Bioinformatics-based analysis of the relationship between STC1 expression and immune infiltration in gastric cancer.

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{"pmcid": "PMC12307138", "section_index": 10, "section_title": "3.1 Baseline information of GC patients", "row_count": 22, "column_count": 3}, "table": {"label": "TABLE 1", "caption": "Baseline information for patients with gastric cancer in TCGA database.", "rows": [["Characteristic", "Levels", "Overall"], ["n", "", "375"], ["Age, n (%)", "<=65", "164 (44.2%)"], [">65", "207 (55.8%)"], ["Gender, n (%)", "Female", "134 (35.7%)"], ["Male", "241 (64.3%)"], ["Pathologic stage, n (%)", "Stage I&II", "164 (46.6%)"], ["Stage III&IV", "188 (53.4%)"], ["T stage, n (%)", "T1&2", "99 (27.0%)"], ["T3&4", "268 (73.0%)"], ["N stage, n (%)", "N0", "111 (31.1%)"], ["N1&2&3", "246 (68.9%)"], ["M stage, n (%)", "M0", "330 (93%)"], ["M1", "25 (7%)"], ["Histologic grade, n (%)", "G1&2", "147 (40.1%)"], ["G3", "219 (59.9%)"], ["Location, n (%)", "Distal", "138 (33.9%)"], ["Non-distal", "223 (66.1%)"], ["Residual tumor, n (%)", "R0", "298 (90.6%)"], ["R1&2", "31 (9.4%)"], ["OS event, n (%)", "Alive", "228 (60.8%)"], ["Dead", "147 (39.2%)"]], "row_count": 22, "column_count": 3, "numeric_cells": 28, "header_rows": 1, "locator": "section[10]/table-wrap[1]#T1"}}, {"id": "asset:table:pmid:40741411:2", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:db7750fed6906a7f58e40e8743fb0e287173971d7856ec3b687ebdd404ec9d59", "bytes": 699, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[14]/table-wrap[1]#T2", "version": null, "note": "Results of KEGG pathway enrichment analysis.", "structure": {"pmcid": "PMC12307138", "section_index": 14, "section_title": "3.5 Association between STC1 expression and TME immune infiltration as well as T-cell exhaustion", "row_count": 6, "column_count": 7}, "table": {"label": "TABLE 2", "caption": "Results of KEGG pathway enrichment analysis.", "rows": [["ID", "Description", "GeneRatio", "BgRatio", "pvalue", "p.adjust", "qvalue"], ["hsa04657", "IL-17 signaling pathway", "9/47", "94/8076", "2.52e-09", "3.55e-07", "2.97e-07"], ["hsa04060", "Cytokine-cytokine receptor interaction", "10/47", "295/8076", "5.66e-06", "3.99e-04", "3.34e-04"], ["hsa05144", "Malaria", "5/47", "50/8076", "9.35e-06", "4.39e-04", "3.67e-04"], ["hsa04630", "JAK-STAT signaling pathway", "7/47", "162/8076", "3.68e-05", "0.001", "0.001"], ["hsa05323", "Rheumatoid arthritis", "5/47", "93/8076", "1.90e-04", "0.005", "0.004"]], "row_count": 6, "column_count": 7, "numeric_cells": 31, "header_rows": 1, "locator": "section[14]/table-wrap[1]#T2"}}], "gaps": ["asset:source:pmid:40741411 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", "tier": null, "blocking_axis": null, "blocked_on": null, "axes": {}, "can_run": {"dsl_operations": [], "assets": ["source:pmid:40741411", "asset:table:pmid:40741411:1", "asset:table:pmid:40741411:2"], "steps": ["read_published_estimate"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": ["xml"], "capabilities": [], "data_gaps": ["source:pmid:40741411"]}, "gaps": ["corpus_record_absent"]}, "review": {"state": "partial", "machine_critique": {"status": "blocked", "providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "full-text-reading-v1", "prompt_hash": "32f80d71a4a470ecad480a263b49d80d443c330a4507bdc8e09a23fe2f8b71ff", "source_hash": "6c7661c6173c644cf77c3b57c071d747d7886d675ab76b8c833dfed0a6ab47d7", "raw_response_sha256": "sha256:c6d7e3cb32d0da5f0c62abb4b632390aa4aa240a5fb1a34ab80eb17df0b2b2f3", "raw_response_chars": 5673}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "e7d6aa169e7add2ecc71a34ba66ce4efb2640e07332addce03bcb5de240c03d3", "source_hash": "6c7661c6173c644cf77c3b57c071d747d7886d675ab76b8c833dfed0a6ab47d7", "raw_response_sha256": "sha256:c270797f2fbeef23e5d8cd7bab52261edfb83cd77530fcba5771ea26e40225cb", "raw_response_chars": 74300}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "d7eef3a1accf26b69c44bc5b6333ff5cd0557ad6b5a7737650e058293c7e584e", "source_hash": "6c7661c6173c644cf77c3b57c071d747d7886d675ab76b8c833dfed0a6ab47d7", "raw_response": "{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The paper states that STC1 expression was significantly higher in GC tissues, independently predicted poor overall survival, and was associated with immune-cell infiltration, especially T-cell exhaustion; it does not state a single headline numerical result for this main finding.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The paper states that STC1 expression was significantly higher in GC tissues, independently predicted poor overall survival, and was associated with immune-cell infiltration, especially T-cell exhaustion; it does not state a single headline numerical result for this main finding.