Identification of novel candidate genes and small molecule drugs in ovarian cancer by bioinformatics strategy.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35836518", "kind": "science-record", "revision": 4, "content_hash": "sha256:3aaca492f855b57948309d7abbbf4e8f93e230c3db532994337d6c3a912b7352", "created_at": "2026-11-01T18:14:54Z", "updated_at": "2026-11-01T22:07:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of novel candidate genes and small molecule drugs in ovarian cancer by bioinformatics strategy.", "doi": "10.21037/tcr-21-2890", "pmid": "35836518", "authors": ["Min Wei", "Xuefei Bai", "Qiaomei Dong"], "journal": "Translational cancer research", "year": 2022, "abstract": "Background: Ovarian cancer (OC) is the most lethal type of malignancies in the female reproductive system. This study aimed to identify novel biomarkers and potential small molecule drugs in OC by integrating two expression profile datasets.\nMethods: GSE18520 and GSE14407 from the Gene Expression Omnibus (GEO) database were selected and the overlapped differentially expressed genes (DEGs) were detected. The Gene Ontology (GO) analysis and Kyoto Encyclopedia of Genes and Genome (KEGG) pathway enrichment analysis were performed to establish the protein-protein interaction (PPI) network of DEGs and identified the hub genes. Gene Expression Profiling Interactive Analysis (GEPIA), Oncomine database and The Human Protein Atlas (HPA) were used to validate the expression of the identified hub genes. The prognostic value of these hub genes were evaluated by the Kaplan Meier plotter online tool. The expression of NCAPG was further explored by immunohistochemistry in our OC tissues. Moreover, CMap database was used to look for prospective small compounds with therapeutic efficacy based on OC RNA-seq.\nResults: A total of 433 DEGs were identified. The DEGs were mainly enriched in negative regulation of transcription and pathways in cancer. A PPI network was constructed with 344 nodes and 1,596 interactions. The top ten module genes were chosen as hub genes. Among which, survival analysis showed that patients with high expression of CCNB1, TOP2A, NUSAP1, NCAPG, KIF20A and DLGAP5 had poorer survival results than those with low expression. These six genes were all overexpressed in OC tissue by means of bioinformatics analysis. In our clinical patients, the expression rate of NCAPG in OC tissues was significantly higher than that in benign serous ovarian cystadenoma and borderline serous ovarian cystadenoma tissues. Meanwhile, several small molecules with potential therapeutic efficacy against OC were identified in our study.\nConclusions: By means of bioinformatics analysis, we identified six real hub genes and indicated a group of candidate small molecule drugs as adjunctive agents for OC. They could be the potential novel biomarkers for the diagnosis and promising therapeutic targets of OC.", "claims": [{"id": "claim-method", "statement": "The GEO2R online tools were utilized to identify the DEGs between OC samples and normal tissue samples with the cutoff threshold of adjust P<0.05 and |log2(fold change)| >2. Chi-square test was used to analyze the difference between three groups.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35836518", "locator": "sections[4] \"Data preprocessing and DEGs screening\" paragraph 2", "quote": "The GEO2R online tools were utilized to identify the DEGs between OC samples and normal tissue samples with the cutoff threshold of adjust P<0.05 and |log2(fold change)| >2."}, {"asset": "source:pmid:35836518", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "Chi-square test was used to analyze the difference between three groups."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-21-2890/dss", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35836518", "locator": "sections[22] \"fn-group\" paragraph 1", "quote": "Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-21-2890/dss"}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 433 DEGs were identified.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35836518", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "A total of 433 DEGs were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 433 DEGs were identified.", "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:35836518"], "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:GSE14407"], "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:GSE14407"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35836518", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tcr-21-2890", "sha256": "sha256:598f12deda27fbb32f3a6bec0d7cc348b9ad0e1788acf3b311a531f0f63c1bd9", "bytes": 28117, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tcr-21-2890", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9273707", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE14407", "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=GSE14407", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE14407", "version": null, "note": "Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-21-2890/dss", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-21-2890/dss", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM359972", "GSM359973", "GSM359974", "GSM359975", "GSM359976", "GSM359977", "GSM359978", "GSM359979", "GSM359980", "GSM359981", "GSM359982", "GSM359983", "GSM359984", "GSM360039", "GSM360040", "GSM360041", "GSM360042", "GSM360043", "GSM360044", "GSM360045", "GSM360046", "GSM360047", "GSM360048", "GSM360049"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Ovarian