{"id":"https://openalex.org/W7225311674","doi":"https://doi.org/10.20944/preprints202611.0483.v1","title":"Contrast In Transcriptomic Associations Between Type 2 Diabetes and Insulin Resistance in Human Subcutaneous Adipose Tissue: An Exploratory Re-Analysis of Two Public Microarray Cohorts","display_name":"Contrast In Transcriptomic Associations Between Type 2 Diabetes and Insulin Resistance in Human Subcutaneous Adipose Tissue: An Exploratory Re-Analysis of Two Public Microarray Cohorts","publication_year":2026,"publication_date":"2026-11-05","ids":{"openalex":"https://openalex.org/W7225311674","doi":"https://doi.org/10.20944/preprints202611.0483.v1"},"language":"en","primary_location":{"id":"doi:10.20944/preprints202611.0483.v1","doi":"https://doi.org/10.20944/preprints202611.0483.v1","is_oa":true,"landing_page_url":"https://doi.org/10.20944/preprints202611.0483.v1","pdf_url":null,"source":{"id":"https://openalex.org/S6309402219","display_name":"Preprints.org","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.20944/preprints202611.0483.v1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5160883666","display_name":"Tejas Menneni","orcid":null,"observed_orcids":[]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Tejas Menneni","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5160883666"],"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/T10528","display_name":"Adipokines, Inflammation, and Metabolic Diseases","score":0.8823000192642212,"subfield":{"id":"https://openalex.org/subfields/2712","display_name":"Endocrinology, Diabetes and Metabolism"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T10528","display_name":"Adipokines, Inflammation, and Metabolic Diseases","score":0.8823000192642212,"subfield":{"id":"https://openalex.org/subfields/2712","display_name":"Endocrinology, Diabetes and Metabolism"},"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/T11457","display_name":"Adipose Tissue and Metabolism","score":0.0649000033736229,"subfield":{"id":"https://openalex.org/subfields/2737","display_name":"Physiology (medical)"},"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/T10885","display_name":"Gene expression and cancer classification","score":0.010499999858438969,"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/type-2-diabetes","display_name":"type 2 diabetes","score":0.9959999918937683},{"id":"https://openalex.org/keywords/insulin-resistance","display_name":"insulin resistance","score":1.0},{"id":"https://openalex.org/keywords/subcutaneous-adipose-tissue","display_name":"subcutaneous adipose tissue","score":0.9980000257492065},{"id":"https://openalex.org/keywords/differential-gene-expression","display_name":"differential gene expression","score":0.9549999833106995},{"id":"https://openalex.org/keywords/cohort-heterogeneity","display_name":"cohort heterogeneity","score":0.5370000004768372},{"id":"https://openalex.org/keywords/sex-adjustment","display_name":"sex adjustment","score":0.6480000019073486},{"id":"https://openalex.org/keywords/classification-performance","display_name":"classification performance","score":0.6389999985694885},{"id":"https://openalex.org/keywords/adipose-tissue-transcriptome","display_name":"adipose tissue transcriptome","score":0.414000004529953}],"concepts":[{"id":"https://openalex.org/C193244246","wikidata":"https://www.wikidata.org/wiki/Q5432696","display_name":"False discovery rate","level":3,"score":0.7188000082969666},{"id":"https://openalex.org/C2777180221","wikidata":"https://www.wikidata.org/wiki/Q3025883","display_name":"Type 2 diabetes","level":3,"score":0.664900004863739},{"id":"https://openalex.org/C2777391703","wikidata":"https://www.wikidata.org/wiki/Q1053470","display_name":"Insulin resistance","level":3,"score":0.6452999711036682},{"id":"https://openalex.org/C186836561","wikidata":"https://www.wikidata.org/wiki/Q1931516","display_name":"Microarray","level":4,"score":0.6039999723434448},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.5533000230789185},{"id":"https://openalex.org/C8415881","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Microarray analysis techniques","level":4,"score":0.5250999927520752},{"id":"https://openalex.org/C77360908","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Significance analysis of microarrays","level":5,"score":0.5034999847412109},{"id":"https://openalex.org/C171089720","wikidata":"https://www.wikidata.org/wiki/Q193583","display_name":"Adipose