The expression and prognostic value of GLYATL1 and its potential role in hepatocellular carcinoma.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:33457003", "kind": "science-record", "revision": 4, "content_hash": "sha256:d5d3c20e258546f77e95417a03475e51f3f9da78e4f94bbfa1a6f6bd5f5b0f00", "created_at": "2026-11-01T17:34:37Z", "updated_at": "2026-11-01T22:02:57Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "The expression and prognostic value of GLYATL1 and its potential role in hepatocellular carcinoma.", "doi": "10.21037/jgo-20-186", "pmid": "33457003", "authors": ["Renguo Guan", "Weifeng Hong", "Jianfeng Huang", "Tianyi Peng", "Zhen Zhao", "Ye Lin", "Min Yu", "Zhixiang Jian"], "journal": "Journal of gastrointestinal oncology", "year": 2020, "abstract": "BACKGROUND: Glycine-N-acyltransferase-like 1 (GLYATL1), which is involved in the detoxification of endogenous and exogenous acyl-CoA, promotes glutamine metabolism in xenobiotic metabolism. Recent evidence suggests an association between GLYATL1 and tumors. However, there are few comprehensive analyses of GLYATL1 in cancers. We evaluated the expression and prognostic value of GLYATL1 and explored the mechanism underlying the association between GLYATL1 and cancers.\nMETHODS: GLYATL1 mRNA expression across cancers was investigated in the Oncomine database and confirmed in the UALCAN and Gene Expression Profiling Interactive Analysis (GEPIA) databases. Next, its prognostic value in different cancers was revealed by PrognoScan and Kaplan-Meier plotter. According to clinicopathologic features, we conducted a subgroup analysis of the prognosis of GLYATL1 in a cohort of hepatocellular carcinoma (HCC) patients from The Cancer Genome Atlas (TCGA) and the GSE116174 dataset. We further investigated the GLYATL1 promoter methylation profile in HCC. Next, a protein-protein interaction (PPI) network was constructed via the Search Tool for the Retrieval of Interacting Genes (STRING) database. Finally, we utilized gene set enrichment analysis (GSEA) to identify significantly enriched pathways and confirmed their associations using the Tumor Immune Estimation Resource (TIMER) and GEPIA databases.\nRESULTS: GLYATL1 is downregulated in many cancers and indicates a poor prognosis. Specifically, low GLYATL1 expression was associated with short overall survival (OS) in HCC patients. Interestingly, GLYATL1 expression was associated with poor OS in stage I-II HCC patients and was revealed as an independent prognostic factor. The promoter methylation level of GLYATL1 in HCC tissue was significantly higher than that in normal liver tissue. The PPI network suggested that GLYATL1 is co-expressed with ten genes, including CNGA3 and GNB5. GSEA revealed that GLYATL1 is predominantly negatively enriched in xenobiotic metabolism, and the gene association analysis in TIMER and GEPIA showed a significantly negative association between the expression of GLYATL1 and the expression of most genes involved in mitochondrial glutamine metabolism, including SLC1A5 and SLC1A11.\nCONCLUSIONS: Our study is the first to shed light on the expression and prognostic value of GLYATL1 in cancers and provide a potential regulatory mechanism underlying HCC development.", "claims": [{"id": "claim-method", "statement": "Finally, we utilized gene set enrichment analysis (GSEA) to identify significantly enriched pathways and confirmed their associations using the Tumor Immune Estimation Resource (TIMER) and GEPIA databases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33457003", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "Finally, we utilized gene set enrichment analysis (GSEA) to identify significantly enriched pathways and confirmed their associations using the Tumor Immune Estimation Resource (TIMER) and GEPIA databases."}], "state": "complete"}, {"id": "claim-data-access", "statement": "GLYATL1 mRNA expression across cancers was investigated in the Oncomine database and confirmed in the UALCAN and Gene Expression Profiling Interactive Analysis (GEPIA) databases.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33457003", "locator": "sections[0] \"Abstract\" paragraph 2", "quote": "GLYATL1 mRNA expression across cancers was investigated in the Oncomine database and confirmed in the UALCAN and Gene Expression Profiling Interactive Analysis (GEPIA) databases."}], "state": "complete"}, {"id": "claim-target-result", "statement": "GLYATL1 is downregulated in many cancers and indicates a poor prognosis.", "kind": "qualitative", "target": null, "evidence": [{"asset": "source:pmid:33457003", "locator": "sections[0] \"Abstract\" paragraph 3", "quote": "GLYATL1 is downregulated in many cancers and indicates a poor prognosis."