Identification of key miRNAs in papillary thyroid carcinoma based on data mining and bioinformatics methods.

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The present study aimed to investigate key miRNAs involved in papillary thyroid carcinoma (PTC). Two independent datasets (GSE73182 and GSE113629) were obtained from the GEO database. The differentially expressed miRNAs (DEmiRNAs) between PTC tissues and normal thyroid tissues were analyzed by GEO2R with the Limma R package. Key miRNAs in PTC were identified by the VennDiagram R package. The targets of the key miRNAs were predicted by miRWalk and were functionally enriched by clusterProfiler R package. Five miRNAs including hsa-miR-146b-5p, hsa-miR-15a-5p, hsa-miR-21-5p, hsa-miR-221-3p and hsa-miR-222-3p were identified as key miRNAs in PTC. The expression levels of these key miRNAs were upregulated in PTC. This finding was also confirmed in the other dataset. Target prediction of miRNAs indicated that hsa-miR-146b-5p, hsa-miR-15a-5p, hsa-miR-21-5p, hsa-miR-221-3p and hsa-miR-222-3p exhibited 2, 41, 3, 14 and 8 target genes, respectively. Enrichment analysis indicated that these key miRNAs were mainly involved in nine biological processes, such as regulation of MAP kinase activity, JNK cascade signaling and regulation of protein serine/threonine kinase activity) and in 28 pathways, including the mitogen associated protein kinase, the sphingolipid, ErbB, Ras and the C-type lectin receptor signaling pathways. In conclusion, the present study identified several key miRNAs in PTC, which serve as potential targets for PTC diagnosis and treatment.", "claims": [{"id": "claim-method", "statement": "The differentially expressed miRNAs (DEmiRNAs) between PTC tissues and normal thyroid tissues were analyzed by GEO2R with the Limma R package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31839944", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The differentially expressed miRNAs (DEmiRNAs) between PTC tissues and normal thyroid tissues were analyzed by GEO2R with the Limma R package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Two independent datasets (GSE73182 and GSE113629) were obtained from the GEO database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31839944", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Two independent datasets (GSE73182 and GSE113629) were obtained from the GEO database."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Five miRNAs including hsa-miR-146b-5p, hsa-miR-15a-5p, hsa-miR-21-5p, hsa-miR-221-3p and hsa-miR-222-3p were identified as key miRNAs in PTC.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:31839944", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "Five miRNAs including hsa-miR-146b-5p, hsa-miR-15a-5p, hsa-miR-21-5p, hsa-miR-221-3p and hsa-miR-222-3p were identified as key miRNAs in PTC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Five miRNAs including hsa-miR-146b-5p, hsa-miR-15a-5p, hsa-miR-21-5p, hsa-miR-221-3p and hsa-miR-222-3p were identified as key miRNAs in PTC.", "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:31839944"], "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. 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