Identification and validation of autophagy-related genes in Hirschsprung's disease.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:39494277", "kind": "science-record", "revision": 4, "content_hash": "sha256:a72cf0f83d3ca9bf1e2cacf894608295d09cd554ed293906020fef8591f1d1ec", "created_at": "2026-11-01T20:29:45Z", "updated_at": "2026-11-01T22:55:32Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and validation of autophagy-related genes in Hirschsprung's disease.", "doi": "10.7717/peerj.18376", "pmid": "39494277", "authors": ["Ting Yao", "Zenghui Hao", "Wei Fan", "Jinbao Han", "Shuyu Wang", "Zaiqun Jiang", "Yunting Wang", "Xiao Qian Yang", "Zhilin Xu"], "journal": "PeerJ", "year": 2024, "abstract": "Background: Hirschsprung's disease (HSCR) is a congenital disorder characterized by aganglionosis in the intermuscular and submucosal nerve plexuses of the gut, leading to impaired gastrointestinal function. Although the precise cause and pathophysiology of HSCR remain elusive, increasing evidence points to a significant role of autophagy in its development, warranting further investigation into its underlying mechanisms.\nMethods: This study utilized publicly available microarray expression profiling datasets, GSE96854 and GSE98502, from the Gene Expression Omnibus (GEO). The R software (version 4.2.0) was employed to identify autophagy-related genes potentially showing differential expression in HSCR. Subsequent analyses included correlation analysis, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment, and protein-protein interaction (PPI) network analysis using the STRING database (version 11.0) and Cytoscape software (version 3.8.2). Ultimately, HSCR samples were used to verify the mRNA levels of important genes by quantitative real-time polymerase chain reaction (qRT-PCR) in a laboratory setting.\nResults: We have discovered 20 genes that are involved in autophagy and show variable expression. Among these genes, 15 are up-regulated and five are down-regulated. The enrichment analysis using the GO and KEGG pathways revealed a notable enrichment in pathways related to the control of autophagy. Nine hub genes were found via the investigation of the PPI network constructed from STRING database and module analysis using Cytoscape. Moreover, the concordance between SIRT1 expression in the HSCR model and the bioinformatics analysis of mRNA chip findings was validated using qRT-PCR.\nConclusion: Utilizing bioinformatics analysis, we identified 20 potential genes associated with Hirschsprung's disease that play a role in autophagy. Notably, the upregulation of SIRT1 may profoundly influence the progression of HSCR by regulating autophagy-related pathways, offering a novel perspective on the disease's pathogenesis.", "claims": [{"id": "claim-method", "statement": "The R software was used for differential expression analysis, employing the limma package (version 3.40.6) with the lmFit function for linear modeling. Adjusted p-values were calculated using the Benjamini–Hochberg method. The datasets were compared using a t-test, and statistical significance was evaluated using a significance level of P < 0.05. The gene expression levels of our clinical samples were compared using a two-tailed Student’s t-test, and a significance threshold of P < 0.05 was utilized to determine statistically significant differences.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39494277", "locator": "sections[4] \"Investigation of genes with altered expression associated with autophagy\" paragraph 2", "quote": "The R software was used for differential expression analysis, employing the limma package (version 3.40.6) with the lmFit function for linear modeling."}, {"asset": "source:pmid:39494277", "locator": "sections[4] \"Investigation of genes with altered expression associated with autophagy\" paragraph 2", "quote": "Adjusted p-values were calculated using the Benjamini–Hochberg method."}, {"asset": "source:pmid:39494277", "locator": "sections[7] \"Further validation of hub gene expression in HSCR colon specimens necessitates the inclusion of additional datasets\" paragraph 2", "quote": "The datasets were compared using a t-test, and statistical significance was evaluated using a significance level of P < 0.05."}, {"asset": "source:pmid:39494277", "locator": "sections[9] \"Statistical analysis\" paragraph 2", "quote": "The gene expression levels of our clinical samples were compared using a two-tailed Student’s t-test, and a significance threshold of P < 0.05 was utilized to determine statistically significant differences."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The clinical data of patients with HSCR are available in the Supplementary Files.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:39494277", "locator": "sections[19] \"Additional Information and Declarations\" paragraph 5", "quote": "The clinical data of patients with HSCR are available in the Supplementary Files."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 20 autophagy-related genes with variable expression in Hirschsprung’s disease.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:39494277", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We have discovered 20 genes that are involved in autophagy and show variable expression."