{"id":"https://openalex.org/W2183284450","doi":null,"title":"Accounting for biological variation in digital gene expression experiments","display_name":"Accounting for biological variation in digital gene expression experiments","publication_year":2009,"publication_date":"2009-01-01","ids":{"openalex":"https://openalex.org/W2183284450","mag":"2183284450"},"language":"en","primary_location":{"id":"pmh:oai:jupiter.its.unimelb.edu.au:11343/35379","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/11343/35379","pdf_url":null,"source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"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":"Honours thesis"},"volume":null,"type":"dissertation","indexed_in":[],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5034469657","display_name":"Davis James McCarthy","orcid":"https://orcid.org/0000-0002-2218-6833","observed_orcids":["https://orcid.org/0000-0002-2218-6833"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Davis J. McCarthy","raw_affiliation_strings":[],"raw_orcid":"https://orcid.org/0000-0002-2218-6833","affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5034469657"],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"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/T10885","display_name":"Gene expression and cancer classification","score":0.9932000041007996,"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":0.9932000041007996,"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":0.004100000020116568,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.0010000000474974513,"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/biological-variation","display_name":"biological variation","score":0.9750000238418579},{"id":"https://openalex.org/keywords/gene-expression","display_name":"gene expression","score":0.8519999980926514},{"id":"https://openalex.org/keywords/rna-seq","display_name":"RNA-seq","score":0.4970000088214874},{"id":"https://openalex.org/keywords/variance-components","display_name":"variance components","score":0.35499998927116394},{"id":"https://openalex.org/keywords/differential-gene-expression","display_name":"differential gene expression","score":0.3240000009536743}],"concepts":[{"id":"https://openalex.org/C117236510","wikidata":"https://www.wikidata.org/wiki/Q7113620","display_name":"Overdispersion","level":4,"score":0.6866936683654785},{"id":"https://openalex.org/C33643355","wikidata":"https://www.wikidata.org/wiki/Q5176731","display_name":"Count data","level":3,"score":0.5942479968070984},{"id":"https://openalex.org/C100906024","wikidata":"https://www.wikidata.org/wiki/Q205692","display_name":"Poisson distribution","level":2,"score":0.5342622995376587},{"id":"https://openalex.org/C199335787","wikidata":"https://www.wikidata.org/wiki/Q743364","display_name":"Negative binomial distribution","level":3,"score":0.49763253331184387},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4854007661342621},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.48250508308410645},{"id":"https://openalex.org/C198531522","wikidata":"https://www.wikidata.org/wiki/Q485146","display_name":"Sample (material)","level":2,"score":0.4261839985847473},{"id":"https://openalex.org/C129848803","wikidata":"https://www.wikidata.org/wiki/Q2564360","display_name":"Sample size determination","level":2,"score":0.4241284728050232},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3995583653450012},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.34278422594070435},{"id":"https://openalex.org/C105795698","wikidata":"https://www.wikidata.org/wiki/Q12483","display_name":"Statistics","level":1,"score":0.2803128957748413},{"id":"https://openalex.org/C33923547","wikidata":"https://www.wikidata.org/wiki/Q395","display_name":"Mathematics","level":0,"score":0.2280220091342926},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.0},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.0}],"mesh":[],"locations_count":2,"locations":[{"id":"pmh:oai:jupiter.its.unimelb.edu.au:11343/35379","doi":null,"is_oa":false,"landing_page_url":"http://hdl.handle.net/11343/35379","pdf_url":null,"source":{"id":"https://openalex.org/S4377196259","display_name":"Minerva Access (University of Melbourne)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I165779595","host_organization_name":"The University of Melbourne","host_organization_lineage":["https://openalex.org/I165779595"],"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":"Honours thesis"},{"id":"mag:2183284450","doi":null,"is_oa":false,"landing_page_url":"https://minerva-access.unimelb.edu.au/bitstream/11343/35379/1/255846_thesis_final.pdf","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":null,"sustainable_development_goals":[],"study_designs":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":58,"referenced_works":["https://openalex.org/W1959492","https://openalex.org/W313178570","https://openalex.org/W1528905581","https://openalex.org/W1532331378","https://openalex.org/W1598266570","https://openalex.org/W1624051667","https://openalex.org/W1670944937","https://openalex.org/W1718902928","https://openalex.org/W1848732551","https://openalex.org/W1973174352","https://openalex.org/W1990601349","https://openalex.org/W1994090617","https://openalex.org/W2002426853","https://openalex.org/W2005129098","https://openalex.org/W2007719232","https://openalex.org/W2010637767","https://openalex.org/W2010888033","https://openalex.org/W2016300187","https://openalex.org/W2038798176","https://openalex.org/W2042722230","https://openalex.org/W2045443950","https://openalex.org/W2047905873","https://openalex.org/W2058839892","https://openalex.org/W2061680337","https://openalex.org/W2072857774","https://openalex.org/W2075379868","https://openalex.org/W2077