Integrated bioinformatics and network pharmacology to identify the therapeutic target and molecular mechanisms of Huangqin decoction on ulcerative Colitis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:34997010", "kind": "science-record", "revision": 4, "content_hash": "sha256:30a62833ff29ffe355eceb1b1f8a138e432c7305b53a7871d1a3b77a5765c7e8", "created_at": "2026-11-01T17:36:42Z", "updated_at": "2026-11-01T22:05:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Integrated bioinformatics and network pharmacology to identify the therapeutic target and molecular mechanisms of Huangqin decoction on ulcerative Colitis.", "doi": "10.1038/s41598-021-03980-8", "pmid": "34997010", "authors": ["Yi Wu", "Xinqiao Liu", "Guiwei Li"], "journal": "Scientific reports", "year": 2022, "abstract": "Huangqin decoction (HQD) is a Traditional Chinese Medicine formula for ulcerative colitis. However, the pharmacology and molecular mechanism of HQD on ulcerative colitis is still unclear. Combined microarray analysis, network pharmacology, and molecular docking for revealing the therapeutic targets and molecular mechanism of HQD against ulcerative colitis. TCMSP, DrugBank, Swiss Target Prediction were utilized to search the active components and effective targets of HQD. Ulcerative colitis effective targets were obtained by microarray data from the GEO database (GSE107499). Co-targets between HQD and ulcerative colitis are obtained by Draw Venn Diagram. PPI (Protein-protein interaction) network was constructed by the STRING database. To obtain the core target, topological analysis is exploited by Cytoscape 3.7.2. GO and KEGG enrichment pathway analysis was performed to Metascape platform, and molecular docking through Autodock Vina 1.1.2 finished. 161 active components with 486 effective targets of HQD were screened. 1542 ulcerative colitis effective targets were obtained with |Log2FC|> 1 and adjusted P-value < 0.05. The Venn analysis was contained 79 co-targets. Enrichment analysis showed that HQD played a role in TNF signaling pathway, IL-17 signaling pathway, Th17 cell differentiation, etc. IL6, TNF, IL1B, PTGS2, ESR1, and PPARG with the highest degree from PPI network were successfully docked with 19 core components of HQD, respectively. According to ZINC15 database, quercetin (ZINC4175638), baicalein (ZINC3871633), and wogonin (ZINC899093) recognized as key compounds of HQD on ulcerative colitis. PTGS2, ESR1, and PPARG are potential therapeutic targets of HQD. HQD can act on multiple targets through multi-pathway, to carry out its therapeutic role in ulcerative colitis.", "claims": [{"id": "claim-method", "statement": "According to the GEO2R web tool, a total of 1542 DEGs were identified, which consist of 1024 upregulated and 518 downregulated genes", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34997010", "locator": "sections[10] \"Identification of DEGs and co-targets\" paragraph 2", "quote": "According to the GEO2R web tool, a total of 1542 DEGs were identified, which consist of 1024 upregulated and 518 downregulated genes"}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data used to support the findings of this study is available.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:34997010", "locator": "sections[25] \"notes\" paragraph 1", "quote": "The data used to support the findings of this study is available."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The study identified 79 co-targets between Huangqin decoction and ulcerative colitis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:34997010", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "The Venn analysis was contained 79 co-targets."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The study identified 79 co-targets between Huangqin decoction and ulcerative colitis.", "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:34997010"], "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:GSE107499"], "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:GSE107499"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:34997010", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-021-03980-8", "sha256": "sha256:fcb67f3bd87ae413adcfa31daadd74ce74d4e62bc1c8f9dcc69f1c0f3f49a4fb", "bytes": 23243, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-021-03980-8", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8741777", "source": "europe_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE107499", "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=GSE107499", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE107499", "version": null, "note": "The data used to support the findings of this study is available.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The data used to support the findings of this study is available.