Bioinformatics and Next-Generation Data Analysis for Identification of Genes and Molecular Pathways Involved in Subjects with Diabetes and Obesity.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36837510", "kind": "science-record", "revision": 4, "content_hash": "sha256:512aaf047a19962a6902b558864cf097fc01af07732457184bbf1586636f30f2", "created_at": "2026-11-01T19:01:27Z", "updated_at": "2026-11-01T22:51:22Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics and Next-Generation Data Analysis for Identification of Genes and Molecular Pathways Involved in Subjects with Diabetes and Obesity.", "doi": "10.3390/medicina59020309", "pmid": "36837510", "authors": ["Prashanth Ganekal", "Basavaraj Vastrad", "Satish Kavatagimath", "Chanabasayya Vastrad", "Shivakumar Kotrashetti"], "journal": "Medicina (Kaunas, Lithuania)", "year": 2023, "abstract": "Background and Objectives: A subject with diabetes and obesity is a class of the metabolic disorder. The current investigation aimed to elucidate the potential biomarker and prognostic targets in subjects with diabetes and obesity. Materials and Methods: The next-generation sequencing (NGS) data of GSE132831 was downloaded from Gene Expression Omnibus (GEO) database. Functional enrichment analysis of DEGs was conducted with ToppGene. The protein-protein interactions network, module analysis, target gene-miRNA regulatory network and target gene-TF regulatory network were constructed and analyzed. Furthermore, hub genes were validated by receiver operating characteristic (ROC) analysis. A total of 872 DEGs, including 439 up-regulated genes and 433 down-regulated genes were observed. Results: Second, functional enrichment analysis showed that these DEGs are mainly involved in the axon guidance, neutrophil degranulation, plasma membrane bounded cell projection organization and cell activation. The top ten hub genes (MYH9, FLNA, DCTN1, CLTC, ERBB2, TCF4, VIM, LRRK2, IFI16 and CAV1) could be utilized as potential diagnostic indicators for subjects with diabetes and obesity. The hub genes were validated in subjects with diabetes and obesity. Conclusion: This investigation found effective and reliable molecular biomarkers for diagnosis and prognosis by integrated bioinformatics analysis, suggesting new and key therapeutic targets for subjects with diabetes and obesity.", "claims": [{"id": "claim-method", "statement": "The limma R/Bioconductor software package was used to perform the identification of DEGs between samples of diabetic obese and normal control in R software [19].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36837510", "locator": "sections[4] \"2.2. Identification of DEGs\" paragraph 2", "quote": "The limma R/Bioconductor software package was used to perform the identification of DEGs between samples of diabetic obese and normal control in R software [19]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets supporting the conclusions of this article are available in the GEO (Gene Expression Omnibus) (https://www.ncbi.nlm.nih.gov/geo/, accessed on 11 June 2020) repository. [(GSE132831) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132831, accessed on 11 June 2020)].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36837510", "locator": "sections[24] \"Data Availability Statement\" paragraph 2", "quote": "The datasets supporting the conclusions of this article are available in the GEO (Gene Expression Omnibus) (https://www.ncbi.nlm.nih.gov/geo/, accessed on 11 June 2020) repository. [(GSE132831) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132831, accessed on 11 June 2020)]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 872 differentially expressed genes, comprising 439 up-regulated and 433 down-regulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36837510", "locator": "sections[11] \"3.1. Identification of DEGs\" paragraph 2", "quote": "The GSE132831 dataset contained 872 DEGs, including 439 up-regulated genes and 433 down-regulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 872 differentially expressed genes, comprising 439 up-regulated and 433 down-regulated genes.", "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:36837510"], "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:GSE132831"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "complete", "blocked_on": null, "description": "Apply the paper's statistical method to the resolved series and compare the result with the published target.", "duration_hours": null, "parameters": {}, "inputs": ["data:geo:GSE132831"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36837510", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/medicina59020309", "sha256": "sha256:c7a70286ba7bfd62434d2056b6e0b163012d87e6352e624c4969ce8f5eba0674", "bytes": 89043, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/medicina59020309", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9967176", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE132831", "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=GSE132831", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE132831", "version": null, "note": "The datasets supporting the conclusions of this article are available in the GEO (Gene Expression Omnibus) (https://www.ncbi.nlm.nih.gov/geo/, accessed on 11 June 2020) repository. [(GSE132831) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132831, accessed on 11 June 2020)].", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The datasets supporting the conclusions of this article are available in the GEO (Gene Expression Omnibus) (https://www.ncbi.nlm.nih.gov/geo/, accessed on 11 June 2020) repository. [(GSE132831) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132831, accessed on 11 June 