Identification of metastasis and prognosis-associated genes for serous ovarian cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32510146", "kind": "science-record", "revision": 8, "content_hash": "sha256:adedd5e491c48527a0a685f614e7381fba30af349dc45b30e1e0a56d1a927235", "created_at": "2026-11-01T15:41:03Z", "updated_at": "2026-11-01T22:44:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of metastasis and prognosis-associated genes for serous ovarian cancer.", "doi": "10.1042/BSR20194324", "pmid": "32510146", "authors": ["Yijun Yang", "Suwan Qi", "Can Shi", "Xiao Han", "Juanpeng Yu", "Lei Zhang", "Shanshan Qin", "Yingchun Gao"], "journal": "Bioscience reports", "year": 2020, "abstract": "Serous ovarian cancer is one of the most fatal gynecological tumors with an extremely low 5-year survival rate. Most patients are diagnosed at an advanced stage with wide metastasis. The dysregulation of genes serves an important role in the metastasis progression of ovarian cancer. Differentially expressed genes (DEGs) between primary tumors and metastases of serous ovarian cancer were screened out in the gene expression profile of GSE73168 from Gene Expression Omnibus (GEO). Cytoscape plugin cytoHubba and weighted gene co-expression network analysis (WGCNA) were utilized to select hub genes. Univariate and multivariate Cox regression analyses were used to screen out prognosis-associated genes. Furthermore, the Oncomine validation, prognostic analysis, methylation mechanism, gene set enrichment analysis (GSEA), TIMER database analysis and administration of candidate molecular drugs were conducted for hub genes. Nine hundred and fifty-seven DEGs were identified in the gene expression profile of GSE73168. After using Cytoscape plugin cytoHubba, 83 genes were verified. In co-expression network, the blue module was most closely related to tumor metastasis. Furthermore, the genes in Cytoscape were analyzed, showing that the blue module and screened 17 genes were closely associated with tumor metastasis. Univariate and multivariate Cox regression revealed that the age, stage and STMN2 were independent prognostic factors. The Cancer Genome Atlas (TCGA) suggested that the up-regulated expression of STMN2 was related to poor prognosis of ovarian cancer. Thus, STMN2 was considered as a new key gene after expression validation, survival analysis and TIMER database validation. GSEA confirmed that STMN2 was probably involved in ECM receptor interaction, focal adhesion, TGF beta signaling pathway and MAPK signaling pathway. Furthermore, three candidate small molecule drugs for tumor metastasis (diprophylline, valinomycin and anisomycin) were screened out. The quantitative reverse transcription-polymerase chain reaction (qRT-PCR) and western blot showed that STMN2 was highly expressed in ovarian cancer tissue and ovarian cancer cell lines. Further studies are needed to investigate these prognosis-associated genes for new therapy target.", "claims": [{"id": "claim-method", "statement": "The raw dataset of GS73168 was analyzed with the GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/), a web tool using ‘limma’ package of R and utilized to screen DEGs between primary and metastasis tumor tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32510146", "locator": "sections[4] \"Identification of differentially expressed genes\" paragraph 2", "quote": "The raw dataset of GS73168 was analyzed with the GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/), a web tool using ‘limma’ package of R and utilized to screen DEGs between primary and metastasis tumor tissues."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used in the current study are available from the Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov) and Cancer Genome Atlas database (https://cancergenome.nih.gov).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32510146", "locator": "sections[35] \"Data Availability\" paragraph 2", "quote": "The data used in the current study are available from the Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov) and Cancer Genome Atlas database (https://cancergenome.nih.gov)."}], "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:32510146"], "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:GSE73168"], "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:GSE73168"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32510146", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1042/BSR20194324", "sha256": "sha256:dbaf5892e3ad89b64da8d08ab892e81542b7e35b33e919468e1b66c5fb5cfae3", "bytes": 35091, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1042/BSR20194324", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7317593", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE73168", "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=GSE73168", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE73168", "version": null, "note": "The data used in the current study are available from the Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov) and Cancer Genome Atlas database (https://cancergenome.nih.gov).", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used in the current study are available from the Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov) and Cancer Genome Atlas database (https://cancergenome.nih.gov).", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1881598", "GSM1881599", "GSM1881600", "GSM1881601", "GSM1881602", "GSM1881603", "GSM1881604", "GSM1881605", "GSM1881606", "GSM1881607", "GSM1881608", "GSM1881609", "GSM1881610", "GSM1881611", "GSM1881612", "GSM1885279", "GSM1885280", "GSM1885281", "GSM1885282", "GSM1885283", "GSM1885284", "GSM1885285", "GSM1885286", "GSM1885287"], "sample_count": 24, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression profile of tumor cells from primary tumors, ascites and metastases of high and low grade serous ovarian cancer patients", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:32510146:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:7ad17d3de6139f370dfed7f48bb4ccc39a6ea52dce5845a8934a044fe1299682", "bytes": 652, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[25]/table-wrap[1]#T1", "version": null, "note": "Univariate and multivariate Cox regression analysis for STMN2 and clinical features", "structure": {"pmcid": "PMC7317593", "section_index": 25, "section_title": "Prognostic analysis of hub gene", "row_count": 6, "column_count": 7}, "table": {"label": "Table 1", "caption": "Univariate and multivariate Cox regression analysis for STMN2 and clinical features", "rows": [["", "Univariate analysis", "Multivariate analysis"], ["Variables", "HR", "95% CI", "P-value", "HR", "95% CI", "P-value"], ["Age", "1.020", "1.007–1.034", "0.0036*", "1.020", "1.006–1.033", "0.0041*"], ["Grade", "1.378", "0.904–2.102", "0.1360", "1.271", "0.832–1.944", "0.2676"], ["Stage", "1.391", "1.023–1.892", "0.0351*", "1.381", "1.008–1.891", "0.0443*"], ["STMN2", "1.345", "1.027–1.762", "0.0312*", "1.050", "1.002–1.101", "0.0412*"]], "row_count": 6, "column_count": 7, "numeric_cells": 26, "header_rows": 2, "locator": "section[25]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:32510146:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:2185b8dc040baecdc0c9c005d4ca07b80cbfdb769a44e7a92d032560bd47903e", "bytes": 464, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[29]/table-wrap[1]#T2", "version": null, "note": "The top three metastasis-related small molecules with highly significant correlations in results of CMap analysis", "structure": {"pmcid": "PMC7317593", "section_index": 29, "section_title": "Related small molecule drug screening", "row_count": 4, "column_count": 5}, "table": {"label": "Table 2", "caption": "The top three metastasis-related small molecules with highly significant correlations in results of CMap analysis", "rows": [["CMap name", "Mean", "N", "Enrichment", "P value"], ["Diprophylline", "−0.511", "5", "−0.703", "0.00505"], ["Valinomycin", "−0.339", "4", "−0.641", "0.03991"], ["Anisomycin", "−0.41", "4", "−0.631", "0.0455"]], "row_count": 4, "column_count": 5, "numeric_cells": 12, "header_rows": 1, "locator": "section[29]/table-wrap[1]#T2"}}], "gaps": ["asset:data:geo:GSE73168 not downloaded", "asset:data:geo:GSE73168 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "The raw dataset of GS73168 was analyzed with the GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/), a web tool using ‘limma’ package of R and utilized to screen DEGs between primary and metastasis tumor tissues."}}, {"id": "method-2", "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"}}], "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": ["GSE73168"], "resolved_accessions": ["GSE73168"], "statements": ["The data used in the current study are available from the Gene Expression Omnibus (https://www.ncbi.nlm.nih.gov) and Cancer Genome Atlas database (https://cancergenome.nih.gov)."], "basis": "The paper names GSE73168 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:32510146", "data:geo:GSE73168", "asset:table:pmid:32510146:1", "asset:table:pmid:32510146:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE73168"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:20:17Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 27357, "completion_tokens": 2048, "cached_tokens": 9224}}, "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:32510146", "type": "paper", "label": "pmid:32510146"}, {"id": "source:pmid:32510146", "type": "manuscript", "label": "PMID 32510146 full text"}, {"id": "data:geo:GSE73168", "type": "dataset", "label": "GEO GSE73168"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32510146", "type": "paper", "label": "pmid:32510146"}, {"id": "source:pmid:32510146", "type": "manuscript", "label": "PMID 32510146 full text"}, {"id": "data:geo:GSE73168", "type": "dataset", "label": "GEO GSE73168"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32510146", "type": "extraction", "used": ["source:pmid:32510146"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE73168", "type": "accession_resolution", "used": ["data:geo:GSE73168"], "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:32510146", "parent_hash": "sha256:696a7932f5258c0564d73c9017fac3e48638fa09d4c73fbc9ec522399c2a7d45", "fork_of": null, "generation": 7}, "gaps": ["asset:data:geo:GSE73168 licence not read", "asset:data:geo:GSE73168 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": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["tion-polymerase chain reaction (qRT-PCR) and western blot showed that STMN2 was highly expressed in ov"], "order_basis": "paper_text_order:2098", "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": ["The raw dataset of GS73168 was analyzed with the GEO2R (https://www.ncbi.nlm.nih.gov/geo/geo2r/), a web tool using ‘limma’ package of R and utilized to screen DEGs between primary and metastasis tumor tissues."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}