788215","https://openalex.org/W2081098333","https://openalex.org/W2085309210","https://openalex.org/W2088879795","https://openalex.org/W2091975751","https://openalex.org/W2097065948","https://openalex.org/W2097117811","https://openalex.org/W2102938998","https://openalex.org/W2105776281","https://openalex.org/W2107233609","https://openalex.org/W2110065044","https://openalex.org/W2114104545","https://openalex.org/W2116166762","https://openalex.org/W2120695425","https://openalex.org/W2121211805","https://openalex.org/W2124985265","https://openalex.org/W2128114769","https://openalex.org/W2128243427","https://openalex.org/W2133203904","https://openalex.org/W2141425631","https://openalex.org/W2145416275","https://openalex.org/W2151238743","https://openalex.org/W2153220158","https://openalex.org/W2158297569","https://openalex.org/W2160697532","https://openalex.org/W2163415691","https://openalex.org/W2168720699","https://openalex.org/W2344240552","https://openalex.org/W2430931147","https://openalex.org/W2741340870","https://openalex.org/W2946039809","https://openalex.org/W3122709706"],"related_works":["https://openalex.org/W2795330452","https://openalex.org/W7120571200","https://openalex.org/W2750956634","https://openalex.org/W2181484905","https://openalex.org/W2086373695","https://openalex.org/W2101682408","https://openalex.org/W2245725572","https://openalex.org/W2611947405","https://openalex.org/W3032322340","https://openalex.org/W4290927905"],"abstract_inverted_index":{"This":[0,355],"thesis":[1],"discusses":[2],"modeling,":[3],"estimation":[4,282],"and":[5,18,24,156,180,228,367],"testing":[6,307,315],"methods":[7,83,258,386],"for":[8,63,114,168,183,207,234,236,249,259,264,289,306,309,317,329],"\u2018digital":[9],"gene":[10,80,97,116,128],"expression\u2019":[11],"(DGE)":[12],"data":[13,202,339,380],"developed":[14],"in":[15,26,100,129,220,239,272,297,321,387],"the":[16,27,35,38,43,52,91,122,130,148,157,201,209,225,245,250,256,261,265,273,284,301,330,335,360,382],"Walter":[17],"Eliza":[19],"Hall":[20],"Institute\u2019s":[21],"Bioinformatics":[22],"Division":[23],"implemented":[25],"software":[28],"package":[29],"edgeR.":[30],"The":[31,110,212,292],"race":[32],"to":[33,59,73,78,164,224,359,371],"complete":[34],"sequence":[36],"of":[37,45,90,93,107,112,121,126,153,170,172,195,244,252,276,283,337,362,384],"entire":[39],"human":[40],"genome":[41],"catalyzed":[42],"development":[44,361],"ultra":[46],"high-throughput":[47],"DNA":[48],"sequencing":[49],"technologies.":[50],"Over":[51],"last":[53],"decade,":[54],"these":[55,385],"technologies":[56],"have":[57,69],"proven":[58],"be":[60,205,346],"extremely":[61],"valuable":[62],"genomics,":[64],"their":[65],"original":[66],"application,":[67],"but":[68,187,255],"recently":[70],"been":[71,190],"shown":[72,191],"offer":[74],"a":[75,95,104,115,144,178,230,325,363],"powerful":[76],"approach":[77,233],"investigating":[79],"expression.":[81,311],"Sequencing":[82],"generate":[84],"DGE":[85,185,240,277,290,298,322,373,379],"data,":[86,186],"that":[87,127,160,192,343],"is,":[88],"\u2018counts\u2019":[89],"number":[92,111],"times":[94],"particular":[96],"is":[98,247],"detected":[99],"an":[101,118],"RNA":[102],"sample,":[103],"discrete":[105],"measure":[106],"expression":[108,124,167,320],"level.":[109],"counts":[113],"gives":[117],"excellent":[119],"indication":[120],"true":[123],"level":[125],"biological":[131,154,193,237],"sample.":[132],"Assessing":[133],"which":[134],"genes":[135,173],"are":[136,177,268],"differentially":[137],"expressed":[138],"between":[139],"experimental":[140],"groups":[141],"nevertheless":[142],"remains":[143],"difficult":[145],"problem,":[146],"given":[147],"small":[149,294],"sample":[150,295],"sizes":[151,296],"typical":[152],"experiments":[155,299],"multiple-testing":[158],"issues":[159],"arise":[161],"when":[162],"trying":[163],"assess":[165],"differential":[166,253,310,319],"tens":[169],"thousands":[171],"simultaneously.":[174],"Poisson":[175,210,226],"models":[176],"natural":[179],"popular":[181],"choice":[182],"modeling":[184,243,372],"it":[188],"has":[189,340,357],"replication":[194],"samples":[196],"introduces":[197],"greater":[198,218],"variability":[199],"into":[200],"than":[203],"can":[204,345],"accounted":[206],"using":[208],"model.":[211,332],"negative":[213],"binomial":[214],"(NB)":[215],"model":[216,267,366],"offers":[217],"flexibility":[219],"handling":[221],"overdispersion":[222],"relative":[223],"model,":[227],"represents":[229],"very":[231],"promising":[232],"accounting":[235],"variation":[238],"experiments.":[241,278],"Accurate":[242],"variance":[246],"vital":[248],"assessment":[251],"expression,":[254],"standard":[257],"estimating":[260],"dispersion":[262,285],"parameter":[263,286,365],"NB":[266,331],"not":[269],"satisfactory,":[270],"especially":[271],"small-sample":[274],"context":[275],"Conditional":[279],"maximum":[280],"likelihood":[281],"proves":[287],"superior":[288],"data.":[291,374],"typically":[293],"make":[300],"usual":[302],"asymptotic":[303],"tests":[304],"inadmissible":[305],"hypotheses":[308],"We":[312],"discuss":[313],"exact":[314,327],"procedures":[316],"assessing":[318],"experiments,":[323],"including":[324],"novel":[326],"test":[328],"Experience":[333],"from":[334],"analysis":[336],"microarray":[338],"taught":[341],"us":[342],"inference":[344],"improved":[347],"substantially":[348],"by":[349],"sharing":[350],"information":[351],"across":[352],"all":[353],"genes.":[354],"knowledge":[356],"led":[358],"common":[364],"empirical":[368],"Bayes":[369],"approaches":[370],"Case":[375],"studies":[376],"on":[377],"real":[378],"show":[381],"success":[383],"practice.":[388]},"counts_by_year":[],"updated_date":"2026-11-03T10:50:19.383937","created_date":"2016-06-24T00:00:00"}