{"id":"https://openalex.org/W3174238723","doi":"https://doi.org/10.1186/s12859-021-04243-z","title":"Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants","display_name":"Transcript annotation tool (TransAT): an R package for retrieving annotations for transcript-specific genetic variants","publication_year":2021,"publication_date":"2021-06-28","ids":{"openalex":"https://openalex.org/W3174238723","doi":"https://doi.org/10.1186/s12859-021-04243-z","mag":"3174238723","pmid":"https://pubmed.ncbi.nlm.nih.gov/34182919"},"language":"en","primary_location":{"id":"doi:10.1186/s12859-021-04243-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04243-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04243-z","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/counter/pdf/10.1186/s12859-021-04243-z","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5032186300","display_name":"Ching\u2010Yu Shih","orcid":null},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":true,"raw_author_name":"Ching-Yu Shih","raw_affiliation_strings":["Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, 10055, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, 10055, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5090291644","display_name":"Amrita Chattopadhyay","orcid":"https://orcid.org/0000-0002-0513-6551"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Amrita Chattopadhyay","raw_affiliation_strings":["Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, 10055, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, 10055, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5029927102","display_name":"Chien\u2010Hui Wu","orcid":"https://orcid.org/0000-0002-6382-1186"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]},{"id":"https://openalex.org/I4210131804","display_name":"National Taiwan University Hospital","ror":"https://ror.org/03nteze27","country_code":"TW","type":"healthcare","lineage":["https://openalex.org/I4210131804"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Chien-Hui Wu","raw_affiliation_strings":["Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, 10055, Taiwan","Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, 10055, Taiwan","institution_ids":["https://openalex.org/I16733864"]},{"raw_affiliation_string":"Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan","institution_ids":["https://openalex.org/I4210131804"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5012873714","display_name":"Yu\u2010Wen Tien","orcid":"https://orcid.org/0000-0002-9126-2705"},"institutions":[{"id":"https://openalex.org/I4210131804","display_name":"National Taiwan University Hospital","ror":"https://ror.org/03nteze27","country_code":"TW","type":"healthcare","lineage":["https://openalex.org/I4210131804"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Yu-Wen Tien","raw_affiliation_strings":["Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Surgery, National Taiwan University Hospital, Taipei, Taiwan","institution_ids":["https://openalex.org/I4210131804"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5025739002","display_name":"Tzu\u2010Pin Lu","orcid":"https://orcid.org/0000-0003-3697-0386"},"institutions":[{"id":"https://openalex.org/I16733864","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95","country_code":"TW","type":"education","lineage":["https://openalex.org/I16733864"]},{"id":"https://openalex.org/I191969501","display_name":"National Taipei University of Nursing and Health Science","ror":"https://ror.org/019z71f50","country_code":"TW","type":"education","lineage":["https://openalex.org/I191969501"]},{"id":"https://openalex.org/I77199428","display_name":"National Taiwan Sport University","ror":"https://ror.org/01zjvhn75","country_code":"TW","type":"education","lineage":["https://openalex.org/I77199428"]}],"countries":["TW"],"is_corresponding":false,"raw_author_name":"Tzu-Pin Lu","raw_affiliation_strings":["Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, 10055, Taiwan. tplu@ntu.edu.tw","Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, 10055, Taiwan. tplu@ntu.edu.tw","Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, 10055, Taiwan"],"raw_orcid":"https://orcid.org/0000-0003-3697-0386","affiliations":[{"raw_affiliation_string":"Bioinformatics