Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:31576231", "kind": "science-record", "revision": 6, "content_hash": "sha256:e8e2e10b5be50454149cffb3ca55a00f08b45f83b9d9a899c3fe19c593dc933c", "created_at": "2026-11-01T15:40:50Z", "updated_at": "2026-11-01T21:22:31Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Engrailed 1 overexpression as a potential prognostic marker in Lower Grade Glioma.", "doi": "10.7717/peerj.7414", "pmid": "31576231", "authors": ["Jin Zhu", "Yu-Qi Zhang"], "journal": "PeerJ", "year": 2019, "abstract": "BACKGROUND: Engrailed 1 (EN1), as a member of homeobox-containing transcription factors, participates in the development of the brain. High expressions of EN1 exist in various tumors. However, the role of EN1 in lower grade glioma (LGG) is still unknown.\nMETHODS: Coefficients of Cox regression were examined by data mining among 13 cancer types using OncoLnc to validate EN1 expressions in LGG patients from The Cancer Genome Atlas database (TCGA). Bioinformatic analysis was performed by using R2 and the UCSC Xena browser based on the data from 273 glioma cases in GSE16011 from GEO datasets and 530 cases of LGG patients in TCGA. Cases in GSE16011 were divided into two groups according to IDH1 mutation status. Cases in TCGA-LGG were classified to subtypes according to histopathological results, IDH1 mutation status and 1p19q status. The Kaplan-Meier survival curves were performed to analyze the relationship between EN1 expressions and clinicopathological characteristics and survival time respectively.\nRESULTS: Cox regression results showed that LGG was ranked statistically first among 13 different cancer types according to the false discovery rate (FDR) correction. Results from GSE16011 showed that: glioma, LGG and LGG with IDH1 mutation patients with high EN1 expressions had significantly shorter 5, 10, and 15-year overall survival time (OS) (p < 0.001). Similar results from TCGA-LGG showed that LGG patients with high EN1 expressions had significantly shorter 15-year OS, irrespective of IDH1 mutation and 1p19q co-deletion (p < 0.001). The astrocytoma subgroup showed highest levels of EN1 expression and shortest 5, 10 and 15-year OS compared with oligoastrocytoma and oligodendroglioma (p < 0.05).\nCONCLUSION: EN1 can be used as a prognostic marker in LGG patients, combined with IDH1 mutation and 1p19q co-deletion.", "claims": [{"id": "claim-method", "statement": "Kaplan–Meier survival analysis was chosen to explore the association between EN1 expression and 5, 10 and 15-year OS in patients with glioma through data mining in R2 using data in GSE16011 (Figs. 2A–2F).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31576231", "locator": "sections[8] \"High EN1 expression might be an indicator of poor OS in patients with glioma and LGG\" paragraph 2", "quote": "Kaplan–Meier survival analysis was chosen to explore the association between EN1 expression and 5, 10 and 15-year OS in patients with glioma through data mining in R2 using data in GSE16011 (Figs. 2A–2F)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:\nThe R2 web-based application (http://r2.amc.nl) was used to generate Kaplan–Meier survival curves of data in GSE16011. Cox coefficients were examined by data mining among 13 TCGA cancer types using OncoLnc (http://www.oncolnc.org/) to compare EN1 expression in different tumors. LGG cohort in TCGA database (TCGA-LGG) was obtained from the UCSC Xena browser: https://portal.gdc.cancer.gov/projects/TCGA-LGG.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:31576231", "locator": "sections[23] \"Data Availability Statement\" paragraphs 1-3", "quote": "The following information was supplied regarding data availability:\nThe R2 web-based application (http://r2.amc.nl) was used to generate Kaplan–Meier survival curves of data in GSE16011. Cox coefficients were examined by data mining among 13 TCGA cancer types using OncoLnc (http://www.oncolnc.org/) to compare EN1 expression in different tumors. LGG cohort in TCGA database (TCGA-LGG) was obtained from the UCSC Xena browser: https://portal.gdc.cancer.gov/projects/TCGA-LGG."}], "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:31576231"], "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:GSE16011"], "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:GSE16011"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:31576231", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.7414", "sha256": "sha256:2d2b46e655cee65a73448714a1e28d4dcc33c571d7446040d2a34d2888c9887c", "bytes": 28190, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.7414", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC6752186", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE16011", "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=GSE16011", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE16011", "version": null, "note": "The following information was supplied regarding data availability:\nThe R2 web-based application (http://r2.amc.nl) was used to generate Kaplan–Meier survival curves of data in GSE16011. Cox coefficients were examined by data mining among 13 TCGA cancer types using OncoLnc (http://www.oncolnc.org/) to compare EN1 expression in different tumors. LGG cohort in TCGA database (TCGA-LGG) was obtained from the UCSC Xena browser: https://portal.gdc.cancer.gov/projects/TCGA-LGG.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:\nThe R2 web-based application (http://r2.amc.nl) was used to generate Kaplan–Meier survival curves of data in GSE16011. Cox coefficients were examined by data mining among 13 TCGA cancer types using OncoLnc (http://www.oncolnc.org/) to compare EN1 expression in different tumors. 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