Novel Molecular Networks and Regulatory MicroRNAs in Type 2 Diabetes Mellitus: Multiomics Integration and Interactomics Study.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38935970", "kind": "science-record", "revision": 3, "content_hash": "sha256:c7748b32212ff57b3014e23ef2c0dcb08748dd5d7d83e007fd0ff64775d6a4eb", "created_at": "2026-11-01T20:29:00Z", "updated_at": "2026-11-01T22:12:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Novel Molecular Networks and Regulatory MicroRNAs in Type 2 Diabetes Mellitus: Multiomics Integration and Interactomics Study.", "doi": "10.2196/32437", "pmid": "38935970", "authors": ["Manoj Khokhar", "Dipayan Roy", "Sojit Tomo", "Ashita Gadwal", "Praveen Sharma", "Purvi Purohit"], "journal": "JMIR bioinformatics and biotechnology", "year": 2022, "abstract": "BACKGROUND: Type 2 diabetes mellitus (T2DM) is a metabolic disorder with severe comorbidities. A multiomics approach can facilitate the identification of novel therapeutic targets and biomarkers with proper validation of potential microRNA (miRNA) interactions.\nOBJECTIVE: The aim of this study was to identify significant differentially expressed common target genes in various tissues and their regulating miRNAs from publicly available Gene Expression Omnibus (GEO) data sets of patients with T2DM using in silico analysis.\nMETHODS: Using differentially expressed genes (DEGs) identified from 5 publicly available T2DM data sets, we performed functional enrichment, coexpression, and network analyses to identify pathways, protein-protein interactions, and miRNA-mRNA interactions involved in T2DM.\nRESULTS: We extracted 2852, 8631, 5501, 3662, and 3753 DEGs from the expression profiles of GEO data sets GSE38642, GSE25724, GSE20966, GSE26887, and GSE23343, respectively. DEG analysis showed that 16 common genes were enriched in insulin secretion, endocrine resistance, and other T2DM-related pathways. Four DEGs, MAML3, EEF1D, NRG1, and CDK5RAP2, were important in the cluster network regulated by commonly targeted miRNAs (hsa-let-7b-5p, hsa-mir-155-5p, hsa-mir-124-3p, hsa-mir-1-3p), which are involved in the advanced glycation end products (AGE)-receptor for advanced glycation end products (RAGE) signaling pathway, culminating in diabetic complications and endocrine resistance.\nCONCLUSIONS: This study identified tissue-specific DEGs in T2DM, especially pertaining to the heart, liver, and pancreas. We identified a total of 16 common DEGs and the top four common targeting miRNAs (hsa-let-7b-5p, hsa-miR-124-3p, hsa-miR-1-3p, and has-miR-155-5p). The miRNAs identified are involved in regulating various pathways, including the phosphatidylinositol-3-kinase-protein kinase B, endocrine resistance, and AGE-RAGE signaling pathways.", "claims": [{"id": "claim-method", "statement": "The DEGs were obtained from the five data sets using the online interactive tool GEO2R [16]. The cutoff for the selection was kept at the default of P<.05. The meta-analysis was based on the functional modules with the MetaDE R package. For this study, we used the “effect size” parameter estimation with a fixed-effects model and an adjusted P value threshold of .05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38935970", "locator": "sections[5] \"Identification and Assortment of Differentially Expressed mRNAs\" paragraph 2", "quote": "The DEGs were obtained from the five data sets using the online interactive tool GEO2R [16]."}, {"asset": "source:pmid:38935970", "locator": "sections[5] \"Identification and Assortment of Differentially Expressed mRNAs\" paragraph 2", "quote": "The cutoff for the selection was kept at the default of P<.05."}, {"asset": "source:pmid:38935970", "locator": "sections[8] \"Integrative Gene Expression Meta-analysis\" paragraph 2", "quote": "The meta-analysis was based on the functional modules with the MetaDE R package."}, {"asset": "source:pmid:38935970", "locator": "sections[8] \"Integrative Gene Expression Meta-analysis\" paragraph 2", "quote": "For this study, we used the “effect size” parameter estimation with a fixed-effects model and an adjusted P value threshold of .05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38935970", "locator": "sections[3] \"Data Collection\" paragraph 2", "quote": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1)."