Identification and prognostic value of DLGAP5 in endometrial cancer.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33312770", "kind": "science-record", "revision": 7, "content_hash": "sha256:a028f9f5ab2ba52a8631d224c92c3640dc539941b3c85423432b219dd0430d10", "created_at": "2026-11-01T15:41:19Z", "updated_at": "2026-11-01T22:02:43Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "Identification and prognostic value of DLGAP5 in endometrial cancer.", "doi": "10.7717/peerj.10433", "pmid": "33312770", "authors": ["Ruoyi Zheng", "Zhengzheng Shi", "Wenzhi Li", "Jianqin Yu", "Yuli Wang", "Qing Zhou"], "journal": "PeerJ", "year": 2020, "abstract": "BACKGROUND: Endometrial cancer poses a serious threat to women's health worldwide, and its pathogenesis, although actively explored, is not fully understood. DLGAP5 is a recently identified cell cycle-regulation gene not reported in endometrial cancer. This study was aiming to analyze the role of DLGAP5 in tumorigenesis and development and to investigate its prognostic significance of patients with endometrial cancer.\nMETHODOLOGY: Microarray datasets (GSE17025, GSE39099 and GSE63678) from the GEO database were used for comparative analysis, and their intersection was obtained by applying the Venn diagram, and DLGAP5 was selected as the target gene. Next, transcriptome data (n = 578) was downloaded from TCGA-UCEC to analyze the mRNA expression profile of DLGAP5. Then, immunohistochemical data provided by HPA were used to identify the different protein expression levels of DLGAP5 in tumor tissues and normal tissues. Subsequently, the prognostic meaning of DLGAP5 in patients with endometrial cancer was explored based on survival data from TCGA-UCEC (n = 541). Finally, the reliability of DLGAP5 expression was verified by RT-qPCR.\nRESULTS: Transcriptome data from TCGA-UCEC, immunohistochemical data from HPA, and RT-qPCR results from clinical samples were used for triple validation to confirm that the expression of DLGAP5 in endometrial cancer tissues was significantly higher than that in normal endometrial tissues. Kaplan-Meier survival analysis announced that the expression level of DLGAP5 was negatively correlated with the overall survival of patients with endometrial cancer.\nCONCLUSIONS: DLGAP5 is a potential oncogene with cell cycle regulation, and its overexpression can predict the poor prognosis of patients with endometrial cancer. As a candidate target for the diagnosis and treatment of endometrial cancer, it is worthwhile to make further study to reveal the carcinogenicity of DLGAP5 and the mechanism of its resistance of organisms.", "claims": [{"id": "claim-method", "statement": "Based on the FPKM value of DLGAP5, HPA was used to analyze the survival of patients with endometrial cancer in TCGA-UCEC by the Kaplan–Meier method with the log-rank test.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33312770", "locator": "sections[7] \"Statistical analysis\" paragraph 2", "quote": "Based on the FPKM value of DLGAP5, HPA was used to analyze the survival of patients with endometrial cancer in TCGA-UCEC by the Kaplan–Meier method with the log-rank test."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The following information was supplied regarding data availability:DLGAP5 data are available at TCGA (https://portal.gdc.cancer.gov/genes/ENSG00000126787) and the immunohistochemical and survival analysis data are available from HPA (https://www.proteinatlas.org/ENSG00000126787-DLGAP5) and from the Kaplan-Meier Plotter (http://kmplot.com/analysis/index.php).NCBI GEO microarray datasets (GSE17025, GSE39099, GSE63678) were processed using the online tool GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r).The raw measurements and R codes are available in the Supplementary Files.The runtime environment for the R codes is based on the GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/), not locally. Running this code in R will cause the program to report an error because the runtime environment does not match. The R code was made available for download primarily to demonstrate the rationale for the work involving this component.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33312770", "locator": "sections[22] \"Data Availability\" paragraph 2", "quote": "The following information was supplied regarding data availability:DLGAP5 data are available at TCGA (https://portal.gdc.cancer.gov/genes/ENSG00000126787) and the immunohistochemical and survival analysis data are available from HPA (https://www.proteinatlas.org/ENSG00000126787-DLGAP5) and from the Kaplan-Meier Plotter (http://kmplot.com/analysis/index.php).NCBI GEO microarray datasets (GSE17025, GSE39099, GSE63678) were processed using the online tool GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r).The raw measurements and R codes are available in the Supplementary Files.The runtime environment for the R codes is based on the GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/), not locally. Running this code in R will cause the program to report an error because the runtime environment does not match. The R code was made available for download primarily to demonstrate the rationale for the work involving this component."