An Analysis Regarding the Association Between the ISLR Gene and Gastric Carcinogenesis.

{"sci_version": "1.2", "schema": "https://corpus.bntrg.co.uk/sci/1.0/sci.schema.json", "id": "pmid:32612640", "kind": "science-record", "revision": 7, "content_hash": "sha256:1d302b71260e0fbdaf31da88e2f7a428e928702728e4483cb7ba1201b680ab09", "created_at": "2026-11-01T15:41:05Z", "updated_at": "2026-11-01T22:01:50Z", "generator": {"name": "corpus-assay-engine", "run_id": "reading-sci-2026-11-01"}, "paper": {"state": "complete", "title": "An Analysis Regarding the Association Between the ISLR Gene and Gastric Carcinogenesis.", "doi": "10.3389/fgene.2020.00620", "pmid": "32612640", "authors": ["Shu Li", "Wei Zhao", "Manyi Sun"], "journal": "Frontiers in genetics", "year": 2020, "abstract": "For datasets of gastric cancer collected by TCGA (The Cancer Genome Atlas) and GEO (Gene Expression Omnibus) repositories, we applied a bioinformatics approach to obtain expression data for the ISLR (immunoglobulin superfamily containing leucine-rich repeat) gene, which is highly expressed in gastric cancer tissues and closely associated with clinical prognosis. Although we did not observe an overall association of ISLR mutation, high expression or copy number variation with survival, hypomethylation of four methylated sites (assessed by the probes cg05195566, cg17258195, cg09664357, and cg07297039) of ISLR was negatively correlated with high expression levels of ISLR and was associated with poor clinical prognosis. In addition, we detected a correlation between ISLR expression and the infiltration levels of several immune cells, especially CD8+ T cells, macrophages and dendritic cells. We also identified a series of genes that were positively and negatively correlated with ISLR expression based on the TCGA-STAD, GSE13861, and GSE29272 datasets. Principal component analysis and random forest analysis were employed to further screen for six hub genes, including ISLR, COL1A2, CDH11, SPARC, COL3A1, and COL1A1, which exhibited a good ability to differentiate between tumor and normal samples. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) pathway and gene set enrichment analysis data also suggested a potential relationship between ISLR gene expression and epithelial-mesenchymal transition (EMT). ISLR expression was negatively correlated with sensitivity to PX-12 and NSC632839. Taken together, these results show that the ISLR gene is involved in gastric carcinogenesis, and the underlying molecular mechanisms may include DNA methylation, EMT, and immune cell infiltration.", "claims": [{"id": "claim-method", "statement": "We conducted OS (overall survival) and DFS (disease-free survival) analyses of gastric cancer cases in the TCGA-STAD cohort according to the expression status of the ISLR gene through GEPIA2. A group cutoff of “quartile” was set, and the Kaplan–Meier curve was plotted. We also pooled the gastric cancer cases in the GSE14210, GSE15459, GSE22377, GSE29272, GSE51105, and GSE62254 datasets for the OS, FP (first progression), and PPS (post progression survival) analyses using the Kaplan–Meier plotter tool (Szasz et al., 2016).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32612640", "locator": "sections[4] \"Survival Curve Analysis\" paragraph 2", "quote": "We conducted OS (overall survival) and DFS (disease-free survival) analyses of gastric cancer cases in the TCGA-STAD cohort according to the expression status of the ISLR gene through GEPIA2. A group cutoff of “quartile” was set, and the Kaplan–Meier curve was plotted. We also pooled the gastric cancer cases in the GSE14210, GSE15459, GSE22377, GSE29272, GSE51105, and GSE62254 datasets for the OS, FP (first progression), and PPS (post progression survival) analyses using the Kaplan–Meier plotter tool (Szasz et al., 2016)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The datasets generated for this study are available on request to the corresponding author.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32612640", "locator": "sections[23] \"Data Availability Statement\" paragraph 2", "quote": "The datasets generated for this study are available on request to the corresponding author."}], "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:32612640"], "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:GSE14210"], "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:GSE14210"], "outputs": ["the replicated result and its comparison"], "instruments": [], "reagents": []}], "materials": [], "instruments": [], "reagents": [], "conditions": {}, "gaps": []}, "data": {"state": "partial", "assets": [{"id": "source:pmid:32612640", "role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.3389/fgene.2020.00620", "sha256": 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analysis", "dsl_operations": [], "missing_operations": [], "expressible": null, "parameters": {}, "data_shapes": [], "evidence": {"score": 1.0, "band": "verbatim", "quote": "We conducted OS (overall survival) and DFS (disease-free survival) analyses of gastric cancer cases in the TCGA-STAD cohort according to the expression status of the ISLR gene through GEPIA2. A group cutoff of “quartile” was set, and the Kaplan–Meier curve was plotted. We also pooled the gastric cancer cases in the GSE14210, GSE15459, GSE22377, GSE29272, GSE51105, and GSE62254 datasets for the OS, FP (first progression), and PPS (post progression survival) analyses using the Kaplan–Meier plotter tool (Szasz et al., 2016)."}}], "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": ["pca_fit"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: pca."}, "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": ["GSE14210", "GSE15459", "GSE22377", "GSE29272", "GSE51105", "and GSE62254"], "resolved_accessions": ["GSE14210", "GSE15459", "GSE22377", "GSE29272", "GSE51105"], "statements": ["The datasets generated for this study are available on request to the corresponding author."], "basis": "The paper names GSE14210, GSE15459, GSE22377, GSE29272, GSE51105 in Gene Expression Omnibus (GEO) and the accession resolves in the repository. No dataset was downloaded and no licence was read."}}, "can_run": {"dsl_operations": ["pca_fit"], "assets": ["source:pmid:32612640", "data:geo:GSE14210", "asset:table:pmid:32612640:1", "asset:table:pmid:32612640:2"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE14210"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T18:21:08Z", "independence": "single_reader"}, "evidence_check": {"method": "verbatim", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 30546, "completion_tokens": 2332, "cached_tokens": 785}}, "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:32612640", "type": "paper", "label": "pmid:32612640"}, {"id": "source:pmid:32612640", "type": "manuscript", "label": "PMID 32612640 full text"}, {"id": "data:geo:GSE14210", "type": "dataset", "label": "GEO GSE14210"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:32612640", "type": "paper", "label": "pmid:32612640"}, {"id": "source:pmid:32612640", "type": "manuscript", "label": "PMID 32612640 full text"}, {"id": "data:geo:GSE14210", "type": "dataset", "label": "GEO GSE14210"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-32612640", "type": "extraction", "used": ["source:pmid:32612640"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE14210", "type": "accession_resolution", "used": ["data:geo:GSE14210"], "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:32612640", "parent_hash": "sha256:d7d548696b6997f5f98e4e6bf5a45065e07db10aa8bda44d2dafa156e10cff63", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE14210 licence not read", "asset:data:geo:GSE14210 not downloaded", "asset:data:geo:GSE15459 licence not read", "asset:data:geo:GSE15459 not downloaded", "asset:data:geo:GSE22377 licence not read", "asset:data:geo:GSE22377 not downloaded", "asset:data:geo:GSE29272 licence not read", "asset:data:geo:GSE29272 not downloaded", "asset:data:geo:GSE51105 licence not read", "asset:data:geo:GSE51105 not downloaded", "execution.not_run", "method.reader_named_unmapped", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "principal_component_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["pca_fit"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.7, "evidence": ["Principal component analysis"], "order_basis": "analysis_only", "id": "assay:1"}]}