and Biostatistics Core, Centre of Genomic and Precision Medicine, National Taiwan University, Taipei, 10055, Taiwan. tplu@ntu.edu.tw","institution_ids":["https://openalex.org/I77199428"]},{"raw_affiliation_string":"Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, 10055, Taiwan. tplu@ntu.edu.tw","institution_ids":["https://openalex.org/I191969501"]},{"raw_affiliation_string":"Department of Public Health, Institute of Epidemiology and Preventive Medicine, National Taiwan University, Taipei, 10055, Taiwan","institution_ids":["https://openalex.org/I16733864"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5032186300"],"corresponding_institution_ids":["https://openalex.org/I16733864"],"apc_list":{"value":1690,"currency":"GBP","value_usd":2072},"apc_paid":{"value":1690,"currency":"GBP","value_usd":2072},"fwci":0.1654,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.59535657,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"22","issue":"1","first_page":"350","last_page":"350"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11642","display_name":"Genomics and Rare Diseases","score":0.8285999894142151,"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":0.8285999894142151,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.056299999356269836,"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/T11287","display_name":"Cancer Genomics and Diagnostics","score":0.007199999876320362,"subfield":{"id":"https://openalex.org/subfields/1306","display_name":"Cancer Research"},"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/annotation","display_name":"Annotation","score":0.7792086601257324},{"id":"https://openalex.org/keywords/single-nucleotide-polymorphism","display_name":"Single-nucleotide polymorphism","score":0.5941953063011169},{"id":"https://openalex.org/keywords/dna-microarray","display_name":"DNA microarray","score":0.5756807327270508},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.5532686114311218},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.5478692650794983},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.5333943963050842},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.4385858178138733},{"id":"https://openalex.org/keywords/snp","display_name":"SNP","score":0.43770310282707214},{"id":"https://openalex.org/keywords/allele-frequency","display_name":"Allele frequency","score":0.43173861503601074},{"id":"https://openalex.org/keywords/allele","display_name":"Allele","score":0.4007992744445801},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2200668454170227},{"id":"https://openalex.org/keywords/genotype","display_name":"Genotype","score":0.17615699768066406}],"concepts":[{"id":"https://openalex.org/C2776321320","wikidata":"https://www.wikidata.org/wiki/Q857525","display_name":"Annotation","level":2,"score":0.7792086601257324},{"id":"https://openalex.org/C153209595","wikidata":"https://www.wikidata.org/wiki/Q501128","display_name":"Single-nucleotide polymorphism","level":4,"score":0.5941953063011169},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.5756807327270508},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.5532686114311218},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.5478692650794983},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.5333943963050842},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.4385858178138733},{"id":"https://openalex.org/C139275648","wikidata":"https://www.wikidata.org/wiki/Q17134011","display_name":"SNP","level":5,"score":0.43770310282707214},{"id":"https://openalex.org/C37463918","wikidata":"https://www.wikidata.org/wiki/Q387981","display_name":"Allele frequency","level":4,"score":0.43173861503601074},{"id":"https://openalex.org/C180754005","wikidata":"https://www.wikidata.org/wiki/Q80726","display_name":"Allele","level":3,"score":0.4007992744445801},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2200668454170227},{"id":"https://openalex.org/C135763542","wikidata":"https://www.wikidata.org/wiki/Q106016","display_name":"Genotype","level":3,"score":0.17615699768066406}],"mesh":[{"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":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D016678","descriptor_name":"Genome","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020641","descriptor_name":"Polymorphism, Single