Bioinformatics analysis-based screening of circRNA gene with mainstream expression trend in colorectal cancer and construction of a coexpression regulatory network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38064496", "kind": "science-record", "revision": 5, "content_hash": "sha256:0a7c5662ad5c2340e8c75cac97c868d62888d2a26cca592d5beed8900105cb5f", "created_at": "2026-11-01T19:03:00Z", "updated_at": "2026-11-01T22:53:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatics analysis-based screening of circRNA gene with mainstream expression trend in colorectal cancer and construction of a coexpression regulatory network.", "doi": "10.1371/journal.pone.0295126", "pmid": "38064496", "authors": ["Lei Xu", "Hongqiang Zhang", "Yu Shao", "Zan Fu"], "journal": "PloS one", "year": 2023, "abstract": "OBJECTIVE: Since circRNA can be utilized as a potential diagnostic marker for cancer, to explore the regulatory mechanism of colorectal cancer (CRC) using bioinformatics, the public database of circRNA was mined.\nMETHODS: CRC differentially expressed miRNAs were screened in the Cancer Genome Atlas (TCGA) database, CRC differentially expressed circRNAs were searched in the Gene Expression Omnibus (GEO) database, the two databases were combined to identify CRC differentially expressed mRNAs, and a circRNA-miRNA‒mRNA regulatory network was constructed by combining a plurality of target prediction databases to identify key genes. The upstream circRNA and regulatory axis of the key genes were identified for gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis to explore the biological functions of circRNA in CRC using the regulatory axis.\nRESULTS: After the screening of the GSE21815 dataset, a total of 22 differentially expressed circRNAs were obtained, with 12 upregulated and 10 downregulated genes. Similarly, the GSE126094 dataset yielded 104 differentially expressed circRNAs, comprising 56 upregulated and 48 downregulated genes. Among the differentially expressed circRNAs, five were identified, with VDAC3 and SETD2 showing downregulated expression, while RAD23B, RPPH1, and MYBL2 exhibited upregulated expression. Following the selection process, five DEcircRNAs, eight target miRNAs, and 105 target DEmRNAs were identified. The protein-protein interaction (PPI) network revealed close relationships among the mRNAs, with E2F2, E2F3, CCND1, TNRC6A, and KAT2B identified as key genes. Notably, CCND1 emerged as a critical gene in the PPI network. Through the upregulation of has-circ-0087862, which binds to miR-892b, the translation inhibition of CCND1 by miR-892b was attenuated, leading to enhanced CCND1 expression. Functional enrichment analysis indicated that CCND1 was involved in protein binding and positive regulation of cellular processes, among other functions.\nCONCLUSION: The differentially expressed genes (DEGs) in CRC markedly affected the survival time of patients. CircRNAs could be utilized as diagnostic markers of CRC, and the key genes in CRC could be screened out by bioinformatics, which would be helpful to understand the drug targets for the treatment of human immunodeficiency virus (HIV)-related CRC patients.", "claims": [{"id": "claim-method", "statement": "Differences between groups were tested using a chi-square test, paired sample Student’‘s t test, independent sample t test, and repeated measures analysis of variance (where applicable).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38064496", "locator": "sections[8] \"2.6 Statistical analysis\" paragraph 2", "quote": "Differences between groups were tested using a chi-square test, paired sample Student’‘s t test, independent sample t test, and repeated measures analysis of variance (where applicable)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE126094 is a dataset with a chip platform GPL19978, consisting of expression profiles of circRNAs in 10 CRC tissues and their corresponding normal tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38064496", "locator": "sections[3] \"2.1 Data source\" paragraph 2", "quote": "GSE126094 is a dataset with a chip platform GPL19978, consisting of expression profiles of circRNAs in 10 CRC tissues and their corresponding normal tissues."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Overexpression of miR-892b in CRC cell SW620 reduced clone formation, cell viability, scratch-healing rate, and invasive-cell number, while increasing E-cadherin and decreasing N-cadherin expression.", "kind": "quantitative", "target": {"value": 0.05, "unit": "p-value", "tolerance": null, "source": "Fig 12 shows that the expression of miR892b and Ecadherin protein increased significantly compared with miR-NC group (P<0.05), while the number of clones, cell viability, scratch healing rate, number of invasive cells and the expression of Ncadherin protein decreased significantly compared with miR-NC group (P<0.05)."}, "evidence": [{"asset": "source:pmid:38064496", "locator": "sections[18] \"3.9 Effect of overexpression of miR892b on proliferation, migration and invasion of CRC cell SW620\" paragraph 2", "quote": "Fig 12 shows that the expression of miR892b and Ecadherin protein increased significantly compared with miR-NC group (P<0.05), while the number of clones, cell viability, scratch healing rate, number of invasive cells and the expression of Ncadherin protein decreased significantly compared with miR-NC group (P<0.05)."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Overexpression of miR-892b in CRC cell SW620 reduced clone formation, cell viability, scratch-healing rate, and invasive-cell number, while increasing E-cadherin and decreasing N-cadherin expression.", "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:38064496"], "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:GSE126094"], "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:GSE126094"], "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:38064496", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": 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