Bioinformatic analysis reveals the importance of epithelial-mesenchymal transition in the development of endometriosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32439908", "kind": "science-record", "revision": 5, "content_hash": "sha256:5484a51666c15fb12d0f2ae5b027282feb2628b267513c45348c171a27232f44", "created_at": "2026-11-01T17:33:41Z", "updated_at": "2026-11-01T22:44:53Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatic analysis reveals the importance of epithelial-mesenchymal transition in the development of endometriosis.", "doi": "10.1038/s41598-020-65606-9", "pmid": "32439908", "authors": ["Meihong Chen", "Yilu Zhou", "Hong Xu", "Charlotte Hill", "Rob M Ewing", "Deming He", "Xiaoling Zhang", "Yihua Wang"], "journal": "Scientific reports", "year": 2020, "abstract": "BACKGROUND: Endometriosis is a frequently occurring disease in women, which seriously affects their quality of life. However, its etiology and pathogenesis are still unclear.\nMETHODS: To identify key genes/pathways involved in the pathogenesis of endometriosis, we recruited 3 raw microarray datasets (GSE11691, GSE7305, and GSE12768) from Gene Expression Omnibus database (GEO), which contain endometriosis tissues and normal endometrial tissues. We then performed in-depth bioinformatic analysis to determine differentially expressed genes (DEGs), followed by gene ontology (GO), Hallmark pathway enrichment and protein-protein interaction (PPI) network analysis. The findings were further validated by immunohistochemistry (IHC) staining in endometrial tissues from endometriosis or control patients.\nRESULTS: We identified 186 DEGs, of which 118 were up-regulated and 68 were down-regulated. The most enriched DEGs in GO functional analysis were mainly associated with cell adhesion, inflammatory response, and extracellular exosome. We found that epithelial-mesenchymal transition (EMT) ranked first in the Hallmark pathway enrichment. EMT may potentially be induced by inflammatory cytokines such as CXCL12. IHC confirmed the down-regulation of E-cadherin (CDH1) and up-regulation of CXCL12 in endometriosis tissues.\nCONCLUSIONS: Utilizing bioinformatics and patient samples, we provide evidence of EMT in endometriosis. Elucidating the role of EMT will improve the understanding of the molecular mechanisms involved in the development of endometriosis.", "claims": [{"id": "claim-method", "statement": "Differential expression analysis was performed on these datasets in limma, and those genes with P value <0.05 and Log[FoldChange] (Log[FC]) > 1 were considered as DEGs.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32439908", "locator": "sections[12] \"Identification of Differentially Expressed Genes (DEGs) using integrated bioinformatics\" paragraph 2", "quote": "Differential expression analysis was performed on these datasets in limma, and those genes with P value <0.05 and Log[FoldChange] (Log[FC]) > 1 were considered as DEGs."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data and materials from this study are available upon a written request.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32439908", "locator": "sections[25] \"notes\" paragraph 1", "quote": "Data and materials from this study are available upon a written request."}], "state": "complete"}, {"id": "claim-target-result", "statement": "We identified 186 DEGs, of which 118 were up-regulated and 68 were down-regulated.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:32439908", "locator": "sections[0] \"Abstract\" paragraph 1", "quote": "We identified 186 DEGs, of which 118 were up-regulated and 68 were down-regulated."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "We identified 186 DEGs, of which 118 were up-regulated and 68 were down-regulated.", "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:32439908"], "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:GSE11691"], "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:GSE11691"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32439908", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1038/s41598-020-65606-9", "sha256": "sha256:881a85be0aaf4a6797a05c0e7ff6626e8967a68c35bfeaf7767affeeab5ca400", "bytes": 28466, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1038/s41598-020-65606-9", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7242372", "source": "ncbi_pmc_fulltext", "coverage": "whole_body_without_references", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE11691", "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=GSE11691", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE11691", "version": null, "note": "Data and materials from this study are available upon a written request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data and materials from this study are available upon a written request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM296875", "GSM296876", "GSM296877", "GSM296878", "GSM296879", "GSM296880", "GSM296881", "GSM296882", "GSM296883", "GSM296884", "GSM296885", "GSM296886", "GSM296887", "GSM296888", "GSM296889", "GSM296890", "GSM296891", "GSM296892"], "sample_count": 18, "group_sizes": null, "group_sizes_basis": null, "platform": "96", "taxon": "Homo sapiens", "title": "Euctopic and ectopic human endometrium (endometriosis)", "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:GSE12768", "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=GSE12768", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE12768", "version": null, "note": "Data and materials from this study are available upon a written request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data and materials from this study are available upon a written request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM320294", "GSM320295", "GSM320296", "GSM320297"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "7304", "taxon": "Homo sapiens", "title": "Gene expression profile for ectopic vs. eutopic endometrium", "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:GSE7305", "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=GSE7305", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE7305", "version": null, "note": "Data and materials from this study are available upon a written request.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data and materials from this study are available upon a written request.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM175766", "GSM175767", "GSM175768", "GSM175769", "GSM175770", "GSM175771", "GSM175772", "GSM175773", "GSM175774", "GSM175775", "GSM175776", "GSM175777", "GSM175778", "GSM175779", "GSM175780", "GSM175781", "GSM175782", "GSM175783", "GSM175784", "GSM175785"], "sample_count": 20, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Human endometriosis vs normal endometrium study - transcriptional profiling", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE11691 not downloaded", "asset:data:geo:GSE11691 licence not read", "asset:data:geo:GSE12768 not downloaded", "asset:data:geo:GSE12768 licence not read", "asset:data:geo:GSE7305 not downloaded", "asset:data:geo:GSE7305 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": "Differential expression analysis was performed on these datasets in limma, and those genes with P value <0.05 and Log[FoldChange] (Log[FC]) > 1 were considered as DEGs."}}, {"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"}}, {"id": "method-3", "family": "network_analysis", "specific": "pathway_enrichment", "label": "Network / pathway analysis", "dsl_operations": ["pathway_enrich"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["edge_list"], "evidence": {"score": 0.7, "band": "medium", "quote": "pathway enrichment"}}], "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. The physical bench the paper used is not, so a physical validation cannot be run here."}, "data": {"tier": "R1", "reachable": true, "accessions": ["GSE11691", "GSE7305", "GSE12768"], "resolved_accessions": ["GSE11691", "GSE7305", "GSE12768"], "statements": ["Data and materials from this study are available upon a written request."], "basis": "The paper names GSE11691, GSE7305, GSE12768 in Gene Expression Omnibus database (GEO) 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:32439908", "data:geo:GSE11691"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE11691"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T16:59:59Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 5, "usage": {"prompt_tokens": 9241, "completion_tokens": 1148, "cached_tokens": 128}}, "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:32439908", "type": "paper", "label": "pmid:32439908"}, {"id": "source:pmid:32439908", "type": "manuscript", "label": "PMID 32439908 full text"}, {"id": "data:geo:GSE11691", "type": "dataset", "label": "GEO GSE11691"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32439908", "type": "paper", "label": "pmid:32439908"}, {"id": "source:pmid:32439908", "type": "manuscript", "label": "PMID 32439908 full text"}, {"id": "data:geo:GSE11691", "type": "dataset", "label": "GEO GSE11691"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32439908", "type": "extraction", "used": ["source:pmid:32439908"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE11691", "type": "accession_resolution", "used": ["data:geo:GSE11691"], "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:32439908", "parent_hash": "sha256:75967d8196b59f617b814df392d52dbaa88327147a6ef244823a06995d831bb0", "fork_of": null, "generation": 4}, "gaps": ["asset:data:geo:GSE11691 licence not read", "asset:data:geo:GSE11691 not downloaded", "asset:data:geo:GSE12768 licence not read", "asset:data:geo:GSE12768 not downloaded", "asset:data:geo:GSE7305 licence not read", "asset:data:geo:GSE7305 not downloaded", "execution.not_run", "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": ["genesis of endometriosis, we recruited 3 raw microarray datasets (GSE11691, GSE7305, and GSE12768) f"], "order_basis": "paper_text_order:356", "id": "assay:1"}, {"role": "data_generation", "definition_id": "ihc", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ysis. The findings were further validated by immunohistochemistry (IHC) staining in endometrial tissues from e", "e further validated by immunohistochemistry (IHC) staining in endometrial tissues from endome", "ed by inflammatory cytokines such as CXCL12. IHC confirmed the down-regulation of E-cadherin"], "order_basis": "paper_text_order:780", "id": "assay:2"}, {"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": ["Differential expression analysis was performed on these datasets in limma, and those genes with P value <0.05 and Log[FoldChange] (Log[FC]) > 1 were considered as DEGs."], "order_basis": "consumes_earlier_output", "id": "assay:3"}]}