{"id":"https://openalex.org/W2278563175","doi":null,"title":"Condition-dependent coexpression in Arabidopsis and the bootstrap estimation of false discovery rate","display_name":"Condition-dependent coexpression in Arabidopsis and the bootstrap estimation of false discovery rate","publication_year":2015,"publication_date":"2015-11-01","ids":{"openalex":"https://openalex.org/W2278563175","mag":"2278563175"},"language":"en","primary_location":{"id":"pmh:oai:utoronto.scholaris.ca:1807/71041","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1807/71041","pdf_url":"https://utoronto.scholaris.ca/bitstreams/26a79689-ed5e-4f8a-99c4-c91490e51538/download","source":{"id":"https://openalex.org/S4306400261","display_name":"TSpace (University of Toronto)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I185261750","host_organization_name":"University of Toronto","host_organization_lineage":["https://openalex.org/I185261750"],"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":"Thesis"},"volume":null,"type":"dissertation","is_traditional":true,"indexed_in":[],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://utoronto.scholaris.ca/bitstreams/26a79689-ed5e-4f8a-99c4-c91490e51538/download","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":null,"display_name":"Hui Lan","orcid":"https://orcid.org/0000-0003-4654-4823","observed_orcids":["https://orcid.org/0000-0003-4654-4823"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Hui Lan","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0003-4654-4823","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6714000105857849,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.6714000105857849,"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/T10885","display_name":"Gene expression and cancer classification","score":0.2777999937534332,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.026000000536441803,"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/gene-co-expression-network","display_name":"gene co-expression network","score":0.7910000085830688},{"id":"https://openalex.org/keywords/seed-germination","display_name":"seed germination","score":0.8379999995231628},{"id":"https://openalex.org/keywords/arabidopsis-thaliana","display_name":"Arabidopsis thaliana","score":0.9909999966621399},{"id":"https://openalex.org/keywords/false-discovery-rate-estimation","display_name":"false discovery rate estimation","score":0.8949999809265137},{"id":"https://openalex.org/keywords/bootstrap-method","display_name":"bootstrapping","score":0.5120000243186951},{"id":"https://openalex.org/keywords/gene-expression-data","display_name":"gene expression data","score":0.33799999952316284}],"concepts":[{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.8964635133743286},{"id":"https://openalex.org/C2779491563","wikidata":"https://www.wikidata.org/wiki/Q157892","display_name":"Arabidopsis","level":4,"score":0.6129293441772461},{"id":"https://openalex.org/C95922358","wikidata":"https://www.wikidata.org/wiki/Q5432725","display_name":"False positive rate","level":2,"score":0.4439952075481415},{"id":"https://openalex.org/C96250715","wikidata":"https://www.wikidata.org/wiki/Q965330","display_name":"Estimation","level":2,"score":0.4402908682823181},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.43836697936058044},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.38588598370552063},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3737383484840393},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.3462975025177002},{"id":"https://openalex.org/C149782125","wikidata":"https://www.wikidata.org/wiki/Q160039","display_name":"Econometrics","level":1,"score":0.3441125452518463},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3428078293800354},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.3330037593841553},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3264211416244507},{"id":"https://openalex.org/C127413603","wikidata":"https://www.wikidata.org/wiki/Q11023","display_name":"Engineering","level":0,"score":0.18160736560821533},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.11225995421409607},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.06572368741035461},{"id":"https://openalex.org/C201995342","wikidata":"https://www.wikidata.org/wiki/Q682496","display_name":"Systems