Bioinformatics Analysis Identified Five Widely Expressed Genes Associated with Prognosis in Sarcoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35414751", "kind": "science-record", "revision": 5, "content_hash": "sha256:c1f522a532b20aea977f5e91a24943c879c58e4d6e02334204ed231c9ded70a2", "created_at": "2026-11-01T18:14:14Z", "updated_at": "2026-11-01T22:48:49Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics Analysis Identified Five Widely Expressed Genes Associated with Prognosis in Sarcoma.", "doi": "10.2147/IJGM.S352048", "pmid": "35414751", "authors": ["Bizhi Tu", "Yaya Jia", "Jun Qian"], "journal": "International journal of general medicine", "year": 2022, "abstract": "Background: Human sarcomas (SARC) are a group of malignant tumors that originated from mesenchymal lineages with more than 60 subtypes. However, potential biomarkers for the diagnosis and prognosis of SARC remain to be investigated.\nMethods: We obtained three GSE raw matrix files (GSE39262, GSE21122, GSE48418) that related to various subtypes of sarcoma from the public GEO database and explored the widely differential expression genes in three obtained GSE files. Then common differential expression genes (CDGEs) were identified. We analyzed the correlation between the expression of the top five interacted genes of CDEGs and genome-wide differences, prognosis, genetic mutation, functional enrichment, immune infiltration, immune checkpoint, and marker genes' expression of N6-methyladenosine (m6A) modification in SARC patients. Besides, a prognostic nomogram was constructed to predict the survival of SARC patients.\nResults: Among the three GSE files, 42 CDGEs were identified, and the top five interacted genes were ASPM, CCNB2, PRC1, AURKA, and SCM2. The expression levels of the five genes were higher in the SARC group than that in the normal group. The transcriptional level of CCNB2, PRC, and SCM2 was correlated to the worse survival of SARC. The constructed nomogram that combined CNB2, PRC1, and SCM2 showed a fairly good incredibility in predicting the survival of SARC (C-index: 0.711). Furthermore, the five genes were widely involved in immune infiltration, immune checkpoint, and m6A modification. In addition, we found a minor survival-related mutation rate (9%) of the five identified genes in SARC patients (p < 0.05).\nConclusion: The results suggested the five identified genes widely participated in the prognosis, immune infiltration, immune checkpoint, and m6A modification of SARC patients. This study provided a theoretical basis for the research about the correlation between the level of five identified genes and sarcoma, but the further mechanism needs to be verified by experiments.", "claims": [{"id": "claim-method", "statement": "Utilizing the limma package in R software, the differential expression of various genes in each GSE profile were analyzed.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35414751", "locator": "sections[3] \"Identification of CDEGs from the GEO Database\" paragraph 2", "quote": "Utilizing the limma package in R software, the differential expression of various genes in each GSE profile were analyzed."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding authors upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35414751", "locator": "sections[22] \"Data Sharing Statement\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding authors upon reasonable request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Among the three GSE files, 42 CDGEs were identified, and the top five interacted genes were ASPM, CCNB2, PRC1, AURKA, and SCM2.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35414751", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Among the three GSE files, 42 CDGEs were identified, and the top five interacted genes were ASPM, CCNB2, PRC1, AURKA, and SCM2."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Among the three GSE files, 42 CDGEs were identified, and the top five interacted genes were ASPM, CCNB2, PRC1, AURKA, and SCM2.", "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:35414751"], "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:GSE21122"], "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:GSE21122"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35414751", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.2147/IJGM.S352048", "sha256": 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