Microarray and bioinformatic analysis reveal the parental genes of m6A modified circRNAs as novel prognostic signatures in colorectal cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35965538", "kind": "science-record", "revision": 4, "content_hash": "sha256:569eb5ade4aedaef7fce7769b321159e03c2440e0c66d36231b3238fbb1da4c9", "created_at": "2026-11-01T18:15:04Z", "updated_at": "2026-11-01T22:07:15Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Microarray and bioinformatic analysis reveal the parental genes of m6A modified circRNAs as novel prognostic signatures in colorectal cancer.", "doi": "10.3389/fonc.2022.939790", "pmid": "35965538", "authors": ["Wenken Liang", "Liyuan Deng", "Chune Mo", "Wei Chen", "Yu Sha", "Jianling Shi", "Xianliang Hou", "Yuping Zhang", "Min Yang", "Minglin Ou"], "journal": "Frontiers in oncology", "year": 2022, "abstract": "Background: Accumulating evidences have revealed that the abnormal N6-methyladenosine (m6A) modification is closely associated with the occurrence, development, progression and prognosis of cancer. It is noteworthy that m6A modification is widely existed in circRNAs and found its key biological functions in regulating circRNAs metabolism. However, the role of m6A modified circRNAs in colorectal cancer (CRC) remains unknown. To better understand the role of circRNAs in the pathogenesis of CRC, we focus on the relationship between m6A-modified circRNAs and their parental genes.\nMethods: Arraystar m6A-circRNA epitranscriptomic microarray was used to identify differentially m6A modified circRNAs between CRC and the control group. In addition, TCGA-COAD and GSE106582 cohort were used to identify differentially expressed mRNAs. In this study, we screened the parental genes for which both circRNAs and mRNAs were down-regulated further to analyze, including gene expression, survival prognosis, enrichment analysis. Additionally, Western Blotting was used to further validate the role of the parental gene in CRC.\nResults: We found that 1405 significantly downregulated circRNAs in CRC by our microarray data. Moreover, we obtained 113 parental genes for which both circRNAs and mRNAs were down-regulated to analyze the relationship with the prognosis of CRC based on TCGA-COAD cohort. And we identified nine potential prognostic genes, including ABCD3, ABHD6, GAB1, MIER1, MYOCD, PDE8A, RPS6KA5, TPM1 and WDR78. And low expression of these genes was associated with poor survival prognosis of the patients with CRC. In addition, we found that TPM1 is downregulated in CRC by western blotting experiment. And the calcium-signaling pathway may involve the process of the CRC progression.\nConclusions: We identified nine potential prognostic genes, after analyzed the relationship between the parental genes of m6A modified circRNAs and the progression of CRC. Above all, our study further validated TPM1 can serve as a potentail signature for CRC patients.", "claims": [{"id": "claim-method", "statement": "In the study, we paid more attention to TPM1 and analyzed the relationship between mRNA expression and the clinical factors of CRC (26), by adopting Wilcoxon test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35965538", "locator": "sections[7] \"Public databases and analysis\" paragraph 3", "quote": "In the study, we paid more attention to TPM1 and analyzed the relationship between mRNA expression and the clinical factors of CRC (26), by adopting Wilcoxon test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The original contributions presented in the study are included in the article/Supplementary material. Further inquiries can be directed to the corresponding authors.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35965538", "locator": "sections[19] \"Data availability statement\" paragraph 2", "quote": "The original contributions presented in the study are included in the article/Supplementary material. Further inquiries can be directed to the corresponding authors."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Nine potential prognostic genes were identified: ABCD3, ABHD6, GAB1, MIER1, MYOCD, PDE8A, RPS6KA5, TPM1 and WDR78.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35965538", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "And we identified nine potential prognostic genes, including ABCD3, ABHD6, GAB1, MIER1, MYOCD, PDE8A, RPS6KA5, TPM1 and WDR78."}, {"asset": "source:pmid:35965538", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "And low expression of these genes was associated with poor survival prognosis of the patients with CRC."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "partial", "objective": "Nine potential prognostic genes were identified: ABCD3, ABHD6, GAB1, MIER1, MYOCD, PDE8A, RPS6KA5, TPM1 and WDR78.", "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:35965538"], "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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Moreover, we obtained 113 parental gen"], "order_basis": "paper_text_order:0", "id": "assay:1"}, {"role": "data_generation", "definition_id": "western_blot", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["rognosis, enrichment analysis. Additionally, Western Blotting was used to further validate the role of the", "e found that TPM1 is downregulated in CRC by western blotting experiment. And the calcium-signaling pathwa", "ation analysis of TPM1 for clinical factors. Western Blotting. (A) TPM1 protein expression in the tumor an"], "order_basis": "paper_text_order:1133", "id": "assay:2"}, {"role": "analysis", "definition_id": "group_comparison", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["In the study, we paid more attention to TPM1 and analyzed the relationship between mRNA expression and the clinical factors of CRC (26), by adopting Wilcoxon test."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}