene,":[113],"pathway,":[114],"disease,":[115,143],"biologic":[117,137,224],"network.":[118],"We":[119],"combined":[120],"analyzed":[122],"large":[124],"publically":[126],"available":[127,243],"datasets":[128],"inform":[130],"interpretation.":[133,247],"Results:":[134],"Across":[135],"well-established":[136],"pathways":[138,182],"genetic":[140],"contributors":[141],"73%":[144],"58%":[146],"have":[147],"different":[149],"protein":[150],"coding":[151],"effect":[152],"selection":[155,228],"for,":[156,185],"respectively,":[157,186],"25%":[158,187],"50%":[160,189],"contained.":[164,193],"Additionally,":[165],"strong":[166],"differences":[167],"human":[169],"expression":[171,232],"levels":[172],"affect":[173],"32%":[174],"18%":[176],"same":[179],"set":[180],"diseases":[184],"Conclusion:":[194],"variants,":[198],"effects":[204],"those":[206],"high-resolution":[209],"will":[210,236],"require":[211],"next":[213],"generations":[214],"knowledge-generating":[216],"systems":[217,235],"can":[219],"take":[220],"into":[221],"account":[222],"factors":[225],"cross-tissue":[230],"gene":[231],"levels.":[233],"Such":[234],"further":[237],"expand":[238],"variety":[240],"information":[242],"genomics":[245]},"counts_by_year":[{"year":2026,"cited_by_count":1},{"year":2025,"cited_by_count":1},{"year":2023,"cited_by_count":2},{"year":2021,"cited_by_count":2},{"year":2020,"cited_by_count":1},{"year":2019,"cited_by_count":2}],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2018-12-22T00:00:00"}
