{"id":"https://openalex.org/W3180021379","doi":"https://doi.org/10.3390/data6070075","title":"Preprocessing of Public RNA-Sequencing Datasets to Facilitate Downstream Analyses of Human Diseases","display_name":"Preprocessing of Public RNA-Sequencing Datasets to Facilitate Downstream Analyses of Human Diseases","publication_year":2021,"publication_date":"2021-07-15","ids":{"openalex":"https://openalex.org/W3180021379","doi":"https://doi.org/10.3390/data6070075","mag":"3180021379"},"language":"en","primary_location":{"id":"doi:10.3390/data6070075","is_oa":true,"landing_page_url":"https://doi.org/10.3390/data6070075","pdf_url":"https://www.mdpi.com/2306-5729/6/7/75/pdf?version=1626330970","source":{"id":"https://openalex.org/S4210226510","display_name":"Data","issn_l":"2306-5729","issn":["2306-5729"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://www.mdpi.com/2306-5729/6/7/75/pdf?version=1626330970","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5025120730","display_name":"Naomi Rapier-Sharman","orcid":"https://orcid.org/0000-0003-4759-7863"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Naomi Rapier-Sharman","raw_affiliation_strings":["Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5069310394","display_name":"John Krapohl","orcid":"https://orcid.org/0000-0003-0364-6387"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"John Krapohl","raw_affiliation_strings":["Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5002032666","display_name":"Ethan Beausoleil","orcid":null},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ethan J. Beausoleil","raw_affiliation_strings":["Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068843528","display_name":"Kennedy Gifford","orcid":null},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Kennedy T. L. Gifford","raw_affiliation_strings":["Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5011900348","display_name":"Benjamin R. Hinatsu","orcid":null},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Benjamin R. Hinatsu","raw_affiliation_strings":["Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5060888140","display_name":"Curtis S. Hoffmann","orcid":"https://orcid.org/0000-0002-4655-7774"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Curtis S. Hoffmann","raw_affiliation_strings":["Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5013182530","display_name":"Makayla Komer","orcid":null},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Makayla Komer","raw_affiliation_strings":["Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5045052471","display_name":"Tiana M. Scott","orcid":"https://orcid.org/0000-0002-6209-8301"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tiana M. Scott","raw_affiliation_strings":["Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA","institution_ids":["https://openalex.org/I100005738"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5081038591","display_name":"Brett E Pickett","orcid":"https://orcid.org/0000-0001-7930-8160"},"institutions":[{"id":"https://openalex.org/I100005738","display_name":"Brigham Young University","ror":"https://ror.org/047rhhm47","country_code":"US","type":"education","lineage":["https://openalex.org/I100005738"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Brett E. Pickett","raw_affiliation_strings":["Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA"],"affiliations":[{"raw_affiliation_string":"Department of Microbiology and Molecular Biology, Brigham Young University, Provo, UT 84602, USA","institution_ids":["https://openalex.org/I100005738"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":9,"corresponding_author_ids":["https://openalex.org/A5081038591"],"corresponding_institution_ids":["https://openalex.org/I100005738"],"apc_list":{"value":1600,"currency":"CHF","value_usd":1732},"apc_paid":{"value":1600,"currency":"CHF","value_usd":1732},"fwci":0.4066,"has_fulltext":false,"cited_by_count":5,"citation_normalized_percentile":{"value":0.59141838,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":98},"biblio":{"volume":"6","issue":"7","first_page":"75","last_page":"75"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11482","display_name":"RNA modifications and cancer","score":0.9990000128746033,"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/T11482","display_name":"RNA modifications and cancer","score":0.9990000128746033,"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/T11316","display_name":"Mycobacterium research and diagnosis","score":0.9975000023841858,"subfield":{"id":"https://openalex.org/subfields/2713","display_name":"Epidemiology"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T10515","display_name":"Cancer-related molecular mechanisms research","score":0.9962999820709229,"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/computational-biology","display_name":"Computational