Gene expression profiles analysis identifies a novel two-gene signature to predict overall survival in diffuse large B-cell lymphoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:30393234", "kind": "science-record", "revision": 7, "content_hash": "sha256:d973b1b04929bdec0cf7d962e22ec92308b7994a3e60b964b7f466ec3cb33889", "created_at": "2026-11-01T15:40:38Z", "updated_at": "2026-11-01T22:00:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene expression profiles analysis identifies a novel two-gene signature to predict overall survival in diffuse large B-cell lymphoma.", "doi": "10.1042/BSR20181293", "pmid": "30393234", "authors": ["Chengtao Sun", "Xianfeng Cheng", "Chaoyu Wang", "Xi Wang", "Bing Xia", "Yizhuo Zhang"], "journal": "Bioscience reports", "year": 2019, "abstract": "Diffuse large B-cell lymphoma (DLBCL) is the most common hematologic malignancy, however, specific tumor-associated genes and signaling pathways are yet to be deciphered. Differentially expressed genes (DEGs) were computed based on gene expression profiles from GSE32018, GSE56315, and The Cancer Genome Atlas (TCGA) DLBC. Overlapping DEGs were then evaluated for gene ontology (GO), pathways enrichment, DNA methylation, protein-protein interaction (PPI) network analysis as well as survival analysis. Seventy-four up-regulated and 79 down-regulated DEGs were identified. From PPI network analysis, majority of the DEGs were involved in cell cycle, oocyte meiosis, and epithelial-to-mesenchymal transition (EMT) pathways. Six hub genes including CDC20, MELK, PBK, prostaglandin D2 synthase (PTGDS), PCNA, and CDK1 were selected using the Molecular Complex Detection (MCODE). CDC20 and PTGDS were able to predict overall survival (OS) in TCGA DLBC and in an additional independent cohort GSE31312. Furthermore, CDC20 DNA methylation negatively regulated CDC20 expression and was able to predict OS in DLBCL. A two-gene panel consisting of CDC20 and PTGDS had a better prognostic value compared with CDC20 or PTGDS alone in the TCGA cohort (P=0.026 and 0.039). Overall, the present study identified a set of novel genes and pathways that may play a significant role in the initiation and progression of DLBCL. In addition, CDC20 and PTGDS will provide useful guidance for therapeutic applications.", "claims": [{"id": "claim-method", "statement": "The receiver operating characteristic (ROC) curve was used to assess the diagnostic effectiveness of the identified hub genes between DLBCL and normal tissue, and was based on the GSE56315 dataset.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30393234", "locator": "sections[6] \"Validation of the diagnostic effectiveness of the identified hub genes for DLBCL\" paragraph 2", "quote": "The receiver operating characteristic (ROC) curve was used to assess the diagnostic effectiveness of the identified hub genes between DLBCL and normal tissue, and was based on the GSE56315 dataset."}], "state": "complete"}, {"id": "claim-data-access", "statement": "All data were extracted from previously published freely available datasets.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:30393234", "locator": "sections[19] \"Data availability\" paragraph 2", "quote": "All data were extracted from previously published freely available datasets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:30393234"], "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. 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"title": "Diffuse Large B-Cell Lymphoma Classification System That Associates Normal B-Cell Subset Phenotypes With Prognosis", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:30393234:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:a3cc75fcdc6f68af5ee5c75555703baf640161c530b24b439b2a0235d66c3e6d", "bytes": 1462, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#T1", "version": null, "note": "GO analysis of DEGs associated with DLBCL", "structure": {"pmcid": "PMC6328866", "section_index": 11, "section_title": "Functional enrichment analysis of DEGs in DLBCL", "row_count": 25, "column_count": 4}, "table": {"label": "Table 1", "caption": "GO analysis of DEGs associated with DLBCL", 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