Integrated transcriptomic and co-expression network analysis identifies HIF1A as a key immune regulator in biliary atresia.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:41502897", "kind": "science-record", "revision": 4, "content_hash": "sha256:f3fc2943f8021746e5bed9b9adfba2c3f3475343248f47c9b4444a3c5c2f4aa6", "created_at": "2026-11-01T20:31:29Z", "updated_at": "2026-11-01T22:57:42Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated transcriptomic and co-expression network analysis identifies HIF1A as a key immune regulator in biliary atresia.", "doi": "10.21037/tp-2025-590", "pmid": "41502897", "authors": ["Chu Wang", "Lijing Xiong", "Yang Li"], "journal": "Translational pediatrics", "year": 2025, "abstract": "Background: Biliary atresia (BA) is a rapidly progressive neonatal cholangiopathy with unclear pathogenesis. This study aimed to elucidate the key molecular mechanisms and regulatory networks underlying BA through integrative transcriptomic analysis, providing insights for early diagnosis and targeted therapy.\nMethods: Three BA-related liver microarray datasets (GSE46960, GSE159720, and GSE15235) were retrieved from the Gene Expression Omnibus (GEO) database and analyzed using a unified pipeline. Differentially expressed genes (DEGs) in the training cohort (GSE46960; 64 BA vs. 14 controls) were identified with limma under Benjamini-Hochberg false discovery rate (BH-FDR) control. Functional enrichment [Gene Ontology (GO)/Kyoto Encyclopedia of Genes and Genomes (KEGG)], xCell-based immune infiltration analysis, and gene-set intersection with Hedgehog and NOTCH developmental pathways were performed. HIF1A-stratified transcriptional programs were evaluated by DEG analysis and Gene Set Enrichment Analysis (GSEA). In the validation cohorts, we assessed expression trends and effect sizes across BA subtypes and HIF1A-defined groups. Weighted gene co-expression network analysis (WGCNA) was then applied to DEGs from the inflammatory subtype (GSE15235) to identify co-expression modules associated with HIF1A.\nResults: We identified 343 DEGs between BA and controls, predominantly enriched in cytokine signaling, immune activation, and fibrosis-related pathways, whereas downregulated genes were linked to erythrocyte function and lipid metabolism. Intersection of DEGs with Hedgehog and NOTCH gene sets highlighted six development-related genes; among them, only HIF1A showed consistent and significant upregulation in independent BA samples. Intersection with immune-related gene sets yielded 29 immune-related DEGs centered on HIF1A in the protein-protein interaction (PPI) network. Across cohorts, high HIF1A expression was associated with enhanced enrichment of neutrophils, monocytes, and T cells, as well as positive correlations with neutrophil markers and major histocompatibility complex (MHC) genes. HIF1A-stratified DEGs were enriched in tumor necrosis factor (TNF) and hypoxia-inducible factor-1 (HIF-1) signaling, inflammatory and cytokine-response pathways, and perturbations of bile acid and adenosine triphosphate (ATP)-binding cassette (ABC) transporter pathways. WGCNA of HIF1A-associated DEGs identified a key co-expression module (MEblue) strongly correlated with HIF1A and enriched for leukocyte chemotaxis and cytokine signaling.\nConclusions: HIF1A may play a central role in the pathogenesis of BA by linking hypoxia responses with immune and fibrotic remodeling, particularly via neutrophil- and cytokine-driven inflammation. These findings suggest that HIF1A and its downstream networks represent promising candidates for early detection and targeted intervention in BA, warranting validation in larger, clinically annotated cohorts and experimental models.", "claims": [{"id": "claim-method", "statement": "Differentially expressed genes (DEGs) were identified with the limma package (R), modeling BA vs. control with the control group as the reference. To control for multiple testing at the gene level, we applied the Benjamini-Hochberg false discovery rate (BH-FDR) to limma’s moderated statistics.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41502897", "locator": "sections[6] \"Differential gene expression analysis\" paragraph 2", "quote": "Differentially expressed genes (DEGs) were identified with the limma package (R), modeling BA vs. control with the control group as the reference. To control for multiple testing at the gene level, we applied the Benjamini-Hochberg false discovery rate (BH-FDR) to limma’s moderated statistics."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Among the three datasets, GSE46960 served as the training set for differential expression and co-expression analyses.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:41502897", "locator": "sections[4] \"GEO data acquisition\" paragraph 4", "quote": "Among the three datasets, GSE46960 served as the training set for differential expression and co-expression analyses."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified 343 DEGs between BA and controls, predominantly enriched in cytokine signaling, immune activation, and fibrosis-related pathways, whereas downregulated genes were linked to erythrocyte function and lipid metabolism.