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified a total of 16 common DEGs and the top four common targeting miRNAs (hsa-let-7b-5p, hsa-miR-124-3p, hsa-miR-1-3p, and has-miR-155-5p).", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38935970", "locator": "sections[0] \"Abstract\" paragraph 5", "quote": "We identified a total of 16 common DEGs and the top four common targeting miRNAs (hsa-let-7b-5p, hsa-miR-124-3p, hsa-miR-1-3p, and has-miR-155-5p)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We identified a total of 16 common DEGs and the top four common targeting miRNAs (hsa-let-7b-5p, hsa-miR-124-3p, hsa-miR-1-3p, and has-miR-155-5p).", "steps": [{"id": "read_published_estimate", "order": 1, "name": "Read the published estimate from the source", "kind": "other", "state": "complete", "blocked_on": null, "description": "The claim, method and evidence span published with the source article.", "duration_hours": null, "parameters": {}, "inputs": ["source:pmid:38935970"], "outputs": ["the published estimate and its evidence"], "instruments": [], "reagents": []}, {"id": "obtain_source_data", "order": 2, "name": "Obtain the source data from the named repository", "kind": "data-preparation", "state": "complete", "blocked_on": null, "description": "The GEO series accession resolves and its sample accessions are listed. This lane did not download the dataset or read its licence.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE20966"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:fixed_effects_pool", "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {"i_squared": "llowed by fixed-effects ImaGEO meta-analysis usin"}, "inputs": ["data:geo:GSE20966"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:fixed_effects_pool"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38935970", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2196/32437", "sha256": "sha256:abf7730f07582c4dfbff245238ec4fc570e5de292b16c97d5cf9895a4d1ea738", "bytes": 63878, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.2196/32437", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11135235", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE20966", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE20966", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE20966", "version": null, "note": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM524151", "GSM524152", "GSM524153", "GSM524154", "GSM524155", "GSM524156", "GSM524157", "GSM524158", "GSM524159", "GSM524160", "GSM524161", "GSM524162", "GSM524163", "GSM524164", "GSM524165", "GSM524166", "GSM524167", "GSM524168", "GSM524169", "GSM524170"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "1352", "taxon": "Homo sapiens", "title": "Gene expression profiles of beta-cell enriched tissue obtained by Laser Capture Microdissection from subjects with type 2 diabetes", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE23343", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE23343", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE23343", "version": null, "note": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM572800", "GSM572801", "GSM572802", "GSM572803", "GSM572804", "GSM572805", "GSM572806", "GSM572807", "GSM572808", "GSM572809", "GSM572810", "GSM572811", "GSM572812", "GSM572813", "GSM572814", "GSM572815", "GSM572816"], "sample_count": 17, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Expression data from human liver with or without type 2 diabetes", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE25724", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE25724", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25724", "version": null, "note": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM631755", "GSM631756", "GSM631757", "GSM631758", "GSM631759", "GSM631760", "GSM631761", "GSM631762", "GSM631763", "GSM631764", "GSM631765", "GSM631766", "GSM631767"], "sample_count": 13, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Expression data from type 2 diabetic and non-diabetic isolated human