Identification of a three-gene-based prognostic model in multiple myeloma using bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34249481", "kind": "science-record", "revision": 8, "content_hash": "sha256:cae101f7dfaa796bc991908faa85f55687d4c8bc69756bcb266c5db20dd0d3aa", "created_at": "2026-11-01T15:41:42Z", "updated_at": "2026-11-01T22:47:03Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of a three-gene-based prognostic model in multiple myeloma using bioinformatics analysis.", "doi": "10.7717/peerj.11320", "pmid": "34249481", "authors": ["Ying Pan", "Ye Meng", "Zhimin Zhai", "Shudao Xiong"], "journal": "PeerJ", "year": 2021, "abstract": "BACKGROUND: Multiple myeloma (MM), the second most hematological malignancy, has high incidence and remains incurable till now. The pathogenesis of MM is poorly understood. This study aimed to identify novel prognostic model for MM on gene expression profiles.\nMETHODS: Gene expression datas of MM (GSE6477, GSE136337) were downloaded from Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) in GSE6477 between case samples and normal control samples were screened by the limma package. Meanwhile, enrichment analysis was conducted, and a protein-protein interaction (PPI) network of these DEGs was established by STRING and cytoscape software. Co-expression modules of genes were built by Weighted Correlation Network Analysis (WGCNA). Key genes were identified both from hub genes and the DEGs. Univariate and multivariate Cox congression were performed to screen independent prognostic genes to construct a predictive model. The predictive power of the model was evaluated by Kaplan-Meier curve and time-dependent receiver operating characteristic (ROC) curves. Finally, univariate and multivariate Cox regression analyse were used to investigate whether the prognostic model could be independent of other clinical parameters.\nRESULTS: GSE6477, including 101 case and 15 normal control, were screened as the datasets. A total of 178 DEGs were identified, including 59 up-regulated and 119 down-regulated genes. In WGCNA analysis, module black and module purple were the most relevant modules with cancer traits, and 92 hub genes in these two modules were selected for further analysis. Next, 47 genes were chosen both from the DEGs and hub genes as key genes. Three genes (LYVE1, RNASE1, and RNASE2) were finally screened by univariate and multivariate Cox regression analyses and used to construct a risk model. In addition, the three-gene prognostic model revealed independent and accurate prognostic capacity in relation to other clinical parameters for MM patients.\nCONCLUSION: In summary, we identified and constructed a three-gene-based prognostic model that could be used to predict overall survival of MM patients.", "claims": [{"id": "claim-method", "statement": "Limma package was used to identify differentially expressed genes (DEGs) (Ritchie et al., 2015), and the threshod value was |log2foldchange| >1.0 and adj.P.Val <0.05. The raw data of GSE6477 and GSE136337 were downloaded from the gene expression omnibus (GEO) website (http://www.ncbi.nlm.nlh.gov/geo/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34249481", "locator": "sections[4] \"Analysis of differentially expressed genes (DEGs)\" paragraph 2", "quote": "Limma package was used to identify differentially expressed genes (DEGs) (Ritchie et al., 2015), and the threshod value was |log2foldchange| >1.0 and adj.P.Val <0.05."}, {"asset": "source:pmid:34249481", "locator": "sections[3] \"Data preparation\" paragraph 2", "quote": "The raw data of GSE6477 and GSE136337 were downloaded from the gene expression omnibus (GEO) website (http://www.ncbi.nlm.nlh.gov/geo/)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The raw data of GSE6477 and GSE136337 were downloaded from the gene expression omnibus (GEO) website. Series matrix were downloaded in GSE136337 for validation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34249481", "locator": "sections[18] \"Additional Information and Declarations\" paragraph 4", "quote": "The raw data of GSE6477 and GSE136337 were downloaded from the gene expression omnibus (GEO) website. Series matrix were downloaded in GSE136337 for validation."}], "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:34249481"], "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:GSE136337"], "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:GSE136337"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34249481", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.11320", "sha256": "sha256:27c3c91dca28df34c97d7611e221712cd94378adc653e3d61596b78e6770cbfe", "bytes": 24756, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.11320", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8247704", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE136337", "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=GSE136337", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE136337", "version": null, "note": "The raw data of GSE6477 and GSE136337 were downloaded from the gene expression omnibus (GEO) website. 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The raw data of GSE6477 and GSE136337 were downloaded from the gene expression omnibus (GEO) website (http://www.ncbi.nlm.nlh.gov/geo/)."}}, {"id": "method-2", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"id": "method-3", "family": "survival_analysis", "specific": "cox_proportional_hazards", "label": "Survival analysis", "dsl_operations": ["cox_ph"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Cox regression"}}, {"id": "method-4", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE6477", "GSE136337"], "resolved_accessions": ["GSE6477", "GSE136337"], "statements": ["The raw data of GSE6477 and GSE136337 were downloaded from the gene expression omnibus (GEO) website. Series matrix were downloaded in GSE136337 for validation."], "basis": "The paper names GSE6477, GSE136337 in gene expression omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:34249481", "data:geo:GSE136337", "asset:table:pmid:34249481:1"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE136337"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:32:00Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 18914, "completion_tokens": 1147, "cached_tokens": 792}}, "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:34249481", "type": "paper", "label": "pmid:34249481"}, {"id": "source:pmid:34249481", "type": "manuscript", "label": "PMID 34249481 full text"}, {"id": "data:geo:GSE136337", "type": "dataset", "label": "GEO GSE136337"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34249481", "type": "paper", "label": "pmid:34249481"}, {"id": "source:pmid:34249481", "type": "manuscript", "label": "PMID 34249481 full text"}, {"id": "data:geo:GSE136337", "type": "dataset", "label": "GEO GSE136337"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34249481", "type": "extraction", "used": ["source:pmid:34249481"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE136337", "type": "accession_resolution", "used": ["data:geo:GSE136337"], "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:34249481", "parent_hash": "sha256:7d6753dfd2b76c9391875bf44e401730f0114be44495ac38c7e792ea5c3369a3", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE136337 licence not read", "asset:data:geo:GSE136337 not downloaded", "asset:data:geo:GSE6477 licence not read", "asset:data:geo:GSE6477 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["Limma package was used to identify differentially expressed genes (DEGs) (Ritchie et al., 2015), and the threshod value was |log2foldchange| >1.0 and adj.P.Val <0.05. The raw data of GSE6477 and GSE136337 were downloaded from the gene expression omnibus (GEO) website (http://www.ncbi.nlm.nlh.gov/geo/)."], "order_basis": "analysis_only", "id": "assay:1"}]}