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:41502897", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "We identified 343 DEGs between BA and controls, predominantly enriched in cytokine signaling, immune activation, and fibrosis-related pathways, whereas downregulated genes were linked to erythrocyte function and lipid metabolism."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified 343 DEGs between BA and controls, predominantly enriched in cytokine signaling, immune activation, and fibrosis-related pathways, whereas downregulated genes were linked to erythrocyte function and lipid metabolism.", "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:41502897"], "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:GSE15235"], "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": {"fdr_threshold": "with Benjamini-Hochberg false discovery rate control"}, "inputs": ["data:geo:GSE15235"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:41502897", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/tp-2025-590", "sha256": "sha256:6c4630d9f4c0b087d2377672832318c19a7723c6367ca7e12b60d95b8d785968", "bytes": 57513, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/tp-2025-590", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC12771227", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE15235", "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=GSE15235", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE15235", "version": null, "note": "Among the three datasets, GSE46960 served as the training set for differential expression and co-expression analyses.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Among the three datasets, GSE46960 served as the training set for differential expression and co-expression analyses.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM380382", "GSM380383", "GSM380384", "GSM380385", "GSM380386", "GSM380387", "GSM380388", "GSM380389", "GSM380390", "GSM380391", "GSM380392", "GSM380393", "GSM380394", "GSM380395", "GSM380396", "GSM380397", "GSM380398", "GSM380399", "GSM380400", "GSM380401", "GSM380402", "GSM380403", "GSM380404", "GSM380405", "GSM380406", "GSM380407", "GSM380408", "GSM380409", "GSM380410", "GSM380411", "GSM380412", "GSM380413", "GSM380414", "GSM380415", "GSM380416", "GSM380417", "GSM380418", "GSM380419", "GSM380420", "GSM380421", "GSM380422", "GSM380423", "GSM380424", "GSM380425", "GSM380426", "GSM380427", "GSM380428"], "sample_count": 47, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Staging of biliary atresia at diagnosis by molecular profiling of the liver", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE159720", "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=GSE159720", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE159720", "version": null, "note": "Among the three datasets, GSE46960 served as the training set for differential expression and co-expression analyses.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Among the three datasets, GSE46960 served as the training set for differential expression and co-expression analyses.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM4838474", "GSM4838475", "GSM4838476", "GSM4838477", "GSM4838478", "GSM4838479", "GSM4838480"], "sample_count": 7, "group_sizes": null, "group_sizes_basis": null, "platform": "18573", "taxon": "Homo sapiens", "title": "Biliary-Atresia-associated Mannosidase-1-alpha-2 gene regulates biliary and ciliary morphogenesis and laterality", "resolution_checked_at": "2026-11-01T20:16:08Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE46960", "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=GSE46960", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE46960", "version": null, "note": "Among the three datasets, GSE46960 served as the training set for differential expression and co-expression analyses.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Among the three datasets, GSE46960 served as the training set for differential expression and co-expression analyses.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM1142048", "GSM1142049", "GSM1142050", "GSM1142051", "GSM1142052", "GSM1142053", "GSM1142054", "GSM1142055", "GSM1142056", "GSM1142057", "GSM1142058", "GSM1142059", "GSM1142060", "GSM1142061", "GSM1142062", "GSM1142064", "GSM1142065", "GSM1142066", "GSM1142067", "GSM1142068", "GSM1142069", "GSM1142070", "GSM1142071", "GSM1142072", "GSM1142074", "GSM1142075", "GSM1142076", "GSM1142077", "GSM1142078", "GSM1142079", "GSM1142080", "GSM1142081", "GSM1142082", "GSM1142083", "GSM1142085", "GSM1142086", "GSM1142087", "GSM1142088", "GSM1142089", "GSM1142090", "GSM1142091", "GSM1142092", "GSM1142093", "GSM1142094", "GSM1142095", "GSM1142097", "GSM1142098", "GSM1142099", "GSM1142100", "GSM1142101", "GSM1142102", "GSM1142103", "GSM1142104", "GSM1142105", "GSM1142106", "GSM1142107", "GSM1142108", "GSM1142109", "GSM1142110", "GSM1142111", "GSM1142112", "GSM1142113", "GSM1142114", "GSM1142115", "GSM1142116", "GSM1142117", "GSM1142118", "GSM1142119", "GSM1142120", "GSM1142121", "GSM1142122", "GSM1142123", "GSM1142124", "GSM1142125", "GSM1142126", "GSM1142127", "GSM1142128", "GSM1142129", "GSM1142130", "GSM1142131", "GSM1142132", "GSM1142133", "GSM1142134", "GSM1142135", "GSM1142136", "GSM1142137", "GSM1142138", "GSM1142139", "GSM1142140", "GSM1142141", "GSM1142142", "GSM1142143", "GSM1142144", "GSM1142145", "GSM1142146"], "sample_count": 