2020)].", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM3893351", "GSM3893352", "GSM3893353", "GSM3893354", "GSM3893355", "GSM3893356", "GSM3893357", "GSM3893358", "GSM3893359", "GSM3893360", "GSM3893361", "GSM3893362", "GSM3893363", "GSM3893364", "GSM3893365", "GSM3893366", "GSM3893367", "GSM3893368", "GSM3893369", "GSM3893370", "GSM3893371", "GSM3893372", "GSM3893373", "GSM3893374", "GSM3893375", "GSM3893376", "GSM3893377", "GSM3893378", "GSM3893379", "GSM3893380", "GSM3893381", "GSM3893382", "GSM3893383", "GSM3893384", "GSM3893385", "GSM3893386", "GSM3893387", "GSM3893388", "GSM3893389", "GSM3893390", "GSM3893391", "GSM3893392", "GSM3893393", "GSM3893394", "GSM3893395", "GSM3893396", "GSM3893397", "GSM3893398", "GSM3893399", "GSM3893400", "GSM3893401", "GSM3893402", "GSM3893403", "GSM3893404", "GSM3893405", "GSM3893406", "GSM3893407", "GSM3893408", "GSM3893409", "GSM3893410", "GSM3893411", "GSM3893412", "GSM3893413", "GSM3893414", "GSM3893415", "GSM3893416", "GSM3893417", "GSM3893418", "GSM3893419", "GSM3893420", "GSM3893421", "GSM3893422", "GSM3893423", "GSM3893424", "GSM3893425", "GSM3893426", "GSM3893427", "GSM3893428", "GSM3893429", "GSM3893430", "GSM3893431", "GSM3893432", "GSM3893433", "GSM3893434", "GSM3893435", "GSM3893436", "GSM3893437", "GSM3893438", "GSM3893439", "GSM3893440", "GSM3893441", "GSM3893442", "GSM3893443", "GSM3893444", "GSM3893445", "GSM3893446", "GSM3893447", "GSM3893448", "GSM3893449", "GSM3893450", "GSM3893451", "GSM3893452", "GSM3893453", "GSM3893454", "GSM3893455", "GSM3893456", "GSM3893457", "GSM3893458", "GSM3893459", "GSM3893460", "GSM3893461", "GSM3893462", "GSM3893463", "GSM3893464", "GSM3893465", "GSM3893466", "GSM3893467", "GSM3893468", "GSM3893469", "GSM3893470", "GSM3893471", "GSM3893472", "GSM3893473", "GSM3893474", "GSM3893475", "GSM3893476", "GSM3893477", "GSM3893478", "GSM3893479", "GSM3893480", "GSM3893481", "GSM3893482", "GSM3893483", "GSM3893484", "GSM3893485", "GSM3893486", "GSM3893487", "GSM3893488", "GSM3893489", "GSM3893490", "GSM3893491", "GSM3893492", "GSM3893493", "GSM3893494", "GSM3893495", "GSM3893496", "GSM3893497", "GSM3893498", "GSM3893499", "GSM3893500", "GSM3893501", "GSM3893502", "GSM3893503", "GSM3893504", "GSM3893505", "GSM3893506", "GSM3893507", "GSM3893508", "GSM3893509", "GSM3893510", "GSM3893511", "GSM3893512", "GSM3893513", "GSM3893514", "GSM3893515", "GSM3893516", "GSM3893517", "GSM3893518", "GSM3893519", "GSM3893520", "GSM3893521", "GSM3893522", "GSM3893523", "GSM3893524", "GSM3893525", "GSM3893526", "GSM3893527", "GSM3893528", "GSM3893529", "GSM3893530", "GSM3893531", "GSM3893532", "GSM3893533", "GSM3893534", "GSM3893535", "GSM3893536", "GSM3893537", "GSM3893538", "GSM3893539", "GSM3893540", "GSM3893541", "GSM3893542", "GSM3893543", "GSM3893544", "GSM3893545", "GSM3893546", "GSM3893547", "GSM3893548", "GSM3893549", "GSM3893550", "GSM3893551", "GSM3893552", "GSM3893553", "GSM3893554", "GSM3893555", "GSM3893556", "GSM3893557", "GSM3893558", "GSM3893559", "GSM3893560", "GSM3893561", "GSM3893562", "GSM3893563", "GSM3893564", "GSM3893565", "GSM3893566", "GSM3893567", "GSM3893568", "GSM3893569", "GSM3893570", "GSM3893571", "GSM3893572", "GSM3893573", "GSM3893574"], "sample_count": 224, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Type 2 Diabetes reduces the enteroendocrine GLP-1 cell lineage in human obesity:  characterization in enriched human enteroendocrine cells", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE132831 not downloaded", "asset:data:geo:GSE132831 licence not read"]}, "analysis": {"state": "complete", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The limma R/Bioconductor software package was used to perform the identification of DEGs between samples of diabetic obese and normal control in R software [19]."}}], "targets": [], "gaps": []}, "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": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "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": ["GSE132831"], "resolved_accessions": ["GSE132831"], "statements": ["The datasets supporting the conclusions of this article are available in the GEO (Gene Expression Omnibus) (https://www.ncbi.nlm.nih.gov/geo/, accessed on 11 June 2020) repository. [(GSE132831) (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132831, accessed on 11 June 2020)]."], "basis": "The paper names GSE132831 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": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36837510", "data:geo:GSE132831"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE132831"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:31:40Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 29698, "completion_tokens": 1145, "cached_tokens": 128}}, "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:36837510", "type": "paper", "label": "pmid:36837510"}, {"id": "source:pmid:36837510", "type": "manuscript", "label": "PMID 36837510 full text"}, {"id": "data:geo:GSE132831", "type": "dataset", "label": "GEO GSE132831"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36837510", "type": "paper", "label": "pmid:36837510"}, {"id": "source:pmid:36837510", "type": "manuscript", "label": "PMID 36837510 full text"}, {"id": "data:geo:GSE132831", "type": "dataset", "label": "GEO GSE132831"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36837510", "type": "extraction", "used": ["source:pmid:36837510"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE132831", "type": "accession_resolution", "used": ["data:geo:GSE132831"], "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:36837510", "parent_hash": "sha256:1afc233f0932a2a55c443185017f14174ce6a0255f15cf2d845966987d608190", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE132831 licence not read", "asset:data:geo:GSE132831 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "amplicon_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["etes and obesity. Materials and Methods: The next-generation sequencing (NGS) data of GSE132831 was downloaded from", "and Methods: The next-generation sequencing (NGS) data of GSE132831 was downloaded from Gene"], "order_basis": "paper_text_order:362", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The limma R/Bioconductor software package was used to perform the identification of DEGs between samples of diabetic obese and normal control in R software [19]."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}