Identification of Driver Genes and miRNAs in Ovarian Cancer through an Integrated In-Silico Approach.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:36829472", "kind": "science-record", "revision": 4, "content_hash": "sha256:bed0601250103a153d9efaea8038756bf4042f671acd8d1a9ec10b6974a4b8ab", "created_at": "2026-11-01T19:01:26Z", "updated_at": "2026-11-01T22:51:20Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Driver Genes and miRNAs in Ovarian Cancer through an Integrated In-Silico Approach.", "doi": "10.3390/biology12020192", "pmid": "36829472", "authors": ["Anam Beg", "Rafat Parveen", "Hassan Fouad", "M E Yahia", "Azza S Hassanein"], "journal": "Biology", "year": 2023, "abstract": "Ovarian cancer is the eighth-most common cancer in women and has the highest rate of death among all gynecological malignancies in the Western world. Increasing evidence shows that miRNAs are connected to the progression of ovarian cancer. In the current study, we focus on the identification of miRNA and its associated genes that are responsible for the early prognosis of patients with ovarian cancer. The microarray dataset GSE119055 used in this study was retrieved via the publicly available GEO database by NCBI for the analysis of DEGs. The miRNA GSE119055 dataset includes six ovarian carcinoma samples along with three healthy/primary samples. In our study, DEM analysis of ovarian carcinoma and healthy subjects was performed using R Software to transform and normalize all transcriptomic data along with packages from Bioconductor. Results: We identified miRNA and its associated hub genes from the samples of ovarian cancer. We discovered the top five upregulated miRNAs (hsa-miR-130b-3p, hsa-miR-18a-5p, hsa-miR-182-5p, hsa-miR-187-3p, and hsa-miR-378a-3p) and the top five downregulated miRNAs (hsa-miR-501-3p, hsa-miR-4324, hsa-miR-500a-3p, hsa-miR-1271-5p, and hsa-miR-660-5p) from the network and their associated genes, which include seven common genes (SCN2A, BCL2, MAF, ZNF532, CADM1, ELAVL2, and ESRRG) that were considered hub genes for the downregulated network. Similarly, for upregulated miRNAs we found two hub genes (PRKACB and TAOK1).", "claims": [{"id": "claim-method", "statement": "The selection of specific DEMs was accomplished using a T static approach with the Linear Models for Microarray “limma” package [20] of Bioconductor.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36829472", "locator": "sections[4] \"2.2. Differentially Expressed MicroRNAs (DEMs) Screening\" paragraph 2", "quote": "The selection of specific DEMs was accomplished using a T static approach with the Linear Models for Microarray “limma” package [20] of Bioconductor."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The dataset used in the current study is publicly available at the NCBI GEO dataset for ovarian cancer. The persistent link can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119055.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36829472", "locator": "sections[23] \"notes\" paragraph 1", "quote": "The dataset used in the current study is publicly available at the NCBI GEO dataset for ovarian cancer. The persistent link can be found at: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE119055."}], "state": "complete"}, {"id": "claim-target-result", "statement": "A total of 4575 miRNAs were found in GSE119055, of which 42 DEMs were distinguished.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36829472", "locator": "sections[10] \"3.1. Identification of DEMs Associated with Ovarian Cancer\" paragraph 2", "quote": "A total of 4575 miRNAs were found in GSE119055, of which 42 DEMs were distinguished."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "A total of 4575 miRNAs were found in GSE119055, of which 42 DEMs were distinguished.", "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:36829472"], "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": "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": {"fdr_threshold": "and Benjamini–Hochberg false discovery rate correction"}, "inputs": ["data:geo:GSE119055"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:36829472", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3390/biology12020192", "sha256": "sha256:30f4552183acb4ace334f0b57b4ccf300edb4c085f67a07606df23e430ffb1c7", "bytes": 30366, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.3390/biology12020192", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC9952540", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE119055", "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=GSE119055", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE119055", "version": null, "note": "The dataset used in the current study is publicly available at the NCBI GEO dataset for ovarian cancer. 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