{"id":"https://openalex.org/W2106046924","doi":"https://doi.org/10.1186/1751-0473-8-8","title":"SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies","display_name":"SVAw - a web-based application tool for automated surrogate variable analysis of gene expression studies","publication_year":2013,"publication_date":"2013-03-11","ids":{"openalex":"https://openalex.org/W2106046924","doi":"https://doi.org/10.1186/1751-0473-8-8","mag":"2106046924","pmid":"https://pubmed.ncbi.nlm.nih.gov/23497726"},"language":"en","primary_location":{"id":"doi:10.1186/1751-0473-8-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-8","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-8","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":true,"oa_status":"hybrid","oa_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-8","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5035578057","display_name":"Mehdi Pirooznia","orcid":"https://orcid.org/0000-0002-4210-6458"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]},{"id":"https://openalex.org/I4210097178","display_name":"Behavioral Pharma (United States)","ror":"https://ror.org/011bspp78","country_code":"US","type":"company","lineage":["https://openalex.org/I4210097178"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Mehdi Pirooznia","raw_affiliation_strings":["Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA. pzandi@jhsph.edu","Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA. pzandi@jhsph.edu","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I4210097178","https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5025229438","display_name":"Fayaz Seifuddin","orcid":"https://orcid.org/0000-0003-3357-7888"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fayaz Seifuddin","raw_affiliation_strings":["Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5051850972","display_name":"Fernando S. Goes","orcid":"https://orcid.org/0000-0001-6262-8264"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Fernando S Goes","raw_affiliation_strings":["Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5020868614","display_name":"Jeffrey T. Leek","orcid":"https://orcid.org/0000-0002-2873-2671"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jeffrey T Leek","raw_affiliation_strings":["Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5065109317","display_name":"Peter P. Zandi","orcid":"https://orcid.org/0000-0001-8423-2623"},"institutions":[{"id":"https://openalex.org/I145311948","display_name":"Johns Hopkins University","ror":"https://ror.org/00za53h95","country_code":"US","type":"education","lineage":["https://openalex.org/I145311948"]},{"id":"https://openalex.org/I2799853436","display_name":"Johns Hopkins Medicine","ror":"https://ror.org/037zgn354","country_code":"US","type":"healthcare","lineage":["https://openalex.org/I2799853436"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Peter P Zandi","raw_affiliation_strings":["Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA","Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA","institution_ids":["https://openalex.org/I145311948"]},{"raw_affiliation_string":"Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD, USA","institution_ids":["https://openalex.org/I2799853436","https://openalex.org/I145311948"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":5,"corresponding_author_ids":["https://openalex.org/A5065109317"],"corresponding_institution_ids":["https://openalex.org/I145311948","https://openalex.org/I2799853436"],"apc_list":null,"apc_paid":null,"fwci":0.7481,"has_fulltext":true,"cited_by_count":7,"citation_normalized_percentile":{"value":0.72175754,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":89,"max":96},"biblio":{"volume":"8","issue":"1","first_page":"8","last_page":"8"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10885","display_name":"Gene expression and cancer classification","score":0.6061999797821045,"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":0.6061999797821045,"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/T10261","display_name":"Genetic Associations and Epidemiology","score":0.1746000051498413,"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/T10845","display_name":"Advanced Causal Inference Techniques","score":0.029899999499320984,"subfield":{"id":"https://openalex.org/subfields/2613","display_name":"Statistics and Probability"},"field":{"id":"https://openalex.org/fields/26","display_name":"Mathematics"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.6414611339569092},{"id":"https://openalex.org/keywords/variable","display_name":"Variable (mathematics)","score":0.5288047790527344},{"id":"https://openalex.org/keywords/data-science","display_name":"Data science","score":0.4495590031147003},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.44586363434791565},{"id":"https://openalex.org/keywords/web-application","display_name":"Web application","score":0.4355444312095642},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.33653032779693604},{"id":"https://openalex.org/keywords/world-wide-web","display_name":"World Wide Web","score":0.2580220699310303},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.1319076120853424},{"id":"https://openalex.org/keywords/mathematics","display_name":"Mathematics","score":0.10750874876976013}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6414611339569092},{"id":"https://openalex.org/C182365436","wikidata":"https://www.wikidata.org/wiki/Q50701","display_name":"Variable (mathematics)","level":2,"score":0.5288047790527344},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.4495590031147003},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.44586363434791565},{"id":"https://openalex.org/C118643609","wikidata":"https://www.wikidata.org/wiki/Q189210","display_name":"Web application","level":2,"score":0.4355444312095642},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.33653032779693604},{"id":"https://openalex.org/C136764020","wikidata":"https://www.wikidata.org/wiki/Q466","display_name":"World