Risk miRNA screening of ovarian cancer based on miRNA functional synergistic network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:24444095", "kind": "science-record", "revision": 9, "content_hash": "sha256:df3492e4e316fd0d1b7f98c93f68cf569c6622bb275f85fca486058c9a45dc79", "created_at": "2026-11-01T15:40:04Z", "updated_at": "2026-11-01T22:42:01Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Risk miRNA screening of ovarian cancer based on miRNA functional synergistic network.", "doi": "10.1186/1757-2215-7-9", "pmid": "24444095", "authors": ["Huanchun Ying", "Jing Lyu", "Tianshu Ying", "Jun Li", "Shanshan Jin", "Jingru Shao", "Lili Wang", "Hongying Xu"], "journal": "Journal of ovarian research", "year": 2014, "abstract": "BACKGROUND: miRNAs are proved to have causal roles in tumorgenesis involving various types of human cancers, but the mechanism is not clear. We aimed to explore the effect of miRNAs on the development of ovarian cancer and the underlying mechanism.\nMETHODS: The miRNA expression profile GSE31801 was downloaded from GEO (Gene Expression Omnibus) database. Firstly, the differentially expressed miRNAs were screened. Target genes of the miRNAs were collected from TargetScan, PicTar, miRanda, and DIANA-microT database, then the miRNA-miRNA co-regulating network was constructed using miRNA pairs with common regulated target genes. Next, the functional modules in the network were studied, the miRNA pairs regulated at least one modules were enriched to form the miRNA functional synergistic network (MFSN).\nRESULTS: Risk miRNA were selected in MFSN according to the topological structure. Transcript factors (TFs) in MFSN were identified, followed by the miRNA-transcript factor networks construction. Totally, 42 up- and 61 down-regulated differentially expressed miRNAs were identified, of which 68 formed 2292 miRNA pairs in the miRNA-miRNA co-regulating network. GO: 0007268 (synaptic transmission) and GO: 0019226 (transmission of nerve impulse) were the two common functions of miRNAs in MFSN, and hsa-miR-579 (36), hsa-miR-942 (31), hsa-miR-105 (31), hsa-miR-150 (34), and hsa-miR-27a* (32) were selected as the hub nodes in MFSN.\nCONCLUSIONS: In all, 17 TFs, including CREM, ERG, and CREB1 were screened as the cancer related TFs in MFSN. Other TFs, such as BIN1, FOXN3, FOXK1, FOXP2, and ESRRG with high degrees may be inhibited in ovarian cancer. MFSN gave us a new shed light on the mechanism studies in ovarian cancer.", "claims": [{"id": "claim-method", "statement": "To screen the differentially expressed miRNAs, limma package in R language [12] was used, with the cut off criterion of adjusted p value less than 0.05, and |log fold change (FC)| larger than 1.5.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24444095", "locator": "sections[5] \"Differentially expressed miRNAs analysis\" paragraph 2", "quote": "To screen the differentially expressed miRNAs, limma package in R language [12] was used, with the cut off criterion of adjusted p value less than 0.05, and |log fold change (FC)| larger than 1.5."}], "state": "complete"}, {"id": "claim-data-access", "statement": "We downloaded the miRNA expression profile data GSE31801 [10] from NCBI (National Center for Biotechnology Information) GEO (Gene Expression Omnibus) (http://www.ncbi.nlm.nih.gov/geo/) database. Chips of miRNA profiling in lymphoblastoid cell lines from 74 women with familial ovarian cancer were available, as well as chips from 47 normal ovarian tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:24444095", "locator": "sections[3] \"Affymetrix microarray analysis\" paragraph 2", "quote": "We downloaded the miRNA expression profile data GSE31801 [10] from NCBI (National Center for Biotechnology Information) GEO (Gene Expression Omnibus) (http://www.ncbi.nlm.nih.gov/geo/) database. Chips of miRNA profiling in lymphoblastoid cell lines from 74 women with familial ovarian cancer were available, as well as chips from 47 normal ovarian tissues."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Differentially expressed miRNAs were identified using the limma package in R, with an adjusted p-value cutoff below 0.05 and |log fold change| greater than 1.5; the source data were the GSE31801 miRNA expression profile downloaded from the NCBI GEO database.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:24444095", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The miRNA expression profile GSE31801 was downloaded from GEO (Gene Expression Omnibus) database."}, {"asset": "source:pmid:24444095", "locator": "sections[5] \"Differentially expressed miRNAs analysis\" paragraph 2", "quote": "To screen the differentially expressed miRNAs, limma package in R language [12] was used, with the cut off criterion of adjusted p value less than 0.05, and |log fold change (FC)| larger than 1.5."}, {"asset": "source:pmid:24444095", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Totally, 42 up- and 61 down-regulated differentially expressed miRNAs were identified, of which 68 formed 2292 miRNA pairs in the miRNA-miRNA co-regulating network."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Differentially expressed miRNAs were identified using the limma package in R, with an adjusted p-value cutoff below 0.05 and |log fold change| greater than 1.5; the source data were the GSE31801 miRNA expression profile downloaded from the NCBI GEO database.", "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:24444095"], "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:GSE31801"], "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:GSE31801"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:24444095", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/1757-2215-7-9", "sha256": "sha256:fc43eeed227c9c1b9a02101d18d229dcf75cd9f8f560587eeb99987503b910f3", "bytes": 26099, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/1757-2215-7-9", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC3902002", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE31801", "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=GSE31801", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31801", "version": null, "note": "We downloaded the miRNA expression profile data GSE31801 [10] from NCBI (National Center for Biotechnology Information) GEO (Gene Expression Omnibus) (http://www.ncbi.nlm.nih.gov/geo/) database. Chips of miRNA profiling in lymphoblastoid cell lines from 74 women with familial ovarian cancer were available, as well as chips from 47 normal ovarian tissues.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded the miRNA expression profile data GSE31801 [10] from NCBI (National Center for Biotechnology Information) GEO (Gene Expression Omnibus) (http://www.ncbi.nlm.nih.gov/geo/) database. 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