Identification of circRNA-miRNA-mRNA Networks for Exploring the Fundamental Mechanism in Lung Adenocarcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32308427", "kind": "science-record", "revision": 8, "content_hash": "sha256:a083cbd87ea88ef348f2218ffbaa930f19fa96ef720583cdd245d4fc354f5410", "created_at": "2026-11-01T15:40:59Z", "updated_at": "2026-11-01T22:01:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of circRNA-miRNA-mRNA Networks for Exploring the Fundamental Mechanism in Lung Adenocarcinoma.", "doi": "10.2147/OTT.S235664", "pmid": "32308427", "authors": ["Liming Liang", "Liang Zhang", "Jiguang Zhang", "Shutang Bai", "Hongdu Fu"], "journal": "OncoTargets and therapy", "year": 2020, "abstract": "BACKGROUND: Circular RNAs (circRNAs) were elucidated to act as competing endogenous RNAs (ceRNAs) and to play significant roles in cancer initiation and progression. We aimed to identify the important circRNAs in lung adenocarcinoma and intended to predict the functions of them via the bioinformatics analysis.\nMETHODS: We extracted data from three Gene Expression Omnibus (GEO) datasets, GSE101586, GSE101684, and GSE104854, and identified the common differentially expressed circRNAs. Agarose gel electrophoresis and Sanger sequencing were used to verify these significant circRNAs. Then, qRT-PCR was performed to validate the expression through matched tissues and cell lines. Afterwards, a ceRNA network was constructed and functional analysis was performed to predict the potential mechanisms of circRNAs.\nRESULTS: Five circRNAs (hsa_circ_0072088, hsa_circ_0082564, hsa_circ_0008274, hsa_circ_0000519 and hsa_circ_0003528) were identified differentially expressed in the three datasets. Following the Agarose gel electrophoresis and qRT-PCR validation, hsa_circ_0072088 and hsa_circ_0008274 were chosen for further analysis. A ceRNA network of hsa_circ_0072088 and hsa_circ_0008274 was built based on the CSCD/TargetScan/MiRTarbase/StarBase 3.0. Then, the functional analysis showed that several meaningful terms were identified, such as \"epithelial to mesenchymal transition (EMT)\", \"Cellular response to TGF-β stimulus\", \"MAPK signaling pathway\", and \"PI3K-AKT signaling pathway\". Finally, several significant circRNA/miRNA/mRNA regulatory axes, which were predicted relating to cancer progress, were noted from the network.\nCONCLUSION: We identified significant circRNAs and meaningful circRNA-miRNA-mRNA networks to provide novel insight into pathogenesis and therapy of lung adenocarcinoma.", "claims": [{"id": "claim-data-access", "statement": "We downloaded raw data and re-organized them as raw counts expression matrix.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32308427", "locator": "sections[5] \"CircRNA Expression Profile Analysis\" paragraph 2", "quote": "We downloaded raw data and re-organized them as raw counts expression matrix."}], "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:32308427"], "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:GSE101586"], "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": {"fold_change": "in Table S2), plus, the fold-change and Student’s t testing"}, "inputs": ["data:geo:GSE101586"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32308427", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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"state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE101684", "version": null, "note": "We downloaded raw data and re-organized them as raw counts expression matrix.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "We downloaded raw data and re-organized them as raw counts expression matrix.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM2711988", "GSM2711989", "GSM2711990", "GSM2711991", "GSM2711992", "GSM2711993", "GSM2711994", "GSM2711995"], "sample_count": 8, "group_sizes": null, "group_sizes_basis": null, "platform": "21825", "taxon": "Homo sapiens", "title": "CircRNA expression profiles in early stage lung adenocarcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE104854", "role": "raw", "format": 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"GPL19978", "Homo sapiens", "Non-coding RNA profiling by array", "Public on Jul 19, 2017", "5", "5"], ["GSE101684", "GPL21825", "Homo sapiens", "Non-coding RNA profiling by array", "Public on Jun 26, 2019", "4", "4"], ["GSE104854", "GPL17303", "Homo sapiens", "Ribosome-free RNA sequencing", "Public on Oct 13, 2017", "3", "3"]], "row_count": 5, "column_count": 7, "numeric_cells": 15, "header_rows": 2, "locator": "section[5]/table-wrap[1]#T0001"}}, {"id": "asset:table:pmid:32308427:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:058e8f9cfd4ac055c63e47b0ae9eadca7b0acba273f49e4c9bc6c6ed97be94e2", "bytes": 568, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[10]/table-wrap[1]#T0002", "version": null, "note": "Basic Information of Differentially Expressed circRNAs", "structure": {"pmcid": "PMC7152915", "section_index": 10, "section_title": "Identification of DECs", "row_count": 6, "column_count": 4}, "table": {"label": "Table 2", "caption": "Basic Information of Differentially Expressed circRNAs", "rows": [["CircRNA ID", "Position", "Spliced Length", "Gene Symbol"], ["hsa_circ_0072088", "chr5:32379220-32388780", "693", "ZFR"], ["hsa_circ_0082564", "chr7:137569740-137570248", "227", "CREB3L2"], ["hsa_circ_0008274", "chr13:96485180-96489456", "244", "UGGT2"], ["hsa_circ_0000519", "chr14:20811436-20811534", "98", "RPPH1"], ["hsa_circ_0003528", "chr5:134032815-134044578", "741", "SEC24A"]], "row_count": 6, "column_count": 4, "numeric_cells": 16, "header_rows": 1, "locator": "section[10]/table-wrap[1]#T0002"}}, {"id": "asset:table:pmid:32308427:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:6d6c970acae54ced5ce574088906c845fc63267066a0cc3d8a7671cde1ddc135", "bytes": 1079, "access": "open", "state": "verified", "reader": "read_table", "reader_status": 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All the cell lines were maintained at 37°C in a humidified atmosphere with 5% C", "e Academic of Science). The 16HBE cells were cultured in DMEM, and A549 and H1299 cells were cultured", "tured in DMEM, and A549 and H1299 cells were cultured in RPMI-1640 medium (Gibco, Invitrogen, Carlsba", "e Academic of Science). The 16HBE cells were cultured in DMEM, and A549 and H1299 cells were cultu"], "order_basis": "paper_text_order:1912", "id": "assay:1"}, {"role": "data_generation", "definition_id": "apoptosis_assay", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.69, "evidence": ["circRNA might play roles in tumor growth and apoptosis. 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