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM2869335", "GSM2869336", "GSM2869337", "GSM2869338", "GSM2869339", "GSM2869340", "GSM2869341", "GSM2869342", "GSM2869343", "GSM2869344", "GSM2869345", "GSM2869346", "GSM2869347", "GSM2869348", "GSM2869349", "GSM2869350", "GSM2869351", "GSM2869352", "GSM2869353", "GSM2869354", "GSM2869355", "GSM2869356", "GSM2869357", "GSM2869358", "GSM2869359", "GSM2869360", "GSM2869361", "GSM2869362", "GSM2869363", "GSM2869364", "GSM2869365", "GSM2869366", "GSM2869367", "GSM2869368", "GSM2869369", "GSM2869370", "GSM2869371", "GSM2869372", "GSM2869373", "GSM2869374", "GSM2869375", "GSM2869376", "GSM2869377", "GSM2869378", "GSM2869379", "GSM2869380", "GSM2869381", "GSM2869382", "GSM2869383", "GSM2869384", "GSM2869385", "GSM2869386", "GSM2869387", "GSM2869388", "GSM2869389", "GSM2869390", "GSM2869391", "GSM2869392", "GSM2869393", "GSM2869394", "GSM2869395", "GSM2869396", "GSM2869397", "GSM2869398", "GSM2869399", "GSM2869400", "GSM2869401", "GSM2869402", "GSM2869403", "GSM2869404", "GSM2869405", "GSM2869406", "GSM2869407", "GSM2869408", "GSM2869409", "GSM2869410", "GSM2869411", "GSM2869412", "GSM2869413", "GSM2869414", "GSM2869415", "GSM2869416", "GSM2869417", "GSM2869418", "GSM2869419", "GSM2869420", "GSM2869421", "GSM2869422", "GSM2869423", "GSM2869424", "GSM2869425", "GSM2869426", "GSM2869427", "GSM2869428", "GSM2869429", "GSM2869430", "GSM2869431", "GSM2869432", "GSM2869433", "GSM2869434", "GSM2869435", "GSM2869436", "GSM2869437", "GSM2869438", "GSM2869439", "GSM2869440", "GSM2869441", "GSM2869442", "GSM2869443", "GSM2869444", "GSM2869445", "GSM2869446", "GSM2869447", "GSM2869448", "GSM2869449", "GSM2869450", "GSM2869451", "GSM2869452", "GSM2869453"], "sample_count": 119, "group_sizes": null, "group_sizes_basis": null, "platform": "15207", "taxon": "Homo sapiens", "title": "Expression data from Ulcerative Colitis subjects", "resolution_checked_at": "2026-11-01T17:30:42Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE107499 not downloaded", "asset:data:geo:GSE107499 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "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": "PPI"}}, {"id": "method-2", "family": null, "specific": null, "label": "GEO2R differential expression analysis with |Log2FC| > 1 and adjusted P-value < 0.05", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "According to the GEO2R web tool, a total of 1542 DEGs were identified, which consist of 1024 upregulated and 518 downregulated genes"}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["build_graph", "centrality_scores", "pathway_enrich"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: ppi_network."}, "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": ["GSE107499"], "resolved_accessions": ["GSE107499"], "statements": ["The data used to support the findings of this study is available."], "basis": "The paper names GSE107499 in GEO and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:34997010", "data:geo:GSE107499"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE107499"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:14:45Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 8100, "completion_tokens": 2867, "cached_tokens": 256}}, "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:34997010", "type": "paper", "label": "pmid:34997010"}, {"id": "source:pmid:34997010", "type": "manuscript", "label": "PMID 34997010 full text"}, {"id": "data:geo:GSE107499", "type": "dataset", "label": "GEO GSE107499"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34997010", "type": "paper", "label": "pmid:34997010"}, {"id": "source:pmid:34997010", "type": "manuscript", "label": "PMID 34997010 full text"}, {"id": "data:geo:GSE107499", "type": "dataset", "label": "GEO GSE107499"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34997010", "type": "extraction", "used": ["source:pmid:34997010"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE107499", "type": "accession_resolution", "used": ["data:geo:GSE107499"], "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:34997010", "parent_hash": "sha256:ba7d860e6f7334f39c71bc4850573f79760301c7476fbb5aa4d86c9a1af49713", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE107499 licence not read", "asset:data:geo:GSE107499 not downloaded", "execution.not_run", "method.reader_named_unmapped", "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": 0.99, "evidence": ["lcerative colitis is still unclear. Combined microarray analysis, network pharmacology, and molecula", "e colitis effective targets were obtained by microarray data from the GEO database (GSE107499). Co-t"], "order_basis": "paper_text_order:308", "id": "assay:1"}, {"role": "analysis", "definition_id": "network_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["PPI"], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}