Identification of Molecular Mechanisms of Ameloblastoma and Drug Repositioning by Integration of Bioinformatics Analysis and Molecular Docking Simulation.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:38812739", "kind": "science-record", "revision": 5, "content_hash": "sha256:346d453bbe73f49e59cc8689333380e03754bd8dff302b54f87588380ca6e12f", "created_at": "2026-11-01T19:20:46Z", "updated_at": "2026-11-01T22:54:25Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification of Molecular Mechanisms of Ameloblastoma and Drug Repositioning by Integration of Bioinformatics Analysis and Molecular Docking Simulation.", "doi": "10.1177/11779322241256459", "pmid": "38812739", "authors": ["Suthipong Chujan", "Nutsira Vajeethaveesin", "Jutamaad Satayavivad", "Nakarin Kitkumthorn"], "journal": "Bioinformatics and biology insights", "year": 2024, "abstract": "Background: Ameloblastoma (AM) is a benign tumor locally originated from odontogenic epithelium that is commonly found in the jaw. This tumor makes aggressive invasions and has a high recurrence rate. This study aimed to investigate the differentially expressed genes (DEGs), biological function alterations, disease targets, and existing drugs for AM using bioinformatics analysis.\nMethods: The data set of AM was retrieved from the GEO database (GSE132474) and identified the DEGs using bioinformatics analysis. The biological alteration analysis was applied to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Protein-protein interaction (PPI) network analysis and hub gene identification were screened through NetworkAnalyst. The transcription factor-protein network was constructed via OmicsNet. We also identified candidate compounds from L1000CDS2 database. The target of AM and candidate compounds were verified using docking simulation.\nResults: Totally, 611 DEGs were identified. The biological function enrichment analysis revealed glycosaminoglycan and GABA (γ-aminobutyric acid) signaling were most significantly up-regulated and down-regulated in AM, respectively. Subsequently, hub genes and transcription factors were screened via the network and showed FOS protein was found in both networks. Furthermore, we evaluated FOS protein to be a therapeutic target in AMs. Candidate compounds were screened and verified using docking simulation. Tanespimycin showed the greatest affinity binding value to bind FOS protein.\nConclusions: This study presented the underlying molecular mechanisms of disease pathogenesis, biological alteration, and important pathways of AMs and provided a candidate compound, Tanespimycin, targeting FOS protein for the treatment of AMs.", "claims": [{"id": "claim-method", "statement": "A moderated t-test was applied to identify DEGs, and Fisher’s exact test was used to test for enrichment in GO terms and KEGG pathways.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38812739", "locator": "sections[11] \"Statistical analysis\" paragraph 2", "quote": "A moderated t-test was applied to identify DEGs, and Fisher’s exact test was used to test for enrichment in GO terms and KEGG pathways."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GSE132474 (GPL16699 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381) was obtained from the GEO data set, The National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov/gds/?term=GSE132474). The study was designed to perform expression and genome variation profiling using an array in AM. The patient samples consist of 8 AM tumor tissues and 8 normal oral tissues.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:38812739", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "GSE132474 (GPL16699 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381) was obtained from the GEO data set, The National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov/gds/?term=GSE132474)."}, {"asset": "source:pmid:38812739", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "The study was designed to perform expression and genome variation profiling using an array in AM."}, {"asset": "source:pmid:38812739", "locator": "sections[3] \"Data collection\" paragraph 2", "quote": "The patient samples consist of 8 AM tumor tissues and 8 normal oral tissues."}], "state": "complete"}, {"id": "claim-target-result", "statement": "Totally, 611 DEGs were identified.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:38812739", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "Totally, 611 DEGs were identified."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "Totally, 611 DEGs were identified.", "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:38812739"], "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:GSE132474"], "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:GSE132474"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:38812739", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1177/11779322241256459", "sha256": "sha256:31924d642e3ac142073a7eee4e837ad26b17e543f072549067ce93c6c5497774", "bytes": 38229, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1177/11779322241256459", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC11135093", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE132474", "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=GSE132474", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE132474", "version": null, "note": "GSE132474 (GPL16699 Agilent-039494 SurePrint G3 Human GE v2 8x60K Microarray 039381) was obtained from the GEO data set, The National Center for Biotechnology Information (NCBI) database (https://www.ncbi.nlm.nih.gov/gds/?term=GSE132474). 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