Bioinformatics analysis of the prognostic biomarkers and predictive accuracy of differentially expressed genes in high-risk multiple myeloma based on Gene Expression Omnibus database mining.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36660705", "kind": "science-record", "revision": 4, "content_hash": "sha256:f4987e1b2ec23fd24847e4379abb5d11f47fbefb3b934d02452e2df43a46c559", "created_at": "2026-11-01T19:01:13Z", "updated_at": "2026-11-01T22:51:04Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis of the prognostic biomarkers and predictive accuracy of differentially expressed genes in high-risk multiple myeloma based on Gene Expression Omnibus database mining.", "doi": "10.21037/atm-22-2656", "pmid": "36660705", "authors": ["Chenxiao Du", "Dongmei Guo", "Yuhui Zhang", "Chao Gao", "Jie Bai"], "journal": "Annals of translational medicine", "year": 2022, "abstract": "Background: Multiple myeloma (MM) is still an intractable disease for modern clinical system, and more researches are necessary for development of more effective therapeutic strategies. This study attempted to screen and validates the biomarkers in the progression of MM via excavating Gene Expression Omnibus (GEO) database. Identification of a biomarker may help not only facilitate early diagnosis and management but also identify individuals at risk for poor prognosis and development of MM.\nMethods: The mRNA expression profile of the GSE87900 dataset was analyzed by GEO2R. Using the SangerBox online program, differentially expressed genes (DEGs) in high-risk MM samples were screened with the filter criteria of P<0.05 and |logFC| >1. The SangerBox online analysis tool was used to analyze the volcano plot. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis was performed for DEGs. Twenty patients with high-risk MM and 20 patients with standard-risk MM from Taian City Central Hospital were included. Real-time quantitative polymerase chain reaction (RT-qPCR) was used to verify the selected key genes in MM tissues.\nResults: A total of 611 DEGs were obtained. GO functional enrichment analysis showed that the DEGs were mainly enriched in the DNA replication process at the biological level, and the top DEGs were CACYBP, PCNA, MCM6, SMC1A, DTL, GINS4, MCM2, CDT1, RRM2, BRCA1, RFC5, MCM4, GINS3, GINS1, MCM10, CDC7, CDAN1, BRIP1, GINS2, CDK1, NFIB, and BARD1. The expression of CDC7 and PCNA was significantly different in high-risk MM and standard-risk MM as determined by RT-qPCR. Receiver operating characteristic (ROC) analysis showed that the areas under the curve predicted by CDC7 and PCNA were 0.900 and 0.8863, respectively, which allowed the identification of CDC7 and PCNA could be a potential biomarker of MM. Kaplan-Meier survival analysis showed that MM patients with high CDC7 and PCNA expression had shorter 2-year overall survival (OS) (P<0.05).\nConclusions: CDC7 and PCNA can be used as biomarkers for the prognosis of high-risk MM and evaluate the prognosis of MM patients, which is helpful for guiding the clinical treatment of MM patients.", "claims": [{"id": "claim-method", "statement": "DEGs of high-risk MM were analyzed using online analytical tools GEO2 R (http://www.ncbi.nlm.nih.gov/geo/geo2r/), which is based on GEOquery (12), and limma (13).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36660705", "locator": "sections[4] \"Analysis of DEGs\" paragraph 2", "quote": "DEGs of high-risk MM were analyzed using online analytical tools GEO2 R (http://www.ncbi.nlm.nih.gov/geo/geo2r/), which is based on GEOquery (12), and limma (13)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Sharing Statement: Available at https://atm.amegroups.com/article/view/10.21037/atm-22-2656/dss", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36660705", "locator": "sections[22] \"Footnotes\" paragraph 2", "quote": "Data Sharing Statement: Available at https://atm.amegroups.com/article/view/10.21037/atm-22-2656/dss"}], "state": "complete"}, {"id": "claim-target-result", "statement": "CDC7 and PCNA can be used as biomarkers for the prognosis of high-risk MM and evaluate the prognosis of MM patients, which is helpful for guiding the clinical treatment of MM patients.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36660705", "locator": "sections[0] \"Abstract\" paragraph 4", "quote": "CDC7 and PCNA can be used as biomarkers for the prognosis of high-risk MM and evaluate the prognosis of MM patients, which is helpful for guiding the clinical treatment of MM patients."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "CDC7 and PCNA can be used as biomarkers for the prognosis of high-risk MM and evaluate the prognosis of MM patients, which is helpful for guiding the clinical treatment of MM patients.", "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:36660705"], "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:GSE87900"], "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:GSE87900"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36660705", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/atm-22-2656", "sha256": 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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:36660705", "data:geo:GSE87900"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE87900"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:23:43Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8341, "completion_tokens": 1180, "cached_tokens": 264}}, "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:36660705", "type": "paper", "label": "pmid:36660705"}, {"id": "source:pmid:36660705", "type": "manuscript", "label": "PMID 36660705 full text"}, {"id": "data:geo:GSE87900", "type": "dataset", "label": "GEO GSE87900"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36660705", "type": "paper", "label": "pmid:36660705"}, {"id": "source:pmid:36660705", "type": "manuscript", "label": "PMID 36660705 full text"}, {"id": "data:geo:GSE87900", "type": "dataset", "label": "GEO GSE87900"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36660705", "type": "extraction", "used": ["source:pmid:36660705"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE87900", "type": "accession_resolution", "used": ["data:geo:GSE87900"], "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:36660705", "parent_hash": "sha256:9ef8155abc86649f643c4b05e23ebb174fec5bc5ec370895cc467ee908023a04", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE87900 licence not read", "asset:data:geo:GSE87900 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["time quantitative polymerase chain reaction (RT-qPCR) was used to verify the selected key genes i", "isk MM and standard-risk MM as determined by RT-qPCR. Receiver operating characteristic (ROC) ana", "e quantitative polymerase chain reaction (RT-qPCR) was used to verify the selected key genes i", "MM and standard-risk MM as determined by RT-qPCR. Receiver operating characteristic (ROC) ana"], "order_basis": "paper_text_order:1246", "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": ["DEGs of high-risk MM were analyzed using online analytical tools GEO2 R (http://www.ncbi.nlm.nih.gov/geo/geo2r/), which is based on GEOquery (12), and limma (13)."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}