tissue","level":2,"score":0.4788999855518341},{"id":"https://openalex.org/C95371953","wikidata":"https://www.wikidata.org/wiki/Q591745","display_name":"DNA microarray","level":4,"score":0.46480000019073486},{"id":"https://openalex.org/C151956035","wikidata":"https://www.wikidata.org/wiki/Q1132755","display_name":"Logistic regression","level":2,"score":0.4494999945163727},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.43140000104904175},{"id":"https://openalex.org/C18431079","wikidata":"https://www.wikidata.org/wiki/Q1502169","display_name":"Gene expression profiling","level":4,"score":0.4171000123023987},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.40070000290870667},{"id":"https://openalex.org/C126322002","wikidata":"https://www.wikidata.org/wiki/Q11180","display_name":"Internal medicine","level":1,"score":0.3824000060558319},{"id":"https://openalex.org/C183905921","wikidata":"https://www.wikidata.org/wiki/Q1038757","display_name":"Multiple comparisons problem","level":2,"score":0.3799999952316284},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.37860000133514404},{"id":"https://openalex.org/C71924100","wikidata":"https://www.wikidata.org/wiki/Q11190","display_name":"Medicine","level":0,"score":0.3767000138759613},{"id":"https://openalex.org/C555293320","wikidata":"https://www.wikidata.org/wiki/Q12206","display_name":"Diabetes mellitus","level":2,"score":0.35580000281333923},{"id":"https://openalex.org/C127716648","wikidata":"https://www.wikidata.org/wiki/Q104053","display_name":"Phenotype","level":3,"score":0.3547999858856201},{"id":"https://openalex.org/C24361400","wikidata":"https://www.wikidata.org/wiki/Q6839217","display_name":"Gene chip analysis","level":5,"score":0.3537999987602234},{"id":"https://openalex.org/C77350462","wikidata":"https://www.wikidata.org/wiki/Q1125472","display_name":"Confounding","level":2,"score":0.34860000014305115},{"id":"https://openalex.org/C143998085","wikidata":"https://www.wikidata.org/wiki/Q162555","display_name":"Oncology","level":1,"score":0.33239999413490295},{"id":"https://openalex.org/C150194340","wikidata":"https://www.wikidata.org/wiki/Q26972","display_name":"Gene expression","level":3,"score":0.3301999866962433},{"id":"https://openalex.org/C104317684","wikidata":"https://www.wikidata.org/wiki/Q7187","display_name":"Gene","level":2,"score":0.3294999897480011},{"id":"https://openalex.org/C2776502983","wikidata":"https://www.wikidata.org/wiki/Q690182","display_name":"Contrast (vision)","level":2,"score":0.3215999901294708},{"id":"https://openalex.org/C2910068830","wikidata":"https://www.wikidata.org/wiki/Q3025883","display_name":"Type 2 Diabetes Mellitus","level":3,"score":0.3075999915599823},{"id":"https://openalex.org/C117220453","wikidata":"https://www.wikidata.org/wiki/Q5172842","display_name":"Correlation","level":2,"score":0.3000999987125397},{"id":"https://openalex.org/C148483581","wikidata":"https://www.wikidata.org/wiki/Q446488","display_name":"Feature selection","level":2,"score":0.2904999852180481},{"id":"https://openalex.org/C54355233","wikidata":"https://www.wikidata.org/wiki/Q7162","display_name":"Genetics","level":1,"score":0.27810001373291016},{"id":"https://openalex.org/C21308566","wikidata":"https://www.wikidata.org/wiki/Q7169365","display_name":"Permutation (music)","level":2,"score":0.26820001006126404},{"id":"https://openalex.org/C2776401178","wikidata":"https://www.wikidata.org/wiki/Q12050496","display_name":"Feature (linguistics)","level":2,"score":0.25540000200271606},{"id":"https://openalex.org/C145059251","wikidata":"https://www.wikidata.org/wiki/Q310899","display_name":"microRNA","level":3,"score":0.2533999979496002}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.20944/preprints202611.0483.v1","doi":"https://doi.org/10.20944/preprints202611.0483.v1","is_oa":true,"landing_page_url":"https://doi.org/10.20944/preprints202611.0483.v1","pdf_url":null,"source":{"id":"https://openalex.org/S6309402219","display_name":"Preprints.org","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.20944/preprints202611.0483.v1","doi":"https://doi.org/10.20944/preprints202611.0483.v1","is_oa":true,"landing_page_url":"https://doi.org/10.20944/preprints202611.0483.v1","pdf_url":null,"source":{"id":"https://openalex.org/S6309402219","display_name":"Preprints.org","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":["https://openalex.org/P4310310987"],"host_organization_lineage_names":["Multidisciplinary Digital Publishing