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 20 autophagy-related genes with variable expression in Hirschsprung’s disease.", "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:39494277"], "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:GSE96854"], "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": {}, "inputs": ["data:geo:GSE96854"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:39494277", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.18376", "sha256": "sha256:0d79f608e3748836f7c687e59bde8b33058a6a74c5225f702b982297de24a7e2", "bytes": 34867, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.18376", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11531261", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE96854", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE96854", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE96854", "version": null, "note": "The clinical data of patients with HSCR are available in the Supplementary Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The clinical data of patients with HSCR are available in the Supplementary Files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2545127", "GSM2545128", "GSM2545129", "GSM2545130", "GSM2545131", "GSM2545132"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "18943", "taxon": "Homo sapiens", "title": "Transcriptomics analysis of Hirschsprung’s disease", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE98502", "role": "raw", "format": "geo-series", "media_type": "application/vnd.ncbi.geo-series+json", "uri": "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE98502", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE98502", "version": null, "note": "The clinical data of patients with HSCR are available in the Supplementary Files.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The clinical data of patients with HSCR are available in the Supplementary Files.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2597481", "GSM2597482", "GSM2597483", "GSM2597484", "GSM2597485", "GSM2597486", "GSM2597487", "GSM2597488", "GSM2597489", "GSM2597490", "GSM2597491", "GSM2597492", "GSM2597493", "GSM2597494", "GSM2597495", "GSM2597496"], "sample_count": 16, "group_sizes": null, "group_sizes_basis": null, "platform": "22361", "taxon": "Homo sapiens", "title": "Gene expression profiling coupled with the Connectivity Map database-mining reveals potential therapeutic drugs for Hirschsprung disease", "resolution_checked_at": "2026-11-01T18:46:34Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE96854 not downloaded", "asset:data:geo:GSE96854 licence not read", "asset:data:geo:GSE98502 not downloaded", "asset:data:geo:GSE98502 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "differential_expression", "specific": "limma_voom", "label": "Differential expression analysis", "dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "reordered", "quote": "The R software was used for differential expression analysis, employing the limma package (version 3.40.6) with the lmFit function for linear modeling. Adjusted p-values were calculated using the Benjamini–Hochberg method. The datasets were compared using a t-test, and statistical significance was evaluated using a significance level of P < 0.05. The gene expression levels of our clinical samples were compared using a two-tailed Student’s t-test, and a significance threshold of P < 0.05 was utilized to determine statistically significant differences."}}, {"id": "method-2", "family": "principal_component_analysis", "specific": "pca", "label": "Principal component analysis", "dsl_operations": ["pca_fit"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["wide_numeric_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "PCA"}}, {"id": "method-3", "family": "clustering", "specific": "hierarchical", "label": "Clustering", "dsl_operations": ["hierarchical_cluster"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["feature_matrix"], "evidence": {"score": 0.8, "band": "high", "quote": "hierarchical clustering"}}, {"id": "method-4", "family": "network_analysis", "specific": "ppi_network", "label": "Network / pathway analysis", "dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "protein-protein interaction"}}, {"id": "method-5", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "targets": [], "gaps": ["method.reader_differs_from_extractor"]}, "capability": {"state": "complete", "requirements": [{"capability_id": "capability:computational_analysis", "label": "Computational analysis platform", "assay_families": ["meta_analysis", "machine_learning", "survival_analysis", "statistical_regression", "pca", "molecular_docking", "network_analysis", "differential_expression", "gwas"], "availability_state": "owned", "tier_unlocked": "R1", "candidate": "Automated Assays Laravel application and simulated adapters"}], "gaps": []}, "readiness": {"state": "complete", "tier": "R1", "blocking_axis": "none", "blocked_on": "nothing:replicable_now", "axes": {"method": {"tier": "R1", "expressible": true, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: limma_voom."}, "capability": {"tier": "R1", "capability_id": "capability:computational_analysis", "availability_state": "owned", "basis": "The computational analysis is owned. 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