}], "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:33312770"], "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:GSE17025"], "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:GSE17025"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33312770", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.7717/peerj.10433", "sha256": "sha256:65270bf8e6ce74512fec045c86dbcc99e482848175a6176600f8f3d10feca3a2", "bytes": 41999, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.7717/peerj.10433", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7703392", "source": "europe_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE17025", "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=GSE17025", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE17025", "version": null, "note": "The following information was supplied regarding data availability:DLGAP5 data are available at TCGA (https://portal.gdc.cancer.gov/genes/ENSG00000126787) and the immunohistochemical and survival analysis data are available from HPA (https://www.proteinatlas.org/ENSG00000126787-DLGAP5) and from the Kaplan-Meier Plotter (http://kmplot.com/analysis/index.php).NCBI GEO microarray datasets (GSE17025, GSE39099, GSE63678) were processed using the online tool GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r).The raw measurements and R codes are available in the Supplementary Files.The runtime environment for the R codes is based on the GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/), not locally. Running this code in R will cause the program to report an error because the runtime environment does not match. The R code was made available for download primarily to demonstrate the rationale for the work involving this component.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:DLGAP5 data are available at TCGA (https://portal.gdc.cancer.gov/genes/ENSG00000126787) and the immunohistochemical and survival analysis data are available from HPA (https://www.proteinatlas.org/ENSG00000126787-DLGAP5) and from the Kaplan-Meier Plotter (http://kmplot.com/analysis/index.php).NCBI GEO microarray datasets (GSE17025, GSE39099, GSE63678) were processed using the online tool GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r).The raw measurements and R codes are available in the Supplementary Files.The runtime environment for the R codes is based on the GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/), not locally. Running this code in R will cause the program to report an error because the runtime environment does not match. 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Running this code in R will cause the program to report an error because the runtime environment does not match. The R code was made available for download primarily to demonstrate the rationale for the work involving this component.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:DLGAP5 data are available at TCGA (https://portal.gdc.cancer.gov/genes/ENSG00000126787) and the immunohistochemical and survival analysis data are available from HPA (https://www.proteinatlas.org/ENSG00000126787-DLGAP5) and from the Kaplan-Meier Plotter (http://kmplot.com/analysis/index.php).NCBI GEO microarray datasets (GSE17025, GSE39099, GSE63678) were processed using the online tool GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r).The raw measurements and R codes are available in the Supplementary Files.The runtime environment for the R codes is based on the GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/), not locally. Running this code in R will cause the program to report an error because the runtime environment does not match. The R code was made available for download primarily to demonstrate the rationale for the work involving this component.