Institute"],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[{"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3","score":0.9537000060081482}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2392771535","https://openalex.org/W324522532","https://openalex.org/W2355391594","https://openalex.org/W4385501910","https://openalex.org/W4403148715","https://openalex.org/W2367193359","https://openalex.org/W2883814301","https://openalex.org/W4322501042","https://openalex.org/W1974520367","https://openalex.org/W2092854273"],"abstract_inverted_index":{"Insulin":[0],"resistance":[1],"has":[2],"a":[3,79,124,141],"key":[4],"role":[5],"in":[6,16,41,46,147,193,206,221,236,244,253,286,296],"type":[7],"2":[8],"diabetes":[9],"(T2D).":[10],"However,":[11,262],"there":[12],"may":[13],"be":[14],"differences":[15,40,324],"transcriptomic":[17],"associations":[18],"of":[19,177,190,203,249,277],"these":[20,339],"phenotypes":[21],"within":[22],"different":[23,303],"studies.":[24],"Here":[25],"we":[26,273],"re-analysed":[27],"data":[28,58],"from":[29,34,59,71,112],"GSE27951":[30,60,113,287],"and":[31,50,61,84,92,157,179,223,251,257,279,323],"GSE20950":[32,62],"microarrays":[33],"adipose":[35,98],"tissue":[36,99],"to":[37,159,167,174],"understand":[38,51,175],"the":[39,72,135,144,187,200,212,219,282,294,307],"differential":[42,80,121],"expression,":[43],"find":[44],"overlaps":[45],"differentially":[47],"expressed":[48],"genes":[49],"classification":[52,161,178,240,268],"performance.":[53,162],"We":[54,77,119,128,139,163],"retrieved":[55],"pre-processed":[56],"microarray":[57],"using":[63,123,134,241,269],"Affymetrix":[64],"Human":[65],"Genome":[66],"U133":[67],"Plus":[68],"2.0":[69],"arrays":[70],"Gene":[73],"Expression":[74],"Omnibus":[75],".":[76],"performed":[78,120,129,140,153,164],"expression":[81,122,148],"between":[82,325],"T2D":[83,194,222,254],"NGT":[85,256],"(n":[86],"=":[87,103],"10":[88,106],"vs":[89,95,101,105,195,208,255,259],"11":[90],"samples)":[91],"insulin":[93],"resistant":[94],"sensitive":[96],"subcutaneous":[97],"(IR":[100],"IS)(n":[102],"9":[104],"samples).":[107],"3":[108,283],"samples":[109],"were":[110,226,234],"removed":[111],"as":[114],"they":[115],"had":[116],"conflicting":[117,284],"annotations.":[118],"probe-wise":[125],"welch":[126],"test.":[127],"false":[130],"discovery":[131],"rate":[132],"correction":[133],"Benjamini":[136],"Hochberg":[137],"method.":[138],"threshold":[142,189,202,215],"on":[143,267],"absolute":[145],"difference":[146],"(log2(1.5)).":[149],"Logistic":[150],"regression":[151],"was":[152],"with":[154],"feature":[155,242],"selection":[156,243],"scaling":[158],"explore":[160],"additional":[165],"analysis":[166],"account":[168],"for":[169,230,318,337],"sex,":[170,319],"perform":[171],"permutation":[172,265],"tests":[173,266],"significance":[176],"look":[180],"at":[181],"alternative":[182],"annotation.":[183],"No":[184],"probes":[185,198,217,225,233,292],"met":[186,199,218],"FDR":[188,201,295],"<":[191,204],"0.05":[192,205],"NGT.":[196],"13,124":[197],"IR":[207,258],"IS.":[209],"Once":[210,228],"adding":[211],"effect":[213],"size":[214],"no":[216],"criteria":[220],"3,501":[224],"selected.":[227],"adjusting":[229],"sex":[231],"3,356":[232],"selected":[235],"IR.":[237],"Cross":[238],"validated":[239,350],"training":[245],"gave":[246],"AUC":[247,334],"values":[248],"0.818":[250],"1.000":[252],"IS":[260],"respectively.":[261],"once":[263],"performing":[264],"100":[270],"label":[271],"shuffles":[272],"found":[274],"empirical":[275],"p-values":[276],"0.0495":[278],"0.0099.":[280],"Changing":[281],"annotations":[285],"did":[288],"not":[289,342],"give":[290],"any":[291],"meeting":[293],"T2D.":[297],"The":[298,311],"two":[299],"cohorts":[300,326],"produced":[301,332],"substantially":[302],"differential-expression":[304],"results":[305],"under":[306],"implemented":[308],"analytical":[309],"workflow.":[310],"large":[312],"IR-associated":[313],"signal":[314],"persisted":[315],"after":[316],"adjustment":[317],"but":[320],"technical":[321],"confounding":[322],"remain":[327],"unresolved.":[328],"Although":[329],"internal":[330],"cross-validation":[331],"high":[333],"values,":[335],"particularly":[336],"IR,":[338],"findings":[340],"do":[341],"establish":[343],"external":[344],"predictive":[345],"validity":[346],"or":[347],"identify":[348],"clinically":[349],"biomarkers.":[351],"Further":[352],"independent":[353],"validation":[354],"is":[355],"required.":[356]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-11-06T00:00:00"}