Identification of Novel Genes and Associated Drugs in Cervical Cancer by Bioinformatics Methods.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35428744", "kind": "science-record", "revision": 4, "content_hash": "sha256:7b03c7d3bf531dfb73ed8c20f9c7f94fcd5fa98d897c16399fd000a043c69a4e", "created_at": "2026-11-01T18:14:15Z", "updated_at": "2026-11-01T22:06:18Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Novel Genes and Associated Drugs in Cervical Cancer by Bioinformatics Methods.", "doi": "10.12659/MSM.934799", "pmid": "35428744", "authors": ["Dan Wang", "Yanling Liu", "Shuyu Cheng", "Guoyan Liu"], "journal": "Medical science monitor : international medical journal of experimental and clinical research", "year": 2022, "abstract": "BACKGROUND Cervical cancer is one of the common gynecological tumors that seriously harm women's health, so it is particularly important to accurately explore the underlying mechanism of its occurrence and clinical prognosis. MATERIAL AND METHODS In the GEO database, GEO2R was used to analyze the differentially expressed genes from the 4 databases: GSE6791, GSE9750, GSE63514, and GSE67522. Then, the DAVID website was used to perform Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses. These protein-protein interaction (PPI) networks of DEGS were visualized and analyzed using the STRING website and the hub genes were further screened using the Cytohubba plugin. Lastly, the functions of the hub genes were further analyzed by Gene Expression Profiling Interactive Analysis (GEPIA) online tools, Human Protein Atlas (HPA) databases, and the QuartataWeb database. RESULTS In the 4 Profile datasets, 101 cancer tissues and 67 normal tissues were collected. Among the 78 differentially expressed genes in the 4 datasets, 51 genes were upregulated and 27 genes were downregulated. The PPIs of these differentially expressed genes were visualized using Cytoscape and the Interaction Gene Search Tool (STRING). Then, further analysis of hub genes using the GEPIA tool and Kaplan-Meier curves that showed upregulation of CDK1 and PRC1 is associated with better survival, while AURKA is associated with worse survival. Among these hub genes, only AURKA was closely related to the prognosis of cervical cancer, and 21 potential drugs were found. CONCLUSIONS These results suggest that AURKA and its drug candidates can improve the individualized diagnosis and treatment of cervical cancer in the future.", "claims": [{"id": "claim-method", "statement": "DEGs between cervical cancer specimens and normal specimens were identified via GEO2R online tools (https://www.ncbi.nlm.nih.gov/geo/geo2r/). The |logFC| ≥1.5 and adjusted P value <0.05 were set as the cut-off criteria.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35428744", "locator": "sections[4] \"Data Identification of DEGs\" paragraph 2", "quote": "DEGs between cervical cancer specimens and normal specimens were identified via GEO2R online tools (https://www.ncbi.nlm.nih.gov/geo/geo2r/). The |logFC| ≥1.5 and adjusted P value <0.05 were set as the cut-off criteria."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Among the 78 differentially expressed genes in the 4 datasets, 51 genes were upregulated and 27 genes were downregulated.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35428744", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Among the 78 differentially expressed genes in the 4 datasets, 51 genes were upregulated and 27 genes were downregulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Among the 78 differentially expressed genes in the 4 datasets, 51 genes were upregulated and 27 genes were downregulated.", "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:35428744"], "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": "blocked", "blocked_on": "data:accession_absent", "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": [], "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": [], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:obtain_source_data blocked on data:accession_absent"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35428744", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.12659/MSM.934799", "sha256": "sha256:efbabc7eb0db6cb59bf80e66967b1479c84130b74d864ea8fc93b092c5224480", "bytes": 26703, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.12659/MSM.934799", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9020271", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}], "gaps": []}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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-2", "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"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.8, "band": "high", "quote": "GO enrichment"}}, {"id": "method-4", "family": null, "specific": null, "label": "GEO2R", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "DEGs between cervical cancer specimens and normal specimens were identified via GEO2R online tools (https://www.ncbi.nlm.nih.gov/geo/geo2r/). The |logFC| ≥1.5 and adjusted P value <0.05 were set as the cut-off criteria."}}], "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": "blocked", "tier": "R4", "blocking_axis": "data", "blocked_on": "data:accession_absent", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": "R4", "reachable": false, "accessions": [], "resolved_accessions": [], "statements": [], "basis": "The paper names no accession to its source data, so the data has to come from the authors."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:35428744"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:None"]}, "gaps": ["data:accession_absent"]}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:42:10Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 7799, "completion_tokens": 2917, "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:35428744", "type": "paper", "label": "pmid:35428744"}, {"id": "source:pmid:35428744", "type": "manuscript", "label": "PMID 35428744 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35428744", "type": "paper", "label": "pmid:35428744"}, {"id": "source:pmid:35428744", "type": "manuscript", "label": "PMID 35428744 full text"}, {"id": "data:geo:None", "type": "dataset", "label": "GEO None"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35428744", "type": "extraction", "used": ["source:pmid:35428744"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-None", "type": "accession_resolution", "used": ["data:geo:None"], "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:35428744", "parent_hash": "sha256:99bf6dc6d4d7e5d32c8b0d9be1d4be6f242e68a552acabce2784c0e6164f3d9f", "fork_of": null, "generation": 3}, "gaps": ["execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique", "step:obtain_source_data blocked on data:accession_absent"], "assays": [{"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["l cancer tissues and normal tissues by using immunohistochemical data from the HPA database. Function and Pro"], "order_basis": "paper_text_order:2619", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}