Database screening of herbal monomers regulating autophagy by constructing a "disease-gene-drug" network.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:25475428", "kind": "science-record", "revision": 9, "content_hash": "sha256:0859222a6a9cbd884704593c2ad8749fb4dc56542823308beda8791e955aa0ce", "created_at": "2026-11-01T15:40:07Z", "updated_at": "2026-11-01T22:42:09Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Database screening of herbal monomers regulating autophagy by constructing a \"disease-gene-drug\" network.", "doi": "10.1186/1472-6882-14-466", "pmid": "25475428", "authors": ["Chenjun Hao", "Zhengpeng Yang", "Bo Gao", "Ming Lu", "Xianzhi Meng", "Xin Qiao", "Dongbo Xue", "Weihui Zhang"], "journal": "BMC complementary and alternative medicine", "year": 2014, "abstract": "BACKGROUND: Studies suggest an important role of autophagy as a target for cancer therapy. We constructed a \"disease-gene-drug\" network using the modular approach of bioinformatics and screened herbal monomers demonstrating functions related to autophagy regulation.\nMETHODS: Based on the microarray results of the gene expression omnibus (GEO) database (GSE2435 and GSE31040, starvation-induced autophagy model), we used the human protein reference database (HPRD) to obtain the protein-protein interaction (PPI) network. In addition, we used the CFinder software to identify several functional modules, performed gene ontology-biological process (GO-BP) functional enrichment analysis using the DAVID software, constructed a herbal monomer-module gene regulatory network using literature search and the Cytoscape software, and then analyzed the relationships between autophagy, genes, and herbal monomers.\nRESULTS: We screened 544 differentially expressed genes related to autophagy, 375 pairs of differentially expressed genes, and 7 gene modules, wherein the functions of module 3 (composed of 7 genes) were enriched in \"cell death\". Using the constructed herbal monomer-module gene regulatory network, we found that 30 herbal monomers can simultaneously regulate these 7 genes, indicating a potential regulatory role in autophagy.\nCONCLUSIONS: Database screening using the disease-gene-drug network can provide new strategies and ideas for the application of herbal medicines in cancer therapy.", "claims": [{"id": "claim-method", "statement": "We used the LIMMA differentially expressed gene screen algorithm to screen genes either upregulated or downregulated in the autophagy condition compared with the control condition, and the fold of change, P-value and false discovery rate (FDR) were calculated.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25475428", "locator": "sections[3] \"Microarray data processing\" paragraph 3", "quote": "We used the LIMMA differentially expressed gene screen algorithm to screen genes either upregulated or downregulated in the autophagy condition compared with the control condition, and the fold of change, P-value and false discovery rate (FDR) were calculated."}], "state": "complete"}, {"id": "claim-data-access", "statement": "which can be obtained from the GEO (Gene Expression Omnibus) database.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:25475428", "locator": "sections[3] \"Microarray data processing\" paragraph 2", "quote": "which can be obtained from the GEO (Gene Expression Omnibus) database."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": null, "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:25475428"], "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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the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC4295301", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE2435", "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=GSE2435", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE2435", "version": null, "note": "which can be obtained from the GEO (Gene Expression Omnibus) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "which can be obtained from the GEO (Gene Expression Omnibus) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM45796", "GSM45797", "GSM45798", "GSM45799", "GSM45800", "GSM45801"], "sample_count": 6, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Autophagy promotes MHC class II presentation of peptides from intracellular source proteins", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "data:geo:GSE31040", "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=GSE31040", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE31040", "version": null, "note": "which can be obtained from the GEO (Gene Expression Omnibus) database.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "which can be obtained from the GEO (Gene Expression Omnibus) database.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM769038", "GSM769039", "GSM769040", "GSM769041", "GSM769042", "GSM769043", "GSM769044", "GSM769045", "GSM769046", "GSM769047", "GSM769048", "GSM769049"], "sample_count": 12, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression analysis of human lymphoblastoid cell lines", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE2435 not downloaded", "asset:data:geo:GSE2435 licence not read", "asset:data:geo:GSE31040 not downloaded", "asset:data:geo:GSE31040 licence not read"]}, "analysis": {"state": "complete", "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": "verbatim", "quote": "We used the LIMMA differentially expressed gene screen algorithm to screen genes either upregulated or downregulated in the autophagy condition compared with the control condition, and the fold of change, P-value and false discovery rate (FDR) were calculated."}}, {"id": "method-2", "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": []}, "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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METHODS: Based on the microarray results of the gene expression omnibus (GEO)", "Methods Microarray data processing Two series of Earle’s balanc", "ach experiment was repeated three times. The microarray experiments performed in this study included", "es were detected based on the HG-U133-Plus-2 Affymetrix Human Genome U133 Plus 2.0 Array. 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