Cancer gene expression profiling identifies the surface of the ovary as a stem cell niche", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE18520", "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=GSE18520", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE18520", "version": null, "note": "Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-21-2890/dss", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-21-2890/dss", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM461348", "GSM461349", "GSM461350", "GSM461351", "GSM461352", "GSM461353", "GSM461354", "GSM461355", "GSM461356", "GSM461357", "GSM461358", "GSM461359", "GSM461360", "GSM461361", "GSM461362", "GSM461363", "GSM461364", "GSM461365", "GSM461366", "GSM461367", "GSM461368", "GSM461369", "GSM461370", "GSM461371", "GSM461372", "GSM461373", "GSM461374", "GSM461375", "GSM461376", "GSM461377", "GSM461378", "GSM461379", "GSM461380", "GSM461381", "GSM461382", "GSM461383", "GSM461384", "GSM461385", "GSM461386", "GSM461387", "GSM461388", "GSM461389", "GSM461390", "GSM461391", "GSM461392", "GSM461393", "GSM461394", "GSM461395", "GSM461396", "GSM461397", "GSM461398", "GSM461399", "GSM461400", "GSM462643", "GSM462644", "GSM462645", "GSM462646", "GSM462647", "GSM462648", "GSM462649", "GSM462650", "GSM462651", "GSM462652"], "sample_count": 63, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Whole-genome oligonucleotide expression analysis of papillary serous ovarian adenocarcinomas", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE14407 not downloaded", "asset:data:geo:GSE14407 licence not read", "asset:data:geo:GSE18520 not downloaded", "asset:data:geo:GSE18520 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "contingency_analysis", "specific": "chi_square", "label": "Categorical (contingency table) analysis", "dsl_operations": ["chi_square_test"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["categorical_cross_tabulation"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The GEO2R online tools were utilized to identify the DEGs between OC samples and normal tissue samples with the cutoff threshold of adjust P<0.05 and |log2(fold change)| >2. Chi-square test was used to analyze the difference between three groups."}}, {"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": "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-4", "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": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "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": ["chi_square_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: chi_square."}, "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": ["GSE18520", "GSE14407"], "resolved_accessions": ["GSE18520", "GSE14407"], "statements": ["Data Sharing Statement: Available at https://tcr.amegroups.com/article/view/10.21037/tcr-21-2890/dss"], "basis": "The paper names GSE18520, GSE14407 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": ["chi_square_test"], "assets": ["source:pmid:35836518", "data:geo:GSE14407"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14407"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:55:12Z", "independence": "single_reader"}, "evidence_check": {"method": "reordered", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8275, "completion_tokens": 1751, "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:35836518", "type": "paper", "label": "pmid:35836518"}, {"id": "source:pmid:35836518", "type": "manuscript", "label": "PMID 35836518 full text"}, {"id": "data:geo:GSE14407", "type": "dataset", "label": "GEO GSE14407"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:35836518", "type": "paper", "label": "pmid:35836518"}, {"id": "source:pmid:35836518", "type": "manuscript", "label": "PMID 35836518 full text"}, {"id": "data:geo:GSE14407", "type": "dataset", "label": "GEO GSE14407"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-35836518", "type": "extraction", "used": ["source:pmid:35836518"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14407", "type": "accession_resolution", "used": ["data:geo:GSE14407"], "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:35836518", "parent_hash": "sha256:382015d107b5620413561da338dae9ef9bb381b9a530e5a70d95cef2062c6617", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE14407 licence not read", "asset:data:geo:GSE14407 not downloaded", "asset:data:geo:GSE18520 licence not read", "asset:data:geo:GSE18520 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": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["expression of NCAPG was further explored by immunohistochemistry in our OC tissues. Moreover, CMap database w", "on of NCAPG in different ovarian tissues The immunohistochemical analysis of NCAPG in serous ovarian cancer."], "order_basis": "paper_text_order:1014", "id": "assay:1"}, {"role": "data_generation", "definition_id": "rna_seq", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["pounds with therapeutic efficacy based on OC RNA-seq. Results: A total of 433 DEGs were identifie"], "order_basis": "paper_text_order:1164", "id": "assay:2"}, {"role": "analysis", "definition_id": "contingency_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["chi_square_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["The GEO2R online tools were utilized to identify the DEGs between OC samples and normal tissue samples with the cutoff threshold of adjust P<0.05 and |log2(fold change)| >2. Chi-square test was used to analyze the difference between three groups."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}