95, "group_sizes": null, "group_sizes_basis": null, "platform": "6244", "taxon": "Homo sapiens", "title": "Comprehensive gene expression profile of human livers from patients with biliary atresia at the time of diagnosis and the corresponding disease and normal controls", "resolution_checked_at": "2026-11-01T18:06:44Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE15235 not downloaded", "asset:data:geo:GSE15235 licence not read", "asset:data:geo:GSE159720 not downloaded", "asset:data:geo:GSE159720 licence not read", "asset:data:geo:GSE46960 not downloaded", "asset:data:geo:GSE46960 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": {"fdr_threshold": "with Benjamini-Hochberg false discovery rate control"}, "data_shapes": ["count_matrix_with_condition"], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Differentially expressed genes (DEGs) were identified with the limma package (R), modeling BA vs. control with the control group as the reference. To control for multiple testing at the gene level, we applied the Benjamini-Hochberg false discovery rate (BH-FDR) to limma’s moderated statistics."}}, {"id": "method-2", "family": "group_comparison", "specific": "wilcoxon", "label": "Group comparison", "dsl_operations": [], "missing_operations": ["group_comparison_wilcoxon"], "expressible": false, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "Wilcoxon"}}, {"id": "method-3", "family": "group_comparison", "specific": "anova", "label": "Group comparison", "dsl_operations": ["group_summary", "welch_t", "bootstrap_mean_difference", "group_comparison_anova"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["two_or_more_groups_continuous"], "evidence": {"score": 0.8, "band": "high", "quote": "analysis of variance"}}, {"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"}}], "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE46960", "GSE159720", "GSE15235"], "resolved_accessions": ["GSE46960", "GSE159720", "GSE15235"], "statements": ["Among the three datasets, GSE46960 served as the training set for differential expression and co-expression analyses."], "basis": "The paper names GSE46960, GSE159720, GSE15235 in Gene Expression Omnibus (GEO) database and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "assets": ["source:pmid:41502897", "data:geo:GSE15235"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE15235"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T20:09:42Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 14312, "completion_tokens": 1445, "cached_tokens": 264}}, "human_critique": null, "stages": [{"id": "extraction", "state": "complete", "reader": "MiniMax-M3.1-Flash", "provider": "minimax"}], "gaps": ["review.independent_reader", "review.machine_critique", "review.human_critique"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "pmid:41502897", "type": "paper", "label": "pmid:41502897"}, {"id": "source:pmid:41502897", "type": "manuscript", "label": "PMID 41502897 full text"}, {"id": "data:geo:GSE15235", "type": "dataset", "label": "GEO GSE15235"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:41502897", "type": "paper", "label": "pmid:41502897"}, {"id": "source:pmid:41502897", "type": "manuscript", "label": "PMID 41502897 full text"}, {"id": "data:geo:GSE15235", "type": "dataset", "label": "GEO GSE15235"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-41502897", "type": "extraction", "used": ["source:pmid:41502897"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE15235", "type": "accession_resolution", "used": ["data:geo:GSE15235"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}, {"id": "agent:minimax-reader", "type": "software", "label": "MiniMax literature reader"}], "source_run_id": "reading-sci-2026-11-01", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:41502897", "parent_hash": "sha256:98b38cb44630e728dcb76c71e9c99d62c9fe9a29704b3460ff17cdb23c2557fe", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE15235 licence not read", "asset:data:geo:GSE15235 not downloaded", "asset:data:geo:GSE159720 licence not read", "asset:data:geo:GSE159720 not downloaded", "asset:data:geo:GSE46960 licence not read", "asset:data:geo:GSE46960 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "microarray", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.93, "evidence": ["ted therapy. Methods: Three BA-related liver microarray datasets (GSE46960, GSE159720, and GSE15235)"], "order_basis": "paper_text_order:423", "id": "assay:1"}, {"role": "analysis", "definition_id": "differential_expression", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["normalise_counts", "differential_expression_fit", "fdr_bh"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Differentially expressed genes (DEGs) were identified with the limma package (R), modeling BA vs. control with the control group as the reference. To control for multiple testing at the gene level, we applied the Benjamini-Hochberg false discovery rate (BH-FDR) to limma’s moderated statistics."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}