biology","score":0.49987053871154785},{"id":"https://openalex.org/keywords/gene-ontology","display_name":"Gene ontology","score":0.45205754041671753},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.4426899254322052},{"id":"https://openalex.org/keywords/disease","display_name":"Disease","score":0.4244942367076874},{"id":"https://openalex.org/keywords/gene","display_name":"Gene","score":0.41373342275619507},{"id":"https://openalex.org/keywords/medicine","display_name":"Medicine","score":0.27350467443466187},{"id":"https://openalex.org/keywords/gene-expression","display_name":"Gene expression","score":0.2300463318824768},{"id":"https://openalex.org/keywords/genetics","display_name":"Genetics","score":0.16695016622543335}],"concepts":[{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.49987053871154785},{"id":"https://openalex.org/C2987395477","wikidata":"https://www.wikidata.org/wiki/Q135085","display_name":"Gene ontology","level":4,"score":0.45205754041671753},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.4426899254322052},{"id":"https://openalex.org/C2779134260","wikidata":"https://www.wikidata.org/wiki/Q12136","display_name":"Disease","level":2,"score":0.4244942367076874},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.41373342275619507},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.27350467443466187},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.2300463318824768},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.16695016622543335},{"id":"https://openalex.org/C142724271","wikidata":"https://www.wikidata.org/wiki/Q7208","display_name":"Pathology","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.3390/data6070075","is_oa":true,"landing_page_url":"https://doi.org/10.3390/data6070075","pdf_url":"https://www.mdpi.com/2306-5729/6/7/75/pdf?version=1626330970","source":{"id":"https://openalex.org/S4210226510","display_name":"Data","issn_l":"2306-5729","issn":["2306-5729"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data","raw_type":"journal-article"},{"id":"pmh:oai:RePEc:gam:jdataj:v:6:y:2021:i:7:p:75-:d:594584","is_oa":false,"landing_page_url":"https://www.mdpi.com/2306-5729/6/7/75/","pdf_url":null,"source":{"id":"https://openalex.org/S4306401271","display_name":"RePEc: Research Papers in Economics","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I77793887","host_organization_name":"Federal Reserve Bank of St. Louis","host_organization_lineage":["https://openalex.org/I77793887"],"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":"article"},{"id":"pmh:oai:doaj.org/article:ab137def0747499bbfa4ef75f295c8e9","is_oa":true,"landing_page_url":"https://doaj.org/article/ab137def0747499bbfa4ef75f295c8e9","pdf_url":null,"source":{"id":"https://openalex.org/S112646816","display_name":"SHILAP Revista de lepidopterolog\u00eda","issn_l":"0300-5267","issn":["0300-5267","2340-4078"],"is_oa":true,"is_in_doaj":true,"is_core":false,"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"journal"},"license":"cc-by-sa","license_id":"https://openalex.org/licenses/cc-by-sa","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Data, Vol 6, Iss 7, p 75 (2021)","raw_type":"article"},{"id":"pmh:oai:mdpi.com:/2306-5729/6/7/75/","is_oa":true,"landing_page_url":"https://dx.doi.org/10.3390/data6070075","pdf_url":null,"source":{"id":"https://openalex.org/S4306400947","display_name":"MDPI (MDPI AG)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I4210097602","host_organization_name":"Multidisciplinary Digital Publishing Institute (Switzerland)","host_organization_lineage":["https://openalex.org/I4210097602"],"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":"Data; Volume 6; Issue 7; Pages: 75","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.3390/data6070075","is_oa":true,"landing_page_url":"https://doi.org/10.3390/data6070075","pdf_url":"https://www.mdpi.com/2306-5729/6/7/75/pdf?version=1626330970","source":{"id":"https://openalex.org/S4210226510","display_name":"Data","issn_l":"2306-5729","issn":["2306-5729"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310310987","host_organization_name":"Multidisciplinary Digital Publishing Institute","host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Data","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Industry, innovation and