Nucleotide","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D023281","descriptor_name":"Genomics","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"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":4,"locations":[{"id":"doi:10.1186/s12859-021-04243-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04243-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04243-z","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:34182919","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/34182919","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:doaj.org/article:37aaa645f3904e41bdf57855d23f317a","is_oa":true,"landing_page_url":"https://doaj.org/article/37aaa645f3904e41bdf57855d23f317a","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":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics, Vol 22, Iss 1, Pp 1-12 (2021)","raw_type":"article"},{"id":"pmh:oai:pubmedcentral.nih.gov:8240296","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/8240296","pdf_url":null,"source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"BMC Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/s12859-021-04243-z","is_oa":true,"landing_page_url":"https://doi.org/10.1186/s12859-021-04243-z","pdf_url":"https://bmcbioinformatics.biomedcentral.com/counter/pdf/10.1186/s12859-021-04243-z","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":[{"display_name":"Good health and well-being","score":0.800000011920929,"id":"https://metadata.un.org/sdg/3"}],"awards":[{"id":"https://openalex.org/G5902745161","display_name":null,"funder_award_id":"MOST-109-2314-B-002 -151 -MY3,  MOST-106-2314-B-002-134-MY2","funder_id":"https://openalex.org/F4320322795","funder_display_name":"Ministry of Science and Technology, Taiwan"},{"id":"https://openalex.org/G6338824196","display_name":null,"funder_award_id":"GTZ300","funder_id":"https://openalex.org/F4320323900","funder_display_name":"National Taiwan University"},{"id":"https://openalex.org/G7937749930","display_name":null,"funder_award_id":"106R8400","funder_id":"https://openalex.org/F4320323900","funder_display_name":"National Taiwan University"}],"funders":[{"id":"https://openalex.org/F4320322795","display_name":"Ministry of Science and Technology, Taiwan","ror":"https://ror.org/02kv4zf79"},{"id":"https://openalex.org/F4320323900","display_name":"National Taiwan University","ror":"https://ror.org/05bqach95"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3174238723.pdf","grobid_xml":"https://content.openalex.org/works/W3174238723.grobid-xml"},"referenced_works_count":44,"referenced_works":["https://openalex.org/W47643599","https://openalex.org/W1988004867","https://openalex.org/W2003986301","https://openalex.org/W2045949302","https://openalex.org/W2047721309","https://openalex.org/W2051978340","https://openalex.org/W2063159635","https://openalex.org/W2069839376","https://openalex.org/W2074699306","https://openalex.org/W2085697325","https://openalex.org/W2088080911","https://openalex.org/W2104549677","https://openalex.org/W2106660071","https://openalex.org/W2107903949","https://openalex.org/W2131478115","https://openalex.org/W2147918436","https://openalex.org/W2152320398","https://openalex.org/W2169567789","https://openalex.org/W2225287204","https://openalex.org/W2228484003","https://openalex.org/W2539164385","https://openalex.org/W2547574709","https://openalex.org/W2587204086","https://openalex.org/W2749599841","https://openalex.org/W2768466792","https://openalex.org/W2791866962","https://openalex.org/W2800987064","https://openalex.org/W2907043693","https://openalex.org/W2912664120","https://openalex.org/W2924923089","https://openalex.org/W2941275129","https://openalex.org/W2947601703","https://openalex.org/W2961680688","https://openalex.org/W2984610317","https://openalex.org/W2986720570","https://openalex.org/W2989134117","https://openalex.org/W3004227146","https://openalex.org/W3004940273","https://openalex.org/W3013501632","https://openalex.org/W3029078495","https://openalex.org/W3032555314","https://openalex.org/W3042211652","https://openalex.org/W3120139692","https://openalex.org/W4206037526"],"related_works":["https://openalex.org/W1997352593","https://openalex.org/W2143489661","https://openalex.org/W3016573916","https://openalex.org/W4281711902","https://openalex.org/W3206555169","https://openalex.org/W2070581548","https://openalex.org/W3157359833","https://openalex.org/W2413660786","https://openalex.org/W3024317680","https://openalex.org/W1511048503"],"abstract_inverted_index":{"BACKGROUND:":[0],"An":[1],"individual's":[2],"genetics":[3],"play":[4],"a":[5,32,50,106,118,179,265],"role":[6],"in":[7,17,68,77,82,98,205,210],"how":[8],"RNA":[9],"transcripts":[10],"are":[11,135,200],"generated":[12],"from":[13,183,192,299],"DNA":[14],"and":[15,23,70,92,101,133,148,175,185,203,220,234,238,310],"consequently":[16],"their":[18],"translation":[19],"into":[20,258],"protein.":[21],"Transcriptional":[22],"translational":[24],"profiling":[25],"of":[26,56,59,124,140,154,308],"patients":[27],"furnishes":[28],"the":[29,44,57,114,122,125,150,190,244,256,306],"information":[30,279],"that":[31,108,170,268],"specific":[33,293],"marker":[34,45],"is":[35,81,121,216,221,230,264],"present;":[36],"however,":[37,138],"it":[38],"fails":[39],"to":[40,49,112,288],"provide":[41,149],"evidence":[42],"whether":[43],"correlates":[46],"with":[47,260],"response":[48],"therapeutic":[51],"agent.":[52],"A":[53],"comparative":[54],"analysis":[55],"frequency":[58,116],"genetic":[60,271],"variants,":[61],"such":[62,130],"as":[63,131,146],"single":[64],"nucleotide":[65],"polymorphisms":[66],"(SNPs),":[67],"diseased":[69],"general":[71],"populations":[72,303],"can":[73,109,142,235,251],"identify":[74],"pathogenic":[75],"variants":[76],"individual":[78],"patients.":[79],"This":[80],"part":[83],"because":[84],"SNPs":[85,191],"have":[86],"considerable":[87],"effects":[88],"on":[89,218,243,313],"protein":[90],"function":[91],"gene":[93],"expression":[94],"when":[95],"they":[96],"occur":[97],"coding":[99],"regions":[100],"regulatory":[102],"sequences,":[103],"respectively.":[104],"Therefore,":[105],"tool":[107,168,267],"help":[110],"users":[111],"obtain":[113],"allele":[115,187,297],"for":[117,178,189,223,273,284],"corresponding":[119,151],"transcript":[120,144,166,181],"need":[123],"day.":[126],"Several":[127],"annotation":[128,167],"tools":[129],"SNPnexus":[132],"VariED":[134],"publicly":[136,193],"available;":[137],"none":[139],"them":[141,287],"use":[143],"IDs":[145],"input":[147],"genomic":[152,176],"positions":[153],"variants.":[155],"RESULTS:":[156],"In":[157],"this":[158],"study,":[159],"we":[160],"developed":[161],"an":[162,206],"R":[163,224,245,259],"package,":[164],"called":[165],"(TransAT),":[169],"provides":[171,270],"(i)":[172],"SNP":[173],"ID":[174,182],"position":[177],"user-provided":[180],"patients,":[184],"(ii)":[186],"frequencies":[188,298],"available":[194,217,231],"global":[195,301],"populations.":[196],"All":[197],"data":[198],"elements":[199],"extracted,":[201],"collected,":[202],"displayed":[204],"easily":[207,277],"downloadable":[208],"format":[209],"two":[211],"simple":[212],"command":[213],"lines.":[214],"TransAT":[215,263],"Windows/Linux/MacOS":[219],"operative":[222],"version":[225],"4.0.4":[226],"or":[227],"later.":[228],"It":[229],"at":[232],"https://github.com/ShihChingYu/TransAT":[233],"be":[236,252,281],"downloaded":[237],"installed":[239],"using":[240],"devtools::install_github(\"ShihChingYu/TransAT\",":[241],"force=T)":[242],"execution":[246],"page.":[247],"Thereafter,":[248],"all":[249],"functions":[250],"executed":[253],"by":[254],"loading":[255],"package":[257],"library(TransAT).":[261],"CONCLUSIONS:":[262],"novel":[266],"seamlessly":[269],"annotations":[272],"queried":[274],"transcripts.":[275],"Such":[276],"obtainable":[278],"would":[280],"greatly":[282],"advantageous":[283],"physicians,":[285],"assisting":[286],"make":[289],"individualized":[290],"decisions":[291],"about":[292],"drug":[294],"treatments.":[295],"Moreover,":[296],"user-chosen":[300],"ethnic":[302],"will":[304],"highlight":[305],"importance":[307],"ethnicity":[309],"its":[311],"effect":[312],"patient":[314],"pathogenicity.":[315]},"counts_by_year":[{"year":2022,"cited_by_count":1}],"updated_date":"2026-05-06T08:25:59.206177","created_date":"2025-10-10T00:00:00"}