Establishment and Comprehensive Analysis of Underlying microRNA-mRNA Interactive Networks in Ovarian Cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35310909", "kind": "science-record", "revision": 4, "content_hash": "sha256:a4982abdbcf0dd6be2648b65fe5b1e88edc71f2d083681ded697253afdc49042", "created_at": "2026-11-01T18:14:06Z", "updated_at": "2026-11-01T22:06:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Establishment and Comprehensive Analysis of Underlying microRNA-mRNA Interactive Networks in Ovarian Cancer.", "doi": "10.1155/2022/5120342", "pmid": "35310909", "authors": ["Gengchen Ye", "Shuyue Feng", "Yufei Yang", "Zhengzhi Cao", "Beilei Zhang", "Fu Wang"], "journal": "Journal of oncology", "year": 2022, "abstract": "Background: The rate of ovarian cancer (OC) is one of the highest in women's reproductive systems. An improperly expressed microRNA (miRNA) has been discovered to have a vital role in the pathophysiology of OC. However, more research into OC's miRNA-message RNA (mRNA) gene interaction network is required.\nMethods: Firstly, the microarray data sets GSE25405 and GSE119055 from the GEO (Gene Expression Omnibus) database were downloaded and then analyzed with the GEO2R tool aiming at identifying DEMs (differential expressed miRNAs) between ovarian malignant tissue and ovarian normal tissue. The whole consistently changed miRNAs were then screened out to be candidate DEMs. For estimating underlying upstream transcription factors, FunRich was employed. miRNet was utilized to determine putative DEMs' downstream target genes. The R program was then used to do the GO annotation as well as the analysis of KEGG pathway enrichment for target genes. The PPI (protein-protein interaction), as well as the DEM-hub gene networks, were created by the Cytoscape software and STRING database. Finally, we chose the GSE74448 dataset to test the precision of hub gene expressions.\nResults: We have screened out six (five upregulated and one downregulated) DEMs. The majority of upregulated and downregulated DEMs are likely regulated by SP1 (specificity protein 1). SP4 (s protein 4), POU2F1 (POU class 2 homeobox 1), MEF2A (myocyte-specific enhancer factor 2A), ARID3A (AT-rich interaction domain 3A), and EGR1 (early growth response 1) can regulate upregulated and downregulated DEMs. We have found 807 target genes (656 upregulated and 151 downregulated DEM), being generally enriched in focal adhesion and proteoglycans in cancer, gastric cancer, hepatocellular carcinoma, as well as breast cancer. The majority of hub genes are projected to be controlled by hsa-miR-429, hsa-miR-140-5p, hsa-miR-199a-5p, and hsa-miR-199a-3p after the DEM-hub gene network was built. VEGFA (vascular endothelial growth factor A), EZH2 (enhancer of zeste 2 polycomb repressive complex 2 subunit), and HIF1A (hypoxia inducible factor 1 subunit alpha) expressions are consistent with the GSE74448 dataset in the first 18 hub genes.\nConclusion: We have built an underlying miRNA-mRNA interacting network in OC, giving us unparalleled insight into the disease's diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "Then, we performed the Student's t-test to screen out DEGs between OC and normal tissue.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35310909", "locator": "sections[9] \"2.7. Expression Analysis of Hub Gene by GSE74448 Data Set\" paragraph 2", "quote": "Then, we performed the Student's t-test to screen out DEGs between OC and normal tissue."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The supplementary information files provide the data used to support the findings of this investigation.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35310909", "locator": "sections[21] \"Data Availability\" paragraph 2", "quote": "The supplementary information files provide the data used to support the findings of this investigation."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We have screened out six (five upregulated and one downregulated) DEMs.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35310909", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We have screened out six (five upregulated and one downregulated) DEMs."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "We have screened out six (five upregulated and one downregulated) DEMs.", "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:35310909"], "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:GSE119055"], "outputs": ["the source data with its repository provenance"], "instruments": [], "reagents": []}, {"id": "run_analysis", "order": 3, "name": "Run the published analysis", "kind": "analysis", "state": "blocked", "blocked_on": "method:student_t", "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:GSE119055"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": ["step:run_analysis blocked on method:student_t"]}, "data": {"state": "partial", "assets": [{"id": "source:pmid:35310909", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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