infrastructure","score":0.6899999976158142,"id":"https://metadata.un.org/sdg/9"}],"awards":[],"funders":[],"has_content":{"grobid_xml":true,"pdf":true},"content_urls":{"pdf":"https://content.openalex.org/works/W3180021379.pdf","grobid_xml":"https://content.openalex.org/works/W3180021379.grobid-xml"},"referenced_works_count":58,"referenced_works":["https://openalex.org/W1497400772","https://openalex.org/W1914535805","https://openalex.org/W1997536991","https://openalex.org/W2013318867","https://openalex.org/W2028484891","https://openalex.org/W2050554833","https://openalex.org/W2077590497","https://openalex.org/W2110417468","https://openalex.org/W2110687686","https://openalex.org/W2112220625","https://openalex.org/W2113630544","https://openalex.org/W2114104545","https://openalex.org/W2128586314","https://openalex.org/W2140141449","https://openalex.org/W2203875694","https://openalex.org/W2233430811","https://openalex.org/W2265193578","https://openalex.org/W2302501749","https://openalex.org/W2346168367","https://openalex.org/W2413782718","https://openalex.org/W2592811885","https://openalex.org/W2754773373","https://openalex.org/W2773787581","https://openalex.org/W2783139678","https://openalex.org/W2805930941","https://openalex.org/W2808491541","https://openalex.org/W2883803739","https://openalex.org/W2884450790","https://openalex.org/W2885660579","https://openalex.org/W2889497351","https://openalex.org/W2896090507","https://openalex.org/W2897114391","https://openalex.org/W2897306773","https://openalex.org/W2898805761","https://openalex.org/W2908901070","https://openalex.org/W2921922051","https://openalex.org/W2949639410","https://openalex.org/W2950563001","https://openalex.org/W2950699040","https://openalex.org/W2952013696","https://openalex.org/W2954940431","https://openalex.org/W2957045816","https://openalex.org/W2987288239","https://openalex.org/W3012238019","https://openalex.org/W3013312197","https://openalex.org/W3016489853","https://openalex.org/W3020909574","https://openalex.org/W3042880443","https://openalex.org/W3044799813","https://openalex.org/W3080853679","https://openalex.org/W3081490830","https://openalex.org/W3087984857","https://openalex.org/W3090723926","https://openalex.org/W3092867846","https://openalex.org/W3093813246","https://openalex.org/W3131213086","https://openalex.org/W3155679615","https://openalex.org/W4210361961"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2082860237","https://openalex.org/W2119695867","https://openalex.org/W2130076355","https://openalex.org/W1990804418","https://openalex.org/W1993764875","https://openalex.org/W2046158694","https://openalex.org/W2788277189","https://openalex.org/W2013243191","https://openalex.org/W2794341036"],"abstract_inverted_index":{"Publicly":[0],"available":[1],"RNA-sequencing":[2],"(RNA-seq)":[3],"data":[4,19,164],"are":[5,159],"a":[6,31,128],"rich":[7],"resource":[8],"for":[9,123],"elucidating":[10],"the":[11,36,46,113,131],"mechanisms":[12],"of":[13,38,43,130],"human":[14,47],"disease;":[15],"however,":[16],"preprocessing":[17],"these":[18],"requires":[20],"considerable":[21],"bioinformatic":[22],"expertise":[23],"and":[24,53,103,119,149,158,170,174],"computational":[25,33],"infrastructure.":[26],"Analyzing":[27],"multiple":[28],"datasets":[29,44,132],"with":[30,76],"consistent":[32],"workflow":[34],"increases":[35],"accuracy":[37],"downstream":[39],"meta-analyses.":[40],"This":[41],"collection":[42],"represents":[45],"intracellular":[48,140],"transcriptional":[49],"response":[50],"to":[51,161,171],"disorders":[52],"diseases":[54],"such":[55],"as":[56,72,74,144,146],"acute":[57,98,105],"lymphoblastic":[58],"leukemia":[59],"(ALL),":[60],"B-cell":[61],"lymphomas,":[62],"chronic":[63],"obstructive":[64],"pulmonary":[65],"disease":[66],"(COPD),":[67],"colorectal":[68],"cancer,":[69],"lupus":[70],"erythematosus;":[71],"well":[73,145],"infection":[75],"pathogens":[77],"including":[78],"Borrelia":[79],"burgdorferi,":[80],"hantavirus,":[81],"influenza":[82],"A":[83],"virus,":[84],"Middle":[85],"East":[86],"respiratory":[87,93,99,106],"syndrome":[88,100,107],"coronavirus":[89,101,108],"(MERS-CoV),":[90],"Streptococcus":[91],"pneumoniae,":[92],"syncytial":[94],"virus":[95],"(RSV),":[96],"severe":[97,104],"(SARS-CoV),":[102],"2":[109],"(SARS-CoV-2).":[110],"We":[111],"calculated":[112],"statistically":[114],"significant":[115],"differentially":[116],"expressed":[117],"genes":[118],"Gene":[120],"Ontology":[121],"terms":[122],"all":[124],"datasets.":[125],"In":[126],"addition,":[127],"subset":[129],"also":[133],"includes":[134],"results":[135],"from":[136],"splice":[137],"variant":[138],"analyses,":[139],"signaling":[141],"pathway":[142],"enrichments":[143],"read":[147],"mapping":[148],"quantification.":[150],"All":[151],"analyses":[152],"were":[153],"performed":[154],"using":[155],"well-established":[156],"algorithms":[157],"provided":[160],"facilitate":[162],"future":[163],"mining":[165],"activities,":[166],"wet":[167],"lab":[168],"studies,":[169],"accelerate":[172],"collaboration":[173],"discovery.":[175]},"counts_by_year":[{"year":2024,"cited_by_count":4},{"year":2022,"cited_by_count":1}],"updated_date":"2026-04-05T17:49:38.594831","created_date":"2021-07-19T00:00:00"}