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM956132", "GSM956133", "GSM956134", "GSM956135"], "sample_count": 4, "group_sizes": null, "group_sizes_basis": null, "platform": "570", "taxon": "Homo sapiens", "title": "Gene expression in the different stages of endometrial cancer", "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:GSE63678", "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=GSE63678", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE63678", "version": null, "note": "The following information was supplied regarding data availability:DLGAP5 data are available at TCGA (https://portal.gdc.cancer.gov/genes/ENSG00000126787) and the immunohistochemical and survival analysis data are available from HPA (https://www.proteinatlas.org/ENSG00000126787-DLGAP5) and from the Kaplan-Meier Plotter (http://kmplot.com/analysis/index.php).NCBI GEO microarray datasets (GSE17025, GSE39099, GSE63678) were processed using the online tool GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r).The raw measurements and R codes are available in the Supplementary Files.The runtime environment for the R codes is based on the GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/), not locally. Running this code in R will cause the program to report an error because the runtime environment does not match. The R code was made available for download primarily to demonstrate the rationale for the work involving this component.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "The following information was supplied regarding data availability:DLGAP5 data are available at TCGA (https://portal.gdc.cancer.gov/genes/ENSG00000126787) and the immunohistochemical and survival analysis data are available from HPA (https://www.proteinatlas.org/ENSG00000126787-DLGAP5) and from the Kaplan-Meier Plotter (http://kmplot.com/analysis/index.php).NCBI GEO microarray datasets (GSE17025, GSE39099, GSE63678) were processed using the online tool GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r).The raw measurements and R codes are available in the Supplementary Files.The runtime environment for the R codes is based on the GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/), not locally. Running this code in R will cause the program to report an error because the runtime environment does not match. The R code was made available for download primarily to demonstrate the rationale for the work involving this component.", "access_statement_kind": "data_availability_statement", "sample_accessions": ["GSM1555075", "GSM1555076", "GSM1555077", "GSM1555078", "GSM1555079", "GSM1555080", "GSM1555081", "GSM1555082", "GSM1555083", "GSM1555084", "GSM1555085", "GSM1555086", "GSM1555087", "GSM1555088", "GSM1555089", "GSM1555090", "GSM1555091", "GSM1555092", "GSM1555093", "GSM1555094", "GSM1555095", "GSM1555096", "GSM1555097", "GSM1555098", "GSM1555099", "GSM1555100", "GSM1555101", "GSM1555102", "GSM1555103", "GSM1555104", "GSM1555105", "GSM1555106", "GSM1555107", "GSM1555108", "GSM1555109"], "sample_count": 35, "group_sizes": null, "group_sizes_basis": null, "platform": "571", "taxon": "Homo sapiens", "title": "Expression data from Vulvar, Cervical, Endometrial Carcinoma tissue", "resolution_checked_at": "2026-11-01T15:39:55Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}, {"id": "asset:table:pmid:33312770:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:cdd483e6510083eae5b03c75808a34bfaaa543048ebf34fbe880e371ffd8047b", "bytes": 672, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[1]#table-1", "version": null, "note": "Thirty-seven DEGs in EC (21 up-regulated and 16 down-regulated), according to the data consolidation analysis of GSE17025, GSE39099 and GSE63678.DEGs in groups are sorted by the magnitude of the | log(fold-change) | value.", "structure": {"pmcid": "PMC7703392", "section_index": 9, "section_title": "DLPAG5 is an up-regulated Differentially Expressed Gene (DEG) in endometrial cancer", "row_count": 3, "column_count": 2}, "table": {"label": "Table 1", "caption": "Thirty-seven DEGs in EC (21 up-regulated and 16 down-regulated), according to the data consolidation analysis of GSE17025, GSE39099 and GSE63678.DEGs in groups are sorted by the magnitude of the | log(fold-change) | value.", "rows": [["Groups", "DEGs"], ["Up-regulated", "ASPM, TOP2A, DLGAP5, RRM2, HK2, PBK, CEP55, SCD, SFN, BIRC5, MELK, PHLDA2, NCAPG, JPT1, TPX2, ENO1, CENPF, PTTG1, CDC20, SLC35F6, SEL1L3"], ["Down-regulated", "OGN, BCHE, PEG3, TNXB, LEPROT, CXCL12, CDO1, HLF, ABCA8, NAALAD2, LMOD1, DCN, TRPC1, TBX3, CYP1B1, FHL1"]], "row_count": 3, "column_count": 2, "numeric_cells": 2, "header_rows": 1, "locator": "section[9]/table-wrap[1]#table-1"}}, {"id": "asset:table:pmid:33312770:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:da2f12850856f88ebabe5bd5c9ffbd1b48e8626ba85409d7c715e5857ac04411", "bytes": 361, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[9]/table-wrap[2]#table-2", "version": null, "note": "The expression of DLGAP5 in GSE17025, GSE39099 and GSE63678.", "structure": {"pmcid": "PMC7703392", "section_index": 9, "section_title": "DLPAG5 is an up-regulated Differentially Expressed Gene (DEG) in endometrial cancer", "row_count": 