islets", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE26168", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26168", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26168", "version": null, "note": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM532819", "GSM532820", "GSM532821", "GSM532822", "GSM532823", "GSM532824", "GSM532825", "GSM532826", "GSM532827", "GSM532828", "GSM532829", "GSM532830", "GSM532831", "GSM532832", "GSM532833", "GSM532834", "GSM532835", "GSM532836", "GSM532837", "GSM532838", "GSM532839", "GSM532840", "GSM532841", "GSM532842", "GSM532843", "GSM532844", "GSM532845", "GSM532846", "GSM532847", "GSM532848", "GSM532849", "GSM532850", "GSM532851", "GSM532852", "GSM532853", "GSM532854", "GSM532855", "GSM532856", "GSM532857", "GSM532858", "GSM532859", "GSM532860", "GSM532861", "GSM532862", "GSM532863", "GSM532864", "GSM532865", "GSM532866", "GSM532867", "GSM532868", "GSM642434", "GSM642435", "GSM642436", "GSM642437", "GSM642438", "GSM642439", "GSM642440", "GSM642441", "GSM642442", "GSM642443"], "sample_count": 60, "group_sizes": null, "group_sizes_basis": null, "platform": "10322;6883", "taxon": "Homo sapiens; Human betaherpesvirus 5; Murid gammaherpesvirus 4; Betapolyomavirus hominis; Rattus norvegicus; Murid betaherpesvirus 1; JC polyomavirus; Human immunodeficiency virus 1; human gammaherpesvirus 4; Human gammaherpesvirus 8; Betapolyomavirus macacae; Mus musculus; Human alphaherpesvirus 1", "title": "Type 2 Diabetes mellitus: mRNA and miRNA profiling", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE26887", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE26887", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE26887", "version": null, "note": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM662158", "GSM662159", "GSM662160", "GSM662161", "GSM662162", "GSM662163", "GSM662164", "GSM662165", "GSM662166", "GSM662167", "GSM662168", "GSM662169", "GSM662170", "GSM662171", "GSM662172", "GSM662173", "GSM662174", "GSM662175", "GSM662176", "GSM662177", "GSM662178", "GSM662179", "GSM662180", "GSM662181"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Transcriptome analysis of diabetic and non diabetic patients affected by post-ischemic heart failure", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE38642", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE38642", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE38642", "version": null, "note": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM946700", "GSM946701", "GSM946702", "GSM946703", "GSM946704", "GSM946705", "GSM946706", "GSM946707", "GSM946708", "GSM946709", "GSM946710", "GSM946711", "GSM946712", "GSM946713", "GSM946714", "GSM946715", "GSM946716", "GSM946717", "GSM946718", "GSM946719", "GSM946720", "GSM946721", "GSM946722", "GSM946723", "GSM946724", "GSM946725", "GSM946726", "GSM946727", "GSM946728", "GSM946729", "GSM946730", "GSM946731", "GSM946732", "GSM946733", "GSM946734", "GSM946735", "GSM946736", "GSM946737", "GSM946738", "GSM946739", "GSM946740", "GSM946741", "GSM946742", "GSM946743", "GSM946744", "GSM946745", "GSM946746", "GSM946747", "GSM946748", "GSM946749", "GSM946750", "GSM946751", "GSM946752", "GSM946753", "GSM946754", "GSM946755", "GSM946756", "GSM946757", "GSM946758", "GSM946759", "GSM946760", "GSM946761", "GSM946762"], "sample_count": 63, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Expression data from human pancreatic islets", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE51674", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE51674", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE51674", "version": null, "note": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1).", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1581506", "GSM1581507", "GSM1581508", "GSM1581509", "GSM1581510", "GSM1581511", "GSM1581512", "GSM1581513", "GSM1581514", "GSM1581517", "GSM3181593", "GSM3181594", "GSM3181595", "GSM3181596", "GSM3181597", "GSM3181598"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "10656", "taxon": "Homo sapiens", "title": "miRNA-27b-3p and miRNA-1228-3p correlate with the progression of Kidney Fibrosis in Diabetic Nephropathy", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE20966 not downloaded", "asset:data:geo:GSE20966 licence not read", "asset:data:geo:GSE23343 not downloaded", "asset:data:geo:GSE23343 licence not read", "asset:data:geo:GSE25724 not downloaded", "asset:data:geo:GSE25724 licence not read", "asset:data:geo:GSE26168 not downloaded", "asset:data:geo:GSE26168 licence not read", "asset:data:geo:GSE26887 not downloaded", "asset:data:geo:GSE26887 licence not read", "asset:data:geo:GSE38642 not downloaded", "asset:data:geo:GSE38642 licence not read", "asset:data:geo:GSE51674 not downloaded", "asset:data:geo:GSE51674 