engineering","level":1,"score":0.0},{"id":"https://openalex.org/C143065580","wikidata":"https://www.wikidata.org/wiki/Q3285695","display_name":"Mutant","level":3,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:utoronto.scholaris.ca:1807/71041","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1807/71041","pdf_url":"https://utoronto.scholaris.ca/bitstreams/26a79689-ed5e-4f8a-99c4-c91490e51538/download","source":{"id":"https://openalex.org/S4306400261","display_name":"TSpace (University of Toronto)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I185261750","host_organization_name":"University of Toronto","host_organization_lineage":["https://openalex.org/I185261750"],"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":"Thesis"},{"id":"mag:2278563175","doi":null,"is_oa":false,"landing_page_url":"https://tspace.library.utoronto.ca/handle/1807/71041?mode=full","pdf_url":null,"source":null,"license":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":null}],"best_oa_location":{"id":"pmh:oai:utoronto.scholaris.ca:1807/71041","doi":null,"is_oa":true,"landing_page_url":"http://hdl.handle.net/1807/71041","pdf_url":"https://utoronto.scholaris.ca/bitstreams/26a79689-ed5e-4f8a-99c4-c91490e51538/download","source":{"id":"https://openalex.org/S4306400261","display_name":"TSpace (University of Toronto)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I185261750","host_organization_name":"University of Toronto","host_organization_lineage":["https://openalex.org/I185261750"],"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":"Thesis"},"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[{"id":"https://openalex.org/F4320314997","display_name":"Strong","ror":"https://ror.org/041vyzr56"},{"id":"https://openalex.org/F4320323654","display_name":"Hospital for Sick Children","ror":"https://ror.org/057q4rt57"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W2278563175.pdf","grobid_xml":"https://content.openalex.org/works/W2278563175.grobid-xml"},"referenced_works_count":108,"referenced_works":["https://openalex.org/W11782418","https://openalex.org/W642783518","https://openalex.org/W1480376833","https://openalex.org/W1524637288","https://openalex.org/W1540618782","https://openalex.org/W1579271636","https://openalex.org/W1589857571","https://openalex.org/W1722998888","https://openalex.org/W1937194836","https://openalex.org/W1944747167","https://openalex.org/W1964877861","https://openalex.org/W1964895626","https://openalex.org/W1965032353","https://openalex.org/W1966327575","https://openalex.org/W1966939967","https://openalex.org/W1978957247","https://openalex.org/W1988233215","https://openalex.org/W1995869668","https://openalex.org/W1997096620","https://openalex.org/W1999084705","https://openalex.org/W2005273845","https://openalex.org/W2007009583","https://openalex.org/W2008003666","https://openalex.org/W2008620264","https://openalex.org/W2009358682","https://openalex.org/W2012110806","https://openalex.org/W2017337756","https://openalex.org/W2019013385","https://openalex.org/W2021959587","https://openalex.org/W2029690199","https://openalex.org/W2031391689","https://openalex.org/W2037187863","https://openalex.org/W2038201838","https://openalex.org/W2040040254","https://openalex.org/W2042088824","https://openalex.org/W2045299822","https://openalex.org/W2053427298","https://openalex.org/W2056014639","https://openalex.org/W2056918383","https://openalex.org/W2065996794","https://openalex.org/W2073727170","https://openalex.org/W2078149659","https://openalex.org/W2078577327","https://openalex.org/W2078929441","https://openalex.org/W2097090208","https://openalex.org/W2097370013","https://openalex.org/W2098458123","https://openalex.org/W2101043436","https://openalex.org/W2105400581","https://openalex.org/W2106209421","https://openalex.org/W2106249858","https://openalex.org/W2109995704","https://openalex.org/W2110065044","https://openalex.org/W2111110205","https://openalex.org/W2113160145","https://openalex.org/W2113263286","https://openalex.org/W2113301399","https://openalex.org/W2113762180","https://openalex.org/W2115111790","https://openalex.org/W2119022968","https://openalex.org/W2119905144","https://openalex.org/W2120080928","https://openalex.org/W2123170032","https://openalex.org/W2125705880","https://openalex.org/W2126498993","https://openalex.org/W2129442808","https://openalex.org/W2133540908","https://openalex.org/W2134375320","https://openalex.org/W2134515324","https://openalex.org/W2137365411","https://openalex.org/W2139845570","https://openalex.org/W2143489962","https://openalex.org/W2144889452","https://openalex.org/W2146087926","https://openalex.org/W2146264532","https://openalex.org/W2147528194","https://openalex.org/W2148762636","https://openalex.org/W2150202616","https://openalex.org/W2150646520","https://openalex.org/W2150926065","https://openalex.org/W2151794037","https://openalex.org/W2153907785","https://openalex.org/W2155471967","https://openalex.org/W2156166308","https://openalex.org/W2156640201","https://openalex.org/W2157308521","https://openalex.org/W2159767718","https://openalex.org/W2159937794","https://openalex.org/W2160807805","https://openalex.org/W2161922735","https://openalex.org/W2161926762","https://openalex.org/W2162505470","https://openalex.org/W2164695855","https://openalex.org/W2165902959","https://openalex.org/W2166574880","https://openalex.org/W2166914686","https://openalex.org/W2167784171","https://openalex.org/W2168223887","https://openalex.org/W2168911096","https://openalex.org/W2171352347","https://openalex.org/W2264709743","https://openalex.org/W2331432542","https://openalex.org/W2797532987","https://openalex.org/W2797563284","https://openalex.org/W2898127611","https://openalex.org/W3099289621","https://openalex.org/W3127652930","https://openalex.org/W4253880200"],"related_works":["https://openalex.org/W2021164824","https://openalex.org/W2267188546","https://openalex.org/W7098569964","https://openalex.org/W2140878613","https://openalex.org/W2104475115","https://openalex.org/W2155497595","https://openalex.org/W2417636043","https://openalex.org/W2358829512","https://openalex.org/W1979153484","https://openalex.org/W4225298434"],"abstract_inverted_index":{"Conventional":[0],"coexpression":[1,21,32,49,89,137,155],"analysis":[2],"looks":[3],"at":[4,30],"gene":[5,31,38,78,126],"expression":[6,79,127,147],"levels":[7],"over":[8,233,256],"diverse":[9],"conditions.":[10],"Although":[11],"such":[12],"``condition":[13],"independent''":[14],"analyses":[15],"provide":[16],"useful":[17],"generalized":[18],"information,":[19],"the":[20,51,65,136,146,159,164,187,204,222,227],"of":[22,53,64,138,141,149,163,167,206,237],"genes":[23,142],"can":[24,143,201],"depend":[25,144],"on":[26,145,158,221],"biological":[27,43],"context.":[28],"Looking":[29],"in":[33,50,56,125],"a":[34,88,120,139,150,214,234],"condition-dependent":[35,48],"fashion":[36],"identifies":[37],"interactions":[39,124,200],"relevant":[40],"to":[41,111,115,184,254,261],"more-specific":[42],"questions.":[44],"This":[45],"thesis":[46,210],"addresses":[47],"context":[52],"seed":[54],"germination":[55,112],"Arabidopsis":[57],"thaliana.":[58],"We":[59,92,192,224],"study":[60],"two":[61,105],"broad":[62],"aspects":[63],"problem:":[66],"(i)":[67],"detecting":[68,73],"pairwise":[69],"interactions,":[70,170],"and":[71,97,113,129,212,251],"(ii)":[72],"three-way":[74,123,169,207],"interactions.":[75,208],"First,":[76],"using":[77],"data":[80,128],"gathered":[81],"exclusively":[82],"from":[83],"mature":[84],"seeds,":[85],"we":[86,118,247],"develop":[87,119],"network,":[90],"SeedNet.":[91,262],"analyze":[93],"its":[94,131],"statistical":[95,238],"properties":[96],"find,":[98],"for":[99,122,177,198,217],"example,":[100],"that":[101,194,226],"SeedNet":[102],"bifurcates":[103],"into":[104],"previously":[106],"undescribed":[107],"components,":[108],"one":[109,114],"corresponding":[110],"non-germination.":[116],"Second,":[117],"detector":[121,250],"demonstrate":[130],"efficacy.":[132],"In":[133],"this":[134],"approach,":[135],"pair":[140],"level":[148],"third":[151],"gene.":[152],"That":[153],"is,":[154],"is":[156,172,182],"conditioned":[157],"transcriptional":[160],"environment.":[161],"Because":[162],"vast":[165],"number":[166],"possible":[168],"there":[171],"an":[173],"extremely":[174],"large":[175],"potential":[176],"false":[178],"positives,":[179],"so":[180],"it":[181],"crucial":[183],"accurately":[185],"estimate":[186],"False":[188],"Discovery":[189],"Rate":[190],"(FDR).":[191],"show":[193,225],"extending":[195],"approaches":[196,242],"used":[197],"two-way":[199],"significantly":[202],"underestimate":[203],"FDR":[205,219,252],"The":[209],"develops":[211],"evaluates":[213],"new":[215],"approach":[216,229],"estimating":[218],"based":[220],"bootstrap.":[223],"bootstrap":[228],"produces":[230],"reasonable":[231],"estimates":[232,253],"wide":[235],"range":[236],"conditions,":[239],"whereas":[240],"conventional":[241],"rapidly":[243],"break":[244],"down.":[245],"Finally,":[246],"use":[248],"our":[249],"add":[255],"64,000":[257],"new,":[258],"highly-confident":[259],"edges":[260]},"counts_by_year":[],"updated_date":"2026-10-16T09:59:22.235173","created_date":"2016-06-24T00:00:00"}