The identification of key genes and pathways in glioblastoma by bioinformatics analysis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37593751", "kind": "science-record", "revision": 3, "content_hash": "sha256:fcd15d9074664868c1726e5cd9e8f7a89432be09b346476851331417af8c7084", "created_at": "2026-11-01T19:02:23Z", "updated_at": "2026-11-01T22:10:07Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The identification of key genes and pathways in glioblastoma by bioinformatics analysis.", "doi": "10.1080/23723556.2023.2246657", "pmid": "37593751", "authors": ["Zahra Farsi", "Najaf Allahyari Fard"], "journal": "Molecular & cellular oncology", "year": 2023, "abstract": "GBM is the most common and aggressive type of brain tumor. It is classified as a grade IV tumor by the WHO, the highest grade. Prognosis is generally poor, with most patients surviving only about a year. Only 5% of patients survive longer than 5 years. Understanding the molecular mechanisms that drive GBM progression is critical for developing better diagnostic and treatment strategies. Identifying key genes involved in GBM pathogenesis is essential to fully understand the disease and develop targeted therapies. In this study two datasets, GSE108474 and GSE50161, were obtained from the Gene Expression Omnibus (GEO) to compare gene expression between GBM and normal samples. Differentially expressed genes (DEGs) were identified and analyzed. To construct a protein-protein interaction (PPI) network of the commonly up-regulated and down-regulated genes, the STRING 11.5 and Cytoscape 3.9.1 were utilized. Key genes were identified through this network analysis. The GEPIA database was used to confirm the expression levels of these key genes and their association with survival. Functional and pathway enrichment analyses on the DEGs were conducted using the Enrichr server. In total, 698 DEGs were identified, consisting of 377 up-regulated genes and 318 down-regulated genes. Within the PPI network, 11 key up-regulated genes and 13 key down-regulated genes associated with GBM were identified. NOTCH1, TOP2A, CD44, PTPRC, CDK4, HNRNPU, and PDGFRA were found to be important targets for potential drug design against GBM. Additionally, functional enrichment analysis revealed the significant impact of Epstein-Barr virus (EBV), Cell Cycle, and P53 signaling pathways on GBM.", "claims": [{"id": "claim-method", "statement": "To identify differentially expressed genes (DEGs) between GBM samples and normal samples, we utilized GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r). Genes with significant differential expression were selected based on the criteria of adjusted P-value <.05 and logFC > 1.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37593751", "locator": "sections[2] \"Material and method\" paragraph 2", "quote": "To identify differentially expressed genes (DEGs) between GBM samples and normal samples, we utilized GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r). Genes with significant differential expression were selected based on the criteria of adjusted P-value <.05 and logFC > 1."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE108474 contained 219 samples, including 28 normal samples, while GSE5016134 had GBM samples and 13 normal samples.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37593751", "locator": "sections[2] \"Material and method\" paragraph 2", "quote": "GSE108474 contained 219 samples, including 28 normal samples, while GSE5016134 had GBM samples and 13 normal samples."}], "state": "complete"}, {"id": "claim-target-result", "statement": "In total, 698 DEGs were identified, consisting of 377 up-regulated genes and 318 down-regulated genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37593751", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "In total, 698 DEGs were identified, consisting of 377 up-regulated genes and 318 down-regulated genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "In total, 698 DEGs were identified, consisting of 377 up-regulated genes and 318 down-regulated genes.", "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:37593751"], "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:GSE108474"], "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:GSE108474"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:37593751", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1080/23723556.2023.2246657", "sha256": "sha256:cca037fc7495378e1ae2e983423b46475a6d47ea4e97f9982cb2d661f7e7db1b", "bytes": 44268, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1080/23723556.2023.2246657", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC10431734", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE108474", "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=GSE108474", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE108474", "version": null, "note": "GSE108474 contained 219 samples, including 28 normal samples, while GSE5016134 had GBM samples and 13 normal samples.", 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"band": "verbatim", "quote": "To identify differentially expressed genes (DEGs) between GBM samples and normal samples, we utilized GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r). Genes with significant differential expression were selected based on the criteria of adjusted P-value <.05 and logFC > 1."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE108474", "GSE50161"], "resolved_accessions": ["GSE108474", "GSE50161"], "statements": ["GSE108474 contained 219 samples, including 28 normal samples, while GSE5016134 had GBM samples and 13 normal samples."], "basis": "The paper names GSE108474, GSE50161 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": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:37593751", "data:geo:GSE108474"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE108474"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:51:01Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 12348, "completion_tokens": 1509, "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:37593751", "type": "paper", "label": "pmid:37593751"}, {"id": "source:pmid:37593751", "type": "manuscript", "label": "PMID 37593751 full text"}, {"id": "data:geo:GSE108474", "type": "dataset", "label": "GEO GSE108474"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:37593751", "type": "paper", "label": "pmid:37593751"}, {"id": "source:pmid:37593751", "type": "manuscript", "label": "PMID 37593751 full text"}, {"id": "data:geo:GSE108474", "type": "dataset", "label": "GEO GSE108474"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-37593751", "type": "extraction", "used": ["source:pmid:37593751"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE108474", "type": "accession_resolution", "used": ["data:geo:GSE108474"], "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:37593751", "parent_hash": "sha256:167ba72db591085b714da4a4ff89beee92796c005042345ba8403ccd9f063c72", "fork_of": null, "generation": 2}, "gaps": ["asset:data:geo:GSE108474 licence not read", "asset:data:geo:GSE108474 not downloaded", "asset:data:geo:GSE50161 licence not read", "asset:data:geo:GSE50161 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["al and method In this study, we selected two microarray profiles from the GEO database with access c", "ples. Both datasets were generated using the Affymetrix Human U133 Plus 2.0 array platform. To ident"], "order_basis": "paper_text_order:1780", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["protein-protein interaction"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}