Weighted gene co-expression network analysis and CIBERSORT screening of key genes related to m6A methylation in Hirschsprung's disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:37144136", "kind": "science-record", "revision": 2, "content_hash": "sha256:9fedf558c15fb88ddc2bdad0d8cfd3008331155359f0dea9840f85990c14f4ec", "created_at": "2026-11-01T19:01:48Z", "updated_at": "2026-11-01T21:30:41Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Weighted gene co-expression network analysis and CIBERSORT screening of key genes related to m6A methylation in Hirschsprung's disease.", "doi": "10.3389/fgene.2023.1183467", "pmid": "37144136", "authors": ["Jiaqian Huang", "Tingwei Chen", "Junjie Wang", "Zhiqiang Wang", "Shungen Huang"], "journal": "Frontiers in genetics", "year": 2023, "abstract": "Hirschsprung's disease (HSCR) is a neural crest disease that results from the failure of enteric neural crest cells (ENCCs) to migrate to the corresponding intestinal segment. The RET gene, which regulates enteric neural crest cell proliferation and migration, is considered one of the main risk factors for HSCR and is commonly used to construct HSCR mouse models. The epigenetic mechanism of m6A modification is involved in HSCR. In this study, we analyzed the GEO database (GSE103070) for differentially expressed genes (DEGs) and focused on m6A-related genes. Comparing the RNA-seq data of Wide Type and RET Null, a total of 326 DEGs were identified, of which 245 genes were associated with m6A. According to the CIBERSORT analysis, the proportion of Memory B-cell in RET Null was significantly higher than that of Wide Type. Venn diagram analysis was used to identify key genes in the selected memory B-cell modules and DEGs associated with m6A. Enrichment analysis showed that seven genes were mainly involved in focal adhesion, HIV infection, actin cytoskeleton organization and regulation of binding. These findings could provide a theoretical basis for molecular mechanism studies of HSCR.", "claims": [{"id": "claim-method", "statement": "Pearson correlation analysis was conducted to evaluate the association between m6A modifications and DEGs in Wide Type and RET Null mouse intestinal tissues, with a threshold of |Pearson R|>0.5 and p < 0.05.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37144136", "locator": "sections[5] \"2.3 Identification of m6A-related genes\" paragraph 2", "quote": "Pearson correlation analysis was conducted to evaluate the association between m6A modifications and DEGs in Wide Type and RET Null mouse intestinal tissues, with a threshold of |Pearson R|>0.5 and p < 0.05."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:37144136", "locator": "sections[16] \"Data availability statement\" paragraph 2", "quote": "The datasets presented in this study can be found in online repositories. The names of the repository/repositories and accession number(s) can be found in the article/Supplementary Material."}], "state": "complete"}, {"id": "claim-target-result", "statement": "To identify differentially expressed genes associated with memory B-cell and related with m6A modifications, we mapped 245 DEGs associated with m6A and 641 genes associated with the most relevant modules of memory B-cell in a Venn diagram (Figure 6A), resulting in seven (COL23A1, FBLIM1, GNG10, MYOCD, NIN, NRARP, and ZKSCAN1) differentially expressed genes.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:37144136", "locator": "sections[14] \"3.5 Identification of key genes\" paragraph 2", "quote": "To identify differentially expressed genes associated with memory B-cell and related with m6A modifications, we mapped 245 DEGs associated with m6A and 641 genes associated with the most relevant modules of memory B-cell in a Venn diagram (Figure 6A), resulting in seven (COL23A1, FBLIM1, GNG10, MYOCD, NIN, NRARP, and ZKSCAN1) differentially expressed genes."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "To identify differentially expressed genes associated with memory B-cell and related with m6A modifications, we mapped 245 DEGs associated with m6A and 641 genes associated with the most relevant modules of memory B-cell in a Venn diagram (Figure 6A), resulting in seven (COL23A1, FBLIM1, GNG10, MYOCD, NIN, NRARP, and ZKSCAN1) differentially expressed genes.", "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:37144136"], "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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