Wide Web","level":1,"score":0.2580220699310303},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.1319076120853424},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.10750874876976013},{"id":"https://openalex.org/C134306372","wikidata":"https://www.wikidata.org/wiki/Q7754","display_name":"Mathematical analysis","level":1,"score":0.0}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.1186/1751-0473-8-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-8","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-8","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},{"id":"pmid:23497726","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/23497726","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":"Source code for biology and medicine","raw_type":null},{"id":"pmh:oai:europepmc.org:2617036","is_oa":true,"landing_page_url":"http://europepmc.org/articles/PMC3614430","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":"","raw_type":"Text"},{"id":"pmh:oai:pubmedcentral.nih.gov:3614430","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/3614430","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":"Source Code Biol Med","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1186/1751-0473-8-8","is_oa":true,"landing_page_url":"https://doi.org/10.1186/1751-0473-8-8","pdf_url":"https://scfbm.biomedcentral.com/counter/pdf/10.1186/1751-0473-8-8","source":{"id":"https://openalex.org/S45786803","display_name":"Source Code for Biology and Medicine","issn_l":"1751-0473","issn":["1751-0473"],"is_oa":false,"is_in_doaj":false,"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":"Source Code for Biology and Medicine","raw_type":"journal-article"},"sustainable_development_goals":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2106046924.pdf","grobid_xml":"https://content.openalex.org/works/W2106046924.grobid-xml"},"referenced_works_count":14,"referenced_works":["https://openalex.org/W1986071441","https://openalex.org/W2024103316","https://openalex.org/W2034562813","https://openalex.org/W2056014573","https://openalex.org/W2096192437","https://openalex.org/W2110853801","https://openalex.org/W2116650193","https://openalex.org/W2137499573","https://openalex.org/W2154201415","https://openalex.org/W2161922342","https://openalex.org/W2167532900","https://openalex.org/W2169353806","https://openalex.org/W2502759836","https://openalex.org/W4300025484"],"related_works":["https://openalex.org/W3018365851","https://openalex.org/W3207484021","https://openalex.org/W3123600015","https://openalex.org/W136259318","https://openalex.org/W48531881","https://openalex.org/W3125961646","https://openalex.org/W3125497426","https://openalex.org/W2354248364","https://openalex.org/W1603875766","https://openalex.org/W3124304773"],"abstract_inverted_index":{"BACKGROUND:":[0],"Surrogate":[1],"variable":[2,89,170],"analysis":[3,48,90,141,154,210],"(SVA)":[4],"is":[5,199,225],"a":[6,83,95,135,157,184,200],"powerful":[7],"method":[8],"to":[9,21,43],"identify,":[10],"estimate,":[11],"and":[12,41,58,70,138,151,155,174,180,214,219,238,241],"utilize":[13],"the":[14,47,55,76,124,132,162,168,192,195,207,242],"components":[15],"of":[16,33,60,68,102,159,164,171,191,211,222],"gene":[17,38,61,165],"expression":[18,39,62,104,166],"heterogeneity":[19,34,69],"due":[20],"unknown":[22,220],"and/or":[23],"unmeasured":[24],"technical,":[25],"genetic,":[26],"environmental,":[27],"or":[28],"demographic":[29],"factors.":[30],"These":[31],"sources":[32,67,221],"are":[35],"common":[36],"in":[37,75,128],"studies,":[40],"failing":[42],"incorporate":[44],"them":[45,74],"into":[46],"can":[49,246],"obscure":[50],"results.":[51],"Using":[52],"SVA":[53,100,116,125,153],"increases":[54],"biological":[56],"accuracy":[57],"reproducibility":[59],"studies":[63],"by":[64],"identifying":[65],"these":[66],"correctly":[71],"accounting":[72],"for":[73,99,148,161,177,194,206,228,235,244],"analysis.":[77],"RESULTS:":[78],"Here":[79],"we":[80,121],"have":[81,122],"developed":[82,110],"web":[84,201,237,251],"application":[85,240],"called":[86],"SVAw":[87,133,198],"(Surrogate":[88],"Web":[91],"app)":[92],"that":[93],"provides":[94,156],"user":[96,139],"friendly":[97,140],"interface":[98],"analyses":[101],"genome-wide":[103],"studies.":[105],"The":[106,232],"software":[107],"has":[108],"been":[109],"based":[111],"on":[112,167],"open":[113],"source":[114],"bioconductor":[115],"package.":[117],"In":[118],"our":[119,250],"software,":[120],"extended":[123],"program":[126],"functionality":[127],"three":[129],"aspects:":[130],"(i)":[131],"performs":[134],"fully":[136],"automated":[137],"workflow;":[142],"(ii)":[143],"It":[144,224],"calculates":[145],"probe/gene":[146],"Statistics":[147],"both":[149,236],"pre":[150],"post":[152],"table":[158],"results":[160],"regression":[163],"primary":[169],"interest":[172],"before":[173],"after":[175],"correcting":[176],"surrogate":[178,208],"variables;":[179],"(iii)":[181],"it":[182],"generates":[183],"comprehensive":[185],"report":[186],"file,":[187],"including":[188],"graphical":[189],"comparison":[190],"outcome":[193],"user.":[196],"CONCLUSIONS:":[197],"server":[202],"freely":[203,226],"accessible":[204],"solution":[205],"variant":[209],"high-throughput":[212],"datasets":[213],"facilitates":[215],"removing":[216],"all":[217],"unwanted":[218],"variation.":[223],"available":[227],"use":[229],"at":[230],"http://psychiatry.igm.jhmi.edu/sva.":[231],"executable":[233],"packages":[234],"standalone":[239],"instruction":[243],"installation":[245],"be":[247],"downloaded":[248],"from":[249],"site.":[252]},"counts_by_year":[{"year":2021,"cited_by_count":1},{"year":2018,"cited_by_count":1},{"year":2015,"cited_by_count":2},{"year":2014,"cited_by_count":1},{"year":2013,"cited_by_count":2}],"updated_date":"2026-06-19T15:47:20.252518","created_date":"2025-10-10T00:00:00"}