4, "column_count": 3}, "table": {"label": "Table 2", "caption": "The expression of DLGAP5 in GSE17025, GSE39099 and GSE63678.", "rows": [["Dataset", "P-Value", "log(fold-change)"], ["GSE17025", "8.01 ×10−11", "3.14"], ["GSE63678", "2.17 ×10−2", "2.46"], ["GSE39099", "1.36 ×10−2", "4.06"]], "row_count": 4, "column_count": 3, "numeric_cells": 9, "header_rows": 1, "locator": "section[9]/table-wrap[2]#table-2"}}], "gaps": ["asset:data:geo:GSE17025 not downloaded", "asset:data:geo:GSE17025 licence not read", "asset:data:geo:GSE39099 not downloaded", "asset:data:geo:GSE39099 licence not read", "asset:data:geo:GSE63678 not downloaded", "asset:data:geo:GSE63678 licence not read"]}, "analysis": 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"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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE17025", "GSE39099", "GSE63678"], "resolved_accessions": ["GSE17025", "GSE39099", "GSE63678"], "statements": ["The following information was supplied regarding data availability:DLGAP5 data are available at TCGA (https://portal.gdc.cancer.gov/genes/ENSG00000126787) and the immunohistochemical and survival analysis data are available from HPA (https://www.proteinatlas.org/ENSG00000126787-DLGAP5) and from the Kaplan-Meier Plotter (http://kmplot.com/analysis/index.php).NCBI GEO microarray datasets (GSE17025, GSE39099, GSE63678) were processed using the online tool GEO2R (http://www.ncbi.nlm.nih.gov/geo/geo2r).The raw measurements and R codes are available in the Supplementary Files.The runtime environment for the R codes is based on the GEO2R online tool (https://www.ncbi.nlm.nih.gov/geo/geo2r/), not locally. Running this code in R will cause the program to report an error because the runtime environment does not match. The R code was made available for download primarily to demonstrate the rationale for the work involving this component."], "basis": "The paper names GSE17025, GSE39099, GSE63678 in NCBI Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["logrank_test"], "assets": ["source:pmid:33312770", "data:geo:GSE17025", "asset:table:pmid:33312770:1", "asset:table:pmid:33312770:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE17025"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:25:27Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 34559, "completion_tokens": 3231, "cached_tokens": 22656}}, "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:33312770", "type": "paper", "label": "pmid:33312770"}, {"id": "source:pmid:33312770", "type": "manuscript", "label": "PMID 33312770 full text"}, {"id": "data:geo:GSE17025", "type": "dataset", "label": "GEO GSE17025"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33312770", "type": "paper", "label": "pmid:33312770"}, {"id": "source:pmid:33312770", "type": "manuscript", "label": "PMID 33312770 full text"}, {"id": "data:geo:GSE17025", "type": "dataset", "label": "GEO GSE17025"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33312770", "type": "extraction", "used": ["source:pmid:33312770"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE17025", "type": "accession_resolution", "used": ["data:geo:GSE17025"], "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:33312770", "parent_hash": "sha256:7fec4251f8f6097269996a29631ca6e8b9129980e8c4790b698a873d750d01cc", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE17025 licence not read", "asset:data:geo:GSE17025 not downloaded", "asset:data:geo:GSE39099 licence not read", "asset:data:geo:GSE39099 not downloaded", "asset:data:geo:GSE63678 licence not read", "asset:data:geo:GSE63678 not downloaded", "execution.not_run", "method.reader_differs_from_extractor", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "data_generation", "definition_id": "qpcr", "definition_version": "99e1195c7d6f", "definition_digest": null, "required_operations": [], "support_state": "partial", "source_hashes": {"assay_lexicon": "99e1195c7d6f"}, "confidence": 0.99, "evidence": ["ability of DLGAP5 expression was verified by RT-qPCR. RESULTS: Transcriptome data from TCGA-UCEC,", "lity of DLGAP5 expression was verified by RT-qPCR. RESULTS: Transcriptome data from TCGA-UCEC,", "samples Back to the clinical samples, taking RT-qPCR to identify the differential expression leve", "ples Back to the clinical samples, taking RT-qPCR to identify the differential expression leve"], "order_basis": "paper_text_order:1159", "id": "assay:1"}, {"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 1.0, "evidence": ["Based on the FPKM value of DLGAP5, HPA was used to analyze the survival of patients with endometrial cancer in TCGA-UCEC by the Kaplan–Meier method with the log-rank test."], "order_basis": "consumes_earlier_output", "id": "assay:2"}]}