Bioinformatical analysis of the key differentially expressed genes and associations with immune cell infiltration in development of endometriosis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:35303800", "kind": "science-record", "revision": 4, "content_hash": "sha256:ac570ed8c376967d3cf82f4cdd9be4124c200e5c4f71f731797c0f071abaf4fd", "created_at": "2026-11-01T18:14:06Z", "updated_at": "2026-11-01T22:06:08Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Bioinformatical analysis of the key differentially expressed genes and associations with immune cell infiltration in development of endometriosis.", "doi": "10.1186/s12863-022-01036-y", "pmid": "35303800", "authors": ["Shengnan Chen", "Xiaoshan Chai", "Xianqing Wu"], "journal": "BMC genomic data", "year": 2022, "abstract": "BACKGROUND: This study explored the key genes related to immune cell infiltration in endometriosis.\nRESULTS: The Gene Expression Omnibus (GEO) datasets (GSE7305, GSE7307, and GSE11691), containing a total of 37 endometriosis and 42 normal tissues, were retrieved and analyzed to determine the differentially expressed genes (DEGs). Gene ontology (GO) annotations and Kyoto Encyclopedia of Genes (KEGG) analysis were performed to identify the pathways that were significantly enriched. The xCell software was used to analyze immune cell infiltration and correlation analyses were performed to uncover the relationship between key genes and immune cells. The analysis identified 1031 DEGs (581 upregulated and 450 downregulated DEGs), while GO analysis revealed altered extracellular matrix organization, collagen-containing extracellular matrix, and glycosaminoglycan binding and KEGG enrichment showed genes related to metabolic pathways, pathways in cancer, phosphatidylinositol 3-kinase-protein kinase B (PI3K-Akt) signaling, proteoglycans in cancer, and the mitogen-activated protein kinase (MAPK) signaling pathway. Furthermore, the protein-protein interaction network revealed 10 hub genes, i.e., IL6, FN1, CDH1, CXCL8, IGF1, CDK1, PTPRC, CCNB1, MKI67, and ESR1. The xCell analysis identified immune cells with significant changes in all three datasets, including CD4+ and CD8+ T cells, CD8+ Tem, eosinophils, monocytes, Th1 cells, memory B-cells, activated dendritic cells (aDCs), and plasmacytoid dendritic cells (pDCs). These 10 hub genes were significantly associated with at least three types of immune cells.\nCONCLUSIONS: Aberrant gene expression was related to abnormal infiltration of different immune cells in endometriosis and was associated with endometriosis development by affecting the tissue microenvironment and growth of ectopic endometrial cells.", "claims": [{"id": "claim-method", "statement": "The Pearson correlation test was employed to analyze the hub genes in the infiltrating immune cells in endometriosis using the R package and the resulting data were visualized using the \"ggplot\" package.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35303800", "locator": "sections[17] \"Association of the hub genes with infiltrating immune cells\" paragraph 2", "quote": "The Pearson correlation test was employed to analyze the hub genes in the infiltrating immune cells in endometriosis using the R package and the resulting data were visualized using the \"ggplot\" package."}], "state": "complete"}, {"id": "claim-data-access", "statement": "Data is available at NCBI GEO, accession numbers: GSE7305: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7305. GSE7307: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7307. GSE11691: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11691.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:35303800", "locator": "sections[23] \"Availability of data and materials\" paragraph 2", "quote": "Data is available at NCBI GEO, accession numbers: GSE7305: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7305. GSE7307: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7307. GSE11691: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11691."}], "state": "complete"}, {"id": "claim-target-result", "statement": "The analysis identified 1031 DEGs and revealed that 10 hub genes were significantly associated with at least three immune-cell types whose infiltration was significantly higher in endometriosis than in normal endometrium.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:35303800", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "The analysis identified 1031 DEGs (581 upregulated and 450 downregulated DEGs), while GO analysis revealed altered extracellular matrix organization, collagen-containing extracellular matrix, and glycosaminoglycan binding and KEGG enrichment showed genes related to metabolic pathways, pathways in cancer, phosphatidylinositol 3-kinase-protein kinase B (PI3K-Akt) signaling, proteoglycans in cancer, and the mitogen-activated protein kinase (MAPK) signaling pathway."}, {"asset": "source:pmid:35303800", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "These 10 hub genes were significantly associated with at least three types of immune cells."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "The analysis identified 1031 DEGs and revealed that 10 hub genes were significantly associated with at least three immune-cell types whose infiltration was significantly higher in endometriosis than in normal endometrium.", "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:35303800"], "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:35303800", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1186/s12863-022-01036-y", "sha256": "sha256:0d6067b18b4a197bcc39a76dd79c2ca2ea23dd6aa0689ee4095d36e9a84e9e40", "bytes": 49261, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1186/s12863-022-01036-y", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC8932180", "source": "europe_pmc_fulltext", "coverage": "whole_body", "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 is available at NCBI GEO, accession numbers: GSE7305: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7305. GSE7307: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7307. GSE11691: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11691.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data is available at NCBI GEO, accession numbers: GSE7305: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7305. GSE7307: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7307. GSE11691: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11691.", "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: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 is available at NCBI GEO, accession numbers: GSE7305: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7305. 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GSE11691: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11691.", "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}}, {"id": "data:geo:GSE7307", "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=GSE7307", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE7307", "version": null, "note": "Data is available at NCBI GEO, accession numbers: GSE7305: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7305. GSE7307: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7307. GSE11691: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE11691.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "Data is available at NCBI GEO, accession numbers: GSE7305: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7305. GSE7307: https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE7307. 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