Exploring the common targets of well-differentiated and dedifferentiated retroperitoneal liposarcoma via gene co-expression analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39430534", "kind": "science-record", "revision": 3, "content_hash": "sha256:272a4498933be1bf30006b97a80cb4e2dcce9e6e1b2bed6e543c2d14e1e2b4f2", "created_at": "2026-11-01T20:29:41Z", "updated_at": "2026-11-01T22:12:58Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Exploring the common targets of well-differentiated and dedifferentiated retroperitoneal liposarcoma via gene co-expression analysis.", "doi": "10.1016/j.heliyon.2024.e38825", "pmid": "39430534", "authors": ["Jialiang Zheng", "Zhenhang Lin", "Zhe Xi", "Yilai Gao", "Yingxue Cheng", "Yihao Li", "Ting Wu", "Wengang Li"], "journal": "Heliyon", "year": 2024, "abstract": "Objective: This study aimed to identify common therapeutic targets for well-differentiated and dedifferentiated retroperitoneal liposarcoma.\nMethods: Patient clinical data were obtained from the Surveillance, Epidemiology, and End Results (SEER) database, and survival differences were analyzed using the log-rank test. Gene expression data were sourced from the Gene Expression Omnibus (GEO) dataset GSE159659, with differential gene expression analysis conducted through GEO2R. Protein-protein interaction networks were developed using STRING and Cytoscape to identify key hub genes. Gene Ontology (GO) and KEGG pathway enrichment analyses were performed using R, and transcription factors associated with the hub genes were predicted with TRRUST.\nResults: Significant survival differences were found between patients with well-differentiated and dedifferentiated retroperitoneal liposarcoma. Ninety-six differentially expressed genes with similar expression patterns were identified in both types. A protein-protein interaction network highlighted 12 hub genes and 24 transcription factors. Enrichment analysis pointed to the importance of lipid localization, storage, cytokine signaling, and metal ion absorption in both liposarcoma subtypes. Four potential therapeutic drugs were successfully predicted.\nConclusion: This study identifies common molecular targets in well-differentiated and dedifferentiated retroperitoneal liposarcoma, providing new avenues for mechanistic studies and potential therapeutic development.", "claims": [{"id": "claim-method", "statement": "Survival differences between patients with well-differentiated and dedifferentiated RPLS were evaluated using the log-rank test, with a significance level set at p < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39430534", "locator": "sections[4] \"Statistics\" paragraph 2", "quote": "Survival differences between patients with well-differentiated and dedifferentiated RPLS were evaluated using the log-rank test, with a significance level set at p < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data pertaining to the SEER can be accessed through the SEER program database (https://seer.cancer.gov/), while genetic information is available in the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/), Cellminer database address is https://discover.nci.nih.gov/cellminer/home.do.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39430534", "locator": "sections[11] \"Data availability statement\" paragraph 2", "quote": "Data pertaining to the SEER can be accessed through the SEER program database (https://seer.cancer.gov/), while genetic information is available in the Gene Expression Omnibus (GEO) database (https://www.ncbi.nlm.nih.gov/geo/), Cellminer database address is https://discover.nci.nih.gov/cellminer/home.do."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "", "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:39430534"], "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:GSE159659"], "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:GSE159659"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39430534", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1016/j.heliyon.2024.e38825", "sha256": "sha256:b9022208e567fb205f905db2824232f9ef82601123ca313e44ae0be1fe02c1c2", "bytes": 24679, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1016/j.heliyon.2024.e38825", "version": null, "note": "Full article fetched from PMC; 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