Integrated bioinformatics analysis for the screening of hub genes and therapeutic drugs in ovarian cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31987036", "kind": "science-record", "revision": 7, "content_hash": "sha256:82ee1e29b3d40368402842143831f3c2d186348f9665c4be825f570796570a8c", "created_at": "2026-11-01T15:40:55Z", "updated_at": "2026-11-01T22:01:13Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated bioinformatics analysis for the screening of hub genes and therapeutic drugs in ovarian cancer.", "doi": "10.1186/s13048-020-0613-2", "pmid": "31987036", "authors": ["Dan Yang", "Yang He", "Bo Wu", "Yan Deng", "Nan Wang", "Menglin Li", "Yang Liu"], "journal": "Journal of ovarian research", "year": 2020, "abstract": "BACKGROUND: Ovarian cancer (OC) ranks fifth as a cause of gynecological cancer-associated death globally. Until now, the molecular mechanisms underlying the tumorigenesis and prognosis of OC have not been fully understood. This study aims to identify hub genes and therapeutic drugs involved in OC.\nMETHODS: Four gene expression profiles (GSE54388, GSE69428, GSE36668, and GSE40595) were downloaded from the Gene Expression Omnibus (GEO), and the differentially expressed genes (DEGs) in OC tissues and normal tissues with an adjusted P-value < 0.05 and a |log fold change (FC)| > 1.0 were first identified by GEO2R and FunRich software. Next, Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) analyses were performed for functional enrichment analysis of these DEGs. Then, the hub genes were identified by the cytoHubba plugin and the other bioinformatics approaches including protein-protein interaction (PPI) network analysis, module analysis, survival analysis, and miRNA-hub gene network construction was also performed. Finally, the GEPIA2 and DGIdb databases were utilized to verify the expression levels of hub genes and to select the candidate drugs for OC, respectively.\nRESULTS: A total of 171 DEGs were identified, including 114 upregulated and 57 downregulated DEGs. The results of the GO analysis indicated that the upregulated DEGs were mainly involved in cell division, nucleus, and protein binding, whereas the biological functions showing enrichment in the downregulated DEGs were mainly negative regulation of transcription from RNA polymerase II promoter, protein complex and apicolateral plasma membrane, and glycosaminoglycan binding. As for the KEGG-pathway, the upregulated DEGs were mainly associated with metabolic pathways, biosynthesis of antibiotics, biosynthesis of amino acids, cell cycle, and HTLV-I infection. Additionally, 10 hub genes (KIF4A, CDC20, CCNB2, TOP2A, RRM2, TYMS, KIF11, BIRC5, BUB1B, and FOXM1) were identified and survival analysis of these hub genes showed that OC patients with the high-expression of CCNB2, TYMS, KIF11, KIF4A, BIRC5, BUB1B, FOXM1, and CDC20 were statistically more likely to have poorer progression free survival. Meanwhile, the expression levels of the hub genes based on GEPIA2 were in accordance with those based on GEO. Finally, DGIdb database was used to identify 62 small molecules as the potentially targeted drugs for OC treatment.\nCONCLUSIONS: In summary, the data may produce new insights regarding OC pathogenesis and treatment. Hub genes and candidate drugs may improve individualized diagnosis and therapy for OC in future.", "claims": [{"id": "claim-data-access", "statement": "The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31987036", "locator": "sections[25] \"Availability of data and materials\" paragraph 2", "quote": "The datasets used and/or analyzed during the current study are available from the corresponding author upon reasonable request."