Identification of hub genes and candidate herbal treatment in obesity through integrated bioinformatic analysis and reverse network pharmacology.

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As there is a lack of effective drugs to treat obesity, we combined bioinformatics and reverse network pharmacology in this study to identify effective herbs to treat obesity. We identified 1011 differentially expressed genes (DEGs) of adipose tissue after weight loss by analyzing five expression profiles (GSE103766, GSE35411, GSE112307, GSE43471, and GSE35710) from the Gene Expression Omnibus (GEO) database. We identified 27 hub genes from the protein-protein interaction (PPI) network by performing MCODE using the Search Tool for the Retrieval of Interacting Genes (STRING) database. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analyses revealed that these hub genes have roles in the extracellular matrix-receptor interaction, cholesterol metabolism, PI3K-Akt signaling pathway, etc. Ten herbs (Aloe, Portulacae Herba, Mori Follum, Silybum Marianum, Phyllanthi Fructus, Pollen Typhae, Ginkgo Semen, Leonuri Herba, Eriobotryae Folium, and Litseae Fructus) targeting the nine hub genes (COL1A1, MMP2, MMP9, SPP1, DNMT3B, MMP7, CETP, COL1A2, and MUC1) using six ingredients were identified as the key herbs. Quercetin and (-)-epigallocatechin-3-gallate were determined to be the key ingredients. Lastly, Ingredients-Targets, Herbs-Ingredients-Targets, and Herbs-Taste-Meridian Tropism networks were constructed using Cytoscape to elucidate this complex relationship. This study could help identify promising therapeutic targets and drugs to treat obesity.", "claims": [{"id": "claim-method", "statement": "DEGs with a threshold criterion of |log FC |> 1 and p-value < 0.0550 in SAT samples were screened using the linear models for microarray data package after incorporating weight-loss intervention51.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36224334", "locator": "sections[15] \"Identification of differentially expressed genes (DEGs)\" paragraph 2", "quote": "DEGs with a threshold criterion of |log FC |> 1 and p-value < 0.0550 in SAT samples were screened using the linear models for microarray data package after incorporating weight-loss intervention51."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The data that support the findings of this study are available in GEO database (http://www.ncbi.nlm.nih.gov/geo), reference number [GSE103766, GSE35411, GSE112307, GSE43471, and GSE35710].", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:36224334", "locator": "sections[27] \"notes\" paragraph 1", "quote": "The data that support the findings of this study are available in GEO database (http://www.ncbi.nlm.nih.gov/geo), reference number [GSE103766, GSE35411, GSE112307, GSE43471, and GSE35710]."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified 1011 differentially expressed genes (DEGs) of adipose tissue after weight loss by analyzing five expression profiles (GSE103766, GSE35411, GSE112307, GSE43471, and GSE35710) from the Gene Expression Omnibus (GEO) database.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:36224334", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We identified 1011 differentially expressed genes (DEGs) of adipose tissue after weight loss by analyzing five expression profiles (GSE103766, GSE35411, GSE112307, GSE43471, and GSE35710) from the Gene Expression Omnibus (GEO) database."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified 1011 differentially expressed genes (DEGs) of adipose tissue after weight loss by analyzing five expression profiles (GSE103766, GSE35411, GSE112307, GSE43471, and GSE35710) from the Gene Expression Omnibus (GEO) database.", "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:36224334"], "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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No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["build_graph", "centrality_scores", "pathway_enrich"], "assets": ["source:pmid:36224334", "data:geo:GSE103766"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE103766"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T18:09:53Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9045, "completion_tokens": 1830, "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:36224334", "type": "paper", "label": "pmid:36224334"}, {"id": "source:pmid:36224334", "type": "manuscript", "label": "PMID 36224334 full text"}, {"id": "data:geo:GSE103766", "type": "dataset", "label": "GEO GSE103766"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:36224334", "type": "paper", "label": "pmid:36224334"}, {"id": "source:pmid:36224334", "type": "manuscript", "label": "PMID 36224334 full text"}, {"id": "data:geo:GSE103766", "type": "dataset", "label": "GEO GSE103766"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-36224334", "type": "extraction", "used": ["source:pmid:36224334"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE103766", "type": "accession_resolution", "used": ["data:geo:GSE103766"], "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:36224334", "parent_hash": "sha256:ef97a49298d7cfc7b12fb9d6a49410b3e59ccf56d8612ce6510cbe3fd911253c", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE103766 licence not read", "asset:data:geo:GSE103766 not downloaded", "asset:data:geo:GSE112307 licence not read", "asset:data:geo:GSE112307 not downloaded", "asset:data:geo:GSE35411 licence not read", "asset:data:geo:GSE35411 not downloaded", "asset:data:geo:GSE35710 licence not read", "asset:data:geo:GSE35710 not downloaded", "asset:data:geo:GSE43471 licence not read", "asset:data:geo:GSE43471 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"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": ["protein-protein interaction"], "order_basis": "analysis_only", "id": "assay:1"}]}