}], "state": "complete"}], "gaps": []}, "experiment": {"state": "complete", "objective": "GLYATL1 is downregulated in many cancers and indicates a poor prognosis.", "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:33457003"], "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:GSE116174"], "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:GSE116174"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:33457003", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.21037/jgo-20-186", "sha256": "sha256:34fb6cb6d8c4f0151e260592412190440e374e3554bc5cca3df46a7dfe8ad583", "bytes": 2426, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.21037/jgo-20-186", "version": null, "note": "Full article fetched from PMC; the checksum covers the rendered section body, not the original XML bytes.", "structure": {"pmcid": "PMC7807277", "source": "ncbi_pmc_fulltext", "coverage": "whole_body", "text_hash_scope": "rendered_section_body"}}, {"id": "data:geo:GSE116174", "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=GSE116174", "sha256": null, "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "GSE116174", "version": null, "note": "GLYATL1 mRNA expression across cancers was investigated in the Oncomine database and confirmed in the UALCAN and Gene Expression Profiling Interactive Analysis (GEPIA) databases.", "structure": {"repository": "GEO", "access_route": "GEO accession URL", "access_statement_verbatim": "GLYATL1 mRNA expression across cancers was investigated in the Oncomine database and confirmed in the UALCAN and Gene Expression Profiling Interactive Analysis (GEPIA) databases.", "access_statement_kind": "repository_route_statement", "sample_accessions": ["GSM3212448", "GSM3212449", "GSM3212450", "GSM3212451", "GSM3212452", "GSM3212453", "GSM3212454", "GSM3212455", "GSM3212456", "GSM3212457", "GSM3212458", "GSM3212459", "GSM3212460", "GSM3212461", "GSM3212462", "GSM3212463", "GSM3212464", "GSM3212465", "GSM3212466", "GSM3212467", "GSM3212468", "GSM3212469", "GSM3212470", "GSM3212471", "GSM3212472", "GSM3212473", "GSM3212474", "GSM3212475", "GSM3212476", "GSM3212477", "GSM3212478", "GSM3212479", "GSM3212480", "GSM3212481", "GSM3212482", "GSM3212483", "GSM3212484", "GSM3212485", "GSM3212486", "GSM3212487", "GSM3212488", "GSM3212489", "GSM3212490", "GSM3212491", "GSM3212492", "GSM3212493", "GSM3212494", "GSM3212495", "GSM3212496", "GSM3212497", "GSM3212498", "GSM3212499", "GSM3212500", "GSM3212501", "GSM3212502", "GSM3212503", "GSM3212504", "GSM3212505", "GSM3212506", "GSM3212507", "GSM3212508", "GSM3212509", "GSM3212510", "GSM3212511"], "sample_count": 64, "group_sizes": null, "group_sizes_basis": null, "platform": "13158", "taxon": "Homo sapiens", "title": "Gene expression profile in human hepatocellular carcinoma", "resolution_checked_at": "2026-11-01T15:39:54Z", "resolution_check": "identifier_resolution_only_no_download_no_licence_read", "downloaded": false, "licence_read": false}}], "gaps": ["asset:data:geo:GSE116174 not downloaded", "asset:data:geo:GSE116174 licence not read"]}, "analysis": {"state": "partial", "methods": [{"id": "method-1", "family": "survival_analysis", "specific": "kaplan_meier", "label": "Survival analysis", "dsl_operations": ["survival_km"], "missing_operations": [], "expressible": true, "parameters": {}, "data_shapes": ["time_to_event_with_censoring"], "evidence": {"score": 0.7, "band": "medium", "quote": "Kaplan-Meier"}}, {"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": null, "specific": null, "label": "gene set enrichment analysis (GSEA)", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "Finally, we utilized gene set enrichment analysis (GSEA) to identify significantly enriched pathways and confirmed their associations using the Tumor Immune Estimation Resource (TIMER) and GEPIA databases."}}], "targets": [], "gaps": ["method.reader_named_unmapped"]}, "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": ["survival_km"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: kaplan_meier."}, "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": ["GSE116174"], "resolved_accessions": ["GSE116174"], "statements": ["GLYATL1 mRNA expression across cancers was investigated in the Oncomine database and confirmed in the UALCAN and Gene Expression Profiling Interactive Analysis (GEPIA) databases."], "basis": "The paper names GSE116174 in GSE116174 and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["survival_km"], "assets": ["source:pmid:33457003", "data:geo:GSE116174"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE116174"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-11-01T17:01:15Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": null}, "calls": 5, "usage": {"prompt_tokens": 2144, "completion_tokens": 1621, "cached_tokens": 256}}, "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:33457003", "type": "paper", "label": "pmid:33457003"}, {"id": "source:pmid:33457003", "type": "manuscript", "label": "PMID 33457003 full text"}, {"id": "data:geo:GSE116174", "type": "dataset", "label": "GEO GSE116174"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:33457003", "type": "paper", "label": "pmid:33457003"}, {"id": "source:pmid:33457003", "type": "manuscript", "label": "PMID 33457003 full text"}, {"id": "data:geo:GSE116174", "type": "dataset", "label": "GEO GSE116174"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-33457003", "type": "extraction", "used": ["source:pmid:33457003"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE116174", "type": "accession_resolution", "used": ["data:geo:GSE116174"], "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:33457003", "parent_hash": "sha256:c3e75660c4cfba9dd6c15049aa8df0d0af036b9231c42cd60f2ffb6f151ca838", "fork_of": null, "generation": 3}, "gaps": ["asset:data:geo:GSE116174 licence not read", "asset:data:geo:GSE116174 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["survival_km"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Kaplan-Meier"], "order_basis": "analysis_only", "id": "assay:1"}]}