}], "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:31987036"], "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:GSE36668"], "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:GSE36668"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31987036", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s13048-020-0613-2", "sha256": 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Cells and high grade serous ovarian cancer", "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:31987036:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:e15014a3866dea1e6b127ea9100be64caa745f1fc54de22234481d156329e5df", "bytes": 738, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[1]#Tab1", "version": null, "note": "Detailed information on the GEO microarray profiles of OC patients", "structure": {"pmcid": "PMC6986075", "section_index": 11, "section_title": "Identification of DEGs in OC", "row_count": 5, "column_count": 7}, "table": {"label": "Table 1", "caption": "Detailed information on the GEO microarray profiles of OC patients", "rows": [["No. of GEO profile", "Type", "Source", "Case", "Control", "Platform", "Annotation platform"], ["GSE54388", "mRNA", "serous ovarian cancer", "16", "6", "GPL570", "Affymetrix Human Genome U133 Plus 2.0 Array"], ["GSE69428", "mRNA", "serous ovarian cancer", "10", "10", "GPL570", "Affymetrix Human Genome U133 Plus 2.0 Array"], ["GSE36668", "mRNA", "serous ovarian cancer", "4", "4", "GPL570", "Affymetrix Human Genome U133 Plus 2.0 Array"], ["GSE40595", "mRNA", "ovarian cancer stroma", "63", "14", "GPL570", "Affymetrix Human Genome U133 Plus 2.0 Array"]], "row_count": 5, "column_count": 7, "numeric_cells": 20, "header_rows": 1, "locator": "section[11]/table-wrap[1]#Tab1"}}, {"id": "asset:table:pmid:31987036:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:bdb0256c9ba674c7f18668fd98ed9072e201b75d7ee7e8ab87df149476f6d820", "bytes": 1523, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[11]/table-wrap[2]#Tab2", "version": null, "note": "Information on the overlapping DEGs screened from the datasets", "structure": {"pmcid": "PMC6986075", "section_index": 11, "section_title": "Identification of DEGs in OC", "row_count": 3, "column_count": 2}, "table": {"label": "Table 2", "caption": "Information on the overlapping DEGs screened from the datasets", "rows": [["DEGs", "Gene name"], ["Upregulated (114)", "WHSC1, VEGFA, TYMS, TSTA3, TPI1, TPD52L2, TOP2A, TNNT1, TMPRSS4, TIMELESS, C20orf24, TBC1D7, TACC3, STC2, SORT1, BOLA2, SLC52A2, SLC4A11, SLC39A4, SLC38A1, SLC2A1, SLC19A1, SHMT2, SCRIB, SAC3D1, S100A2, RRM2, RNASEH2A, RACGAP1, PXDN, PUF60, PTTG1, PSAT1, PPP1R14B, PIK3R3, PBK, OVOL2, NR2F6, NOV, NDUFB9, NDC80, NCAPG, MYCL, MUC16, MT1F, MRPS15, MRPL12, MLF2, MCM4, MCAM, MAL, LSM4, LPCAT1, C1orf186, LAPTM4B, KLK8, KLK7, KLK6, KLHL14, KIF4A, KIF11, KIAA0101, ISG15, IRAK1, IDH2, HN1, HMGB3, HMGA1, H2AFX, GPSM2, FOXM1, FGF18, FEN1, FDPS, ESRP1, EPT1, ENO1, E2F8, DYRK2, DTL, DSC2, DPP3, DHCR24, DGAT1, DDX39A, DBN1, CYC1, CTPS1, CRABP2, COPE, COL4A1, CLPTM1L, CLDN3, CHD7, CDH6, CDCA3, CDC20, CD47, CCNE1, CCNB2, C9orf16, C1orf106, BUB1B, BOLA2B, BIRC5, BAK1, AURKAIP1, ATP6V1B1, ASS1, ARL4C, ARF3, APOA1, AIF1L, ABHD11"], ["Downregulated (57)", "ZEB2, ZBTB20, WHAMMP2, WHAMMP3, WDR17, TLE4, THBD, TFPI, SYTL3, SNCAIP, SMIM14, SLC4A4, SCD5, RUNX1T1, RUNDC3B, RNASE4, PTPN13, PRKAR1A, PLCL2, PIP5K1B, PDK4, PDGFRA, NDNF, NBEA, N4BP2L2, N4BP2L1, MPDZ, MITF, MEF2C, MAF, FAM153A, FAM153B, FAM153C, KLHDC1, KLF2, KAT2B, KANSL1L, ITM2A, IL6ST, GPRASP1, GNG11, FOXP2, DPYD, DPY19L2P2, DMD, DCN, CXorf57, CIRBP, CHGB, CELF2, CDC14A, BNC2, ARMCX1, ALDH1A1, ABCA8, ABCA5, AASS"]], "row_count": 3, "column_count": 2, "numeric_cells": 4, "header_rows": 1, "locator": "section[11]/table-wrap[2]#Tab2"}}, {"id": "asset:table:pmid:31987036:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:1e4e627789939a6491b78389d5f0b7425c94a66e31cf920f072c1dadbf138843", "bytes": 4888, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[16]/table-wrap[1]#Tab3", "version": null, "note": "Candidate drugs targeted by the hub genes", "structure": {"pmcid": "PMC6986075", "section_index": 16, "section_title": "Drug-gene interaction", "row_count": 63, "column_count": 6}, "table": {"label": "Table 3", "caption": "Candidate drugs targeted by the hub genes", "rows": [["No.", "Gene", "Drug", "Interaction types", "Sources", "PMIDs"], ["1", "TYMS", "ETOPOSIDE", "–", "PharmGKB", "–"], ["2", "TYMS", "IRINOTECAN", "–", "CIViC", "20,628,391"], ["3", "TYMS", "VINCRISTINE", "–", "NCI", "2,804,079"], ["4", "TYMS", "FOLIC ACID", "–", "PharmGKB", "–"], ["5", "TYMS", "TOPOTECAN", "–", "NCI", "10,803,925"], ["6", "TYMS", "CYTARABINE", "–", "PharmGKB", "–"], ["7", "TYMS", "MITOMYCIN", "–", "NCI", "15,218,314"], ["8", "TYMS", "PREDNISONE", "–", "PharmGKB", "–"], ["9", "TYMS", "TRIFLURIDINE", "inhibitor", "DrugBank", "18,600,528; 16,902,987; 20,372,850; 19,816,940; 19,886,911; 4,719,131; 6,436,227; 15,571,283; 17,179,993; 14,719,072; 16,010,590; 15,125,867; 11,752,352; 18,798,063; 6,010,427"], ["10", "TYMS", "DAUNORUBICIN", "–", "NCI", "2,967,076"], ["11", "TYMS", "HYDROCORTISONE", "–", "NCI", "2,707,640"], ["12", "TYMS", "PRALATREXATE", "inhibitor", "DrugBank", "23,409,799"], ["13", "TYMS", "PHENTOLAMINE", "–", "NCI", "2,866,100"], ["14", "TYMS", "TRIMETHOPRIM", "inhibitor", "DrugBank", "8,538,681; 10,090,784; 10,592,235; 17,139,284; 8,920,005; 17,016,423; 19,622,858"], ["15", "TYMS", "INDOMETHACIN", "–", "NCI", "2,707,640"], ["16", "TYMS", "GEMCITABINE", "inhibitor", "DrugBank", "16,563,096; 15,795,320; 17,166,391; 16,818,276; 11,752,352; 15,655,942; 16,818,496"], ["17", "TYMS", "ASPARAGINASE", "–", "PharmGKB", "–"], ["18", "TYMS", "CAPECITABINE", "inhibitor", "ClearityFoundationBiomarkers; ClearityFoundationClinicalTrial; GuideToPharmacologyInteractions; ChemblInteractions; DrugBank", "15,134,221; 16,926,630; 15,866,500; 15,132,128; 11,752,352; 15,709,193"], ["19", "TYMS", "FLOXURIDINE", "inhibitor", "TdgClinicalTrial; ClearityFoundationClinicalTrial; ChemblInteractions; TEND; DrugBank", "10,697,523; 10,891,536; 10,697,524; 10,482,907; 10,553,409"], ["20", "TYMS", "LEUCOVORIN", "–", "TdgClinicalTrial; TEND", "–"], ["21", "TYMS", "TAMOXIFEN", "–", "NCI", "9,615,734"], ["22", "TYMS", "VERAPAMIL", "–", "NCI", "3,436,366"], ["23", "TYMS", "RALTITREXED", "inhibitor", "PharmGKB; TdgClinicalTrial; GuideToPharmacologyInteractions; TEND; DrugBank", "18,773,878; 10,598,555; 10,430,100; 10,592,235; 11,752,352; 10,499,608; 10,482,907; 10,047,461; 10,496,350"], ["24", "TYMS", "PEMETREXED DISODIUM", "inhibitor", "ChemblInteractions", "–"], ["25", "TYMS", "DEXAMETHASONE", "–", "NCI", "2,707,640; 3,398,844"], ["26", "TYMS", "INTERFERON GAMA-1B", "–", "NCI", "1,557,656"], ["27", "TYMS", 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