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "meta_analysis", "specific": "fixed_effects", "label": "Meta-analysis / evidence synthesis", "dsl_operations": [], "missing_operations": ["fixed_effects_pool"], "expressible": false, "parameters": {"i_squared": "llowed by fixed-effects ImaGEO meta-analysis usin"}, "data_shapes": ["study_level_effect_estimates"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The DEGs were obtained from the five data sets using the online interactive tool GEO2R [16]. The cutoff for the selection was kept at the default of P<.05. The meta-analysis was based on the functional modules with the MetaDE R package. For this study, we used the “effect size” parameter estimation with a fixed-effects model and an adjusted P value threshold of .05."}}], "targets": [], "gaps": ["method.fixed_effects_pool"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": false, "required_operations": [], "missing_operations": ["fixed_effects_pool"], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: fixed_effects."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE38642", "GSE25724", "GSE20966", "GSE26887", "GSE23343", "GSE51674", "GSE26168"], "resolved_accessions": ["GSE38642", "GSE25724", "GSE20966", "GSE26887", "GSE23343", "GSE51674", "GSE26168"], "statements": ["We searched several keywords, including “type 2 diabetes mellitus,” “tissue,” “pancreas,” “liver,” “heart,” “expression profiling by array,” and “Homo sapiens,” in the GEO data sets, among which five were selected for this study: GSE38642 [9-11], GSE25724 [12], GSE20966 [13], GSE26887 [14], and GSE23343 [15] (Table 1)."], "basis": "The paper names GSE38642, GSE25724, GSE20966, GSE26887, GSE23343, GSE51674, GSE26168 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:38935970", "data:geo:GSE20966"], "steps": []}, "must_build": {"dsl_operations": [{"operation": "fixed_effects_pool", "unlocks_papers": null, "priority": null}], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE20966"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T19:22:41Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 19737, "completion_tokens": 2722, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:38935970", "type": "paper", "label": "pmid:38935970"}, {"id": "source:pmid:38935970", "type": "manuscript", "label": "PMID 38935970 full text"}, {"id": "data:geo:GSE20966", "type": "dataset", "label": "GEO GSE20966"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:38935970", "type": "paper", "label": "pmid:38935970"}, {"id": "source:pmid:38935970", "type": "manuscript", "label": "PMID 38935970 full text"}, {"id": "data:geo:GSE20966", "type": "dataset", "label": "GEO GSE20966"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-38935970", "type": "extraction", "used": ["source:pmid:38935970"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE20966", "type": "accession_resolution", "used": ["data:geo:GSE20966"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:38935970", "parent_hash": "sha256:b85391b7e69788d9decf8a6f89b0f682e5f7eaef8e676f81b1156267d09f8ad0", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE20966 licence not read", "asset:data:geo:GSE20966 not downloaded", "asset:data:geo:GSE23343 licence not read", "asset:data:geo:GSE23343 not downloaded", "asset:data:geo:GSE25724 licence not read", "asset:data:geo:GSE25724 not downloaded", "asset:data:geo:GSE26168 licence not read", "asset:data:geo:GSE26168 not downloaded", "asset:data:geo:GSE26887 licence not read", "asset:data:geo:GSE26887 not downloaded", "asset:data:geo:GSE38642 licence not read", "asset:data:geo:GSE38642 not downloaded", "asset:data:geo:GSE51674 licence not read", "asset:data:geo:GSE51674 not downloaded", "execution.not_run", "method.fixed_effects_pool", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:run_analysis blocked on method:fixed_effects_pool"], "assays": [{"role": "analysis", "definition_id": "meta_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The DEGs were obtained from the five data sets using the online interactive tool GEO2R [16]. The cutoff for the selection was kept at the default of P<.05. The meta-analysis was based on the functional modules with the MetaDE R package. For this study, we used the “effect size” parameter estimation with a fixed-effects model and an adjusted P value threshold of .05."], "order_basis": "analysis_only", "id": "assay:1"}]}