Gene co-expression network reveals shared modules predictive of stage and grade in serous ovarian cancers.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:28562334", "kind": "science-record", "revision": 6, "content_hash": "sha256:722d9a06084ecadd37dce48f82cb38a4c6d3fb495853487af4a84a832b9a4fd8", "created_at": "2026-11-01T15:40:26Z", "updated_at": "2026-11-01T21:20:56Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Gene co-expression network reveals shared modules predictive of stage and grade in serous ovarian cancers.", "doi": "10.18632/oncotarget.17785", "pmid": "28562334", "authors": ["Qian Sun", "Haiyue Zhao", "Cong Zhang", "Ting Hu", "Jianli Wu", "Xingguang Lin", "Danfeng Luo", "Changyu Wang", "Li Meng", "Ling Xi", "Kezhen Li", "Junbo Hu", "Ding Ma", "Tao Zhu"], "journal": "Oncotarget", "year": 2017, "abstract": "Serous ovarian cancer (SOC) is the most lethal gynecological cancer. Clinical studies have revealed an association between tumor stage and grade and clinical prognosis. Identification of meaningful clusters of co-expressed genes or representative biomarkers related to stage or grade may help to reveal mechanisms of tumorigenesis and cancer development, and aid in predicting SOC patient prognosis. We therefore performed a weighted gene co-expression network analysis (WGCNA) and calculated module-trait correlations based on three public microarray datasets (GSE26193, GSE9891, and TCGA), which included 788 samples and 10402 genes. We detected four modules related to one or more clinical features significantly shared across all modeling datasets, and identified one stage-associated module and one grade-associated module. Our analysis showed that MMP2, COL3A1, COL1A2, FBN1, COL5A1, COL5A2, and AEBP1 are top hub genes related to stage, while CDK1, BUB1, BUB1B, BIRC5, AURKB, CENPA, and CDC20 are top hub genes related to grade. Gene and pathway enrichment analyses of the regulatory networks involving hub genes suggest that extracellular matrix interactions and mitotic signaling pathways are crucial determinants of tumor stage and grade. The relationships between gene expression modules and tumor stage or grade were validated in five independent datasets. These results could potentially be developed into a more objective scoring system to improve prediction of SOC outcomes.", "claims": [{"id": "claim-method", "statement": "Gene co-expression network analysis was performed using the R package WGCNA [9].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28562334", "locator": "sections[13] \"Gene co-expression network construction\" paragraph 2", "quote": "Gene co-expression network analysis was performed using the R package WGCNA [9]."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The ovarian cancer datasets were adopted from the curatedOvarianData Bioconductor package [16].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:28562334", "locator": "sections[12] \"Datasets filtering\" paragraph 2", "quote": "The ovarian cancer datasets were adopted from the curatedOvarianData Bioconductor package [16]."}], "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:28562334"], "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:GSE26193"], "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:GSE26193"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:28562334", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.18632/oncotarget.17785", "sha256": 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"section[6]/table-wrap[1]#T2", "version": null, "note": "The top 25 hub genes of the blue module through ten datasets and the high-quality STRING subnetwork", "structure": {"pmcid": "PMC5522121", "section_index": 6, "section_title": "Identification of universal hub genes in the blue and yellow modules", "row_count": 26, "column_count": 12}, "table": {"label": "Table 2", "caption": "The top 25 hub genes of the blue module through ten datasets and the high-quality STRING subnetwork", "rows": [["Number", "d1", "d2", "d3", "d4", "d5", "d6", "d7", "d8", "d9", "d10", "STRING_600"], ["1", "FBN1", "FBN1", "FBN1", "FBN1", "FBN1", "FBN1", "FBN1", "FBN1", "FBN1", "FBN1", "JUN"], ["2", "COL5A1", "COL5A1", "COL5A1", "COL5A2", "COL5A1", "COL5A1", "COL5A1", "COL5A2", "COL5A2", "COL5A2", "BMP4"], ["3", "COL5A2", "AEBP1", "AEBP1", "COL5A1", "COL5A2", "COL5A2", "COL5A2", "COL5A1", "COL5A1", "COL5A1", "BMP2"], ["4", "AEBP1", "COL5A2", "COL5A2", "AEBP1", "AEBP1", "AEBP1", "AEBP1", "AEBP1", "AEBP1", 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"section_index": 6, "section_title": "Identification of universal hub genes in the blue and yellow modules", "row_count": 26, "column_count": 12}, "table": {"label": "Table 3", "caption": "The top 25 hub genes of the yellow module through ten datasets and the high-quality STRING subnetwork", "rows": [["number", "multi1", "multi2", "multi3", "multi4", "multi5", "multi6", "multi7", "multi8", "multi9", "multi10", "STRING_600"], ["1", "TPX2", "TPX2", "TPX2", "KIF4A", "TPX2", "TPX2", "TPX2", "KIF4A", "KIF4A", "KIF4A", "CDK1"], ["2", "CENPA", "KIF4A", "CENPA", "CENPA", "BUB1", "KIF4A", "CENPA", "CENPA", "CENPA", "TPX2", "PLK1"], ["3", "DLGAP5", "CENPA", "KIF4A", "TPX2", "KIF4A", "NUSAP1", "DLGAP5", "TPX2", "TPX2", "NUSAP1", "PCNA"], ["4", "KIF4A", "BUB1", "MELK", "BUB1", "RACGAP1", "KIF15", "KIF4A", "BUB1", "BUB1", "CENPA", "CDK2"], ["5", "BUB1", "MELK", "BUB1", "UBE2C", "DLGAP5", "HJURP", "BUB1", "NUSAP1", "DLGAP5", "MELK", "CCNB1"], ["6", "NUSAP1", "DLGAP5", "NUSAP1", "MELK", "MELK", "BUB1", "UBE2C", "KIF15", "MELK", "BUB1", "CDC20"], ["7", "KIF15", "NUSAP1", "HJURP", "RACGAP1", "UBE2C", "CENPA", "NUSAP1", "DLGAP5", "RACGAP1", "KIF15", "AURKB"], ["8", "NCAPH", "UBE2C", "RACGAP1", "NCAPH", "CENPA", "NCAPH", "KIF15", "UBE2C", "KIF15", "DLGAP5", "AURKA"], ["9", "UBE2C", "ASPM", "ASPM", "KIF15", "NUSAP1", "MELK", "NCAPH", "MELK", "HJURP", "CCNB2", "MAD2L1"], ["10", "RACGAP1", "HJURP", "NCAPH", "ASPM", "KIF15", "DLGAP5", "MELK", "RACGAP1", "UBE2C", "HJURP", "MCM5"], ["11", "ASPM", "KIF15", "DLGAP5", "CCNB2", "KIF23", "RACGAP1", "CCNB2", "HJURP", "CCNB2", "BIRC5", "CDC6"], ["12", "HJURP", "CCNB2", "KIF15", "HJURP", "BIRC5", "UBE2C", "HJURP", "ASPM", "ASPM", "RACGAP1", "BUB1"], ["13", "KIF23", "RACGAP1", "BUB1B", "DLGAP5", "BUB1B", "ASPM", "RACGAP1", "BUB1B", "NUSAP1", "BUB1B", "TOP2A"], ["14", "MELK", "BUB1B", "UBE2C", "NUSAP1", "ASPM", "BUB1B", "KIF23", "NCAPH", "BUB1B", "ASPM", "BUB1B"], ["15", "KIF20A", "NCAPH", "KIF20A", "BIRC5", "HJURP", "ZWINT", "BIRC5", "ZWINT", 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