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:24:45.200883+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "b791d27f8ffd0b9cad2e679498b3f3e06a5f66f7e0c899f03c90adfecb4645c9", "source_hash": "6c7661c6173c644cf77c3b57c071d747d7886d675ab76b8c833dfed0a6ab47d7", "raw_response": "<think>We need answer JSON only. Need identify single numerical result headline number for registered target/main finding. Source text perhaps no headline numerical result stated. Numbers in methods/results: 875 DE genes, 723 up, 152 down, but target is headline numerical result paper states for main finding. Is \"headline numerical result\" perhaps 875? User asks \"find the single numerical result that a replication of the registered target has to reproduce. Report headline number only: value paper itself states for registered target\". Registered target main finding = STC1 expression significantly higher in GC and predicted poor OS etc. Source text provides no quantitative effect size / HR / p value for headline. There are numbers unrelated to main registered target (DE genes 875). Need set false, parent 0 unit/evidence empty, target_result say text states qualitative findings instead. Must exact contiguous quote only if evidence. Since false leave empty.\n\nNeed ensure target_result wording perhaps \"The text states STC1 expression was significantly higher in GC tissues and independently predicted poor overall survival, but gives no numerical result for this registered target.\" This is okay. JSON object. parent_value number 0. number_stated false. Unit \"\", evidence \"\". Could there be interpretation where 875 is headline numerical result? Let's inspect supplied paper text. It includes abstract and detailed sections, but only numerical result is 875 DE genes. The task specifically says target: \"the headline numerical result the paper states for its main finding\". Main finding in abstract is STC1 higher, poor OS, immune associations, no numbers. Likely trap: don't report 875, thresholds, software version. So false.\n\nNeed maybe evidence must be exact quotation, but only if number stated. User says if no number, leave evidence empty. target_result can mention what text states, perhaps quote exact wording? Could be: \"The text states: “STC1 expression was significantly higher in GC tissues and independently predicted poor overall survival.”\" This is exact and useful. But does requirement exact contiguous quote pertain evidence only? likely. We can put target_result statement. Ensure JSON valid curly quotes allowed. Let's formulate concise.\n\nPotential issue: They might regard \"There were altogether 875 differentially expressed genes...\" as numerical result and headline numerical result? Registered target is main finding, not pathway DEG count. Main finding relates STC1 expression and prognosis/immune infiltration. There is no specific number. Correct.\n\nJSON only, no markdown.</think>\n\n{\"parent_value\":0,\"unit\":\"\",\"evidence\":\"\",\"target_result\":\"The text states, “STC1 expression was significantly higher in GC tissues and independently predicted poor overall survival,” but gives no numerical result for the registered target.\",\"number_stated\":false}", "reading": {"parent_value": 0, "unit": "", "evidence": "", "target_result": "The text states, “STC1 expression was significantly higher in GC tissues and independently predicted poor overall survival,” but gives no numerical result for the registered target.", "number_stated": false, "source_locator": null}, "recorded_at": "2026-10-31T15:24:48.506283+00:00"}], "agreement": false, "disagreements": {"analysis_methods": {"minimax": ["Differential expression analysis", "Kaplan-Meier survival analysis", "Log-rank test", "Univariate Cox regression", "Multivariate Cox regression", "Bonferroni correction", "Nomogram-based survival probability prediction", "ssGSEA", "TIMER", "Single-cell RNA sequencing analysis", "Gene Set Enrichment Analysis (GSEA)"], "minimax_alt": ["Data-driven optimal cutoff for STC1 expression using the “survminer” package", "Kaplan-Meier survival curves", "Log-rank test", "Univariate and multivariate Cox regression", "Bonferroni correction", "Nomogram for predicting survival probability", "Single-sample Gene Set Enrichment Analysis (ssGSEA)", "TIMER", "Single-cell RNA sequencing analysis using Seurat (version 4.0), PCA, t-SNE, and SingleR cell-type annotation", "DESeq2 differential expression analysis", "Gene Set Enrichment Analysis (GSEA) using clusterProfiler and ggplot2"], "decisive": false}, "statistical_method": {"minimax": "Kaplan-Meier survival curves with the Log-rank test and univariate and multivariate Cox regression analyses", "minimax_alt": "Univariate and multivariate Cox regression", "decisive": true}}, "agreement_basis": {"policy": "decisive_fields", "decisive_fields": ["work_type", "number_stated", "parent_value", "unit"]}, "blinded": true}, "human_critique": {"status": "not_run", "reviewer": null, "signed_at": null, "conflict_checked": false, "commentary": null}, "stages": [{"key": "target_materials", "status": "pending", "reason": null, "evidence": null}, {"key": "independent_readings", "status": "blocked", "reason": "The independent readings are incomplete or disagree; the source evidence must resolve the difference.", "evidence": {"provider_errors": []}}, {"key": "source_resolution", "status": "pending", "reason": null, "evidence": null}, {"key": "protocol_reconstruction", "status": "pending", "reason": null, "evidence": null}, {"key": "control_execution", "status": "pending", "reason": null, "evidence": null}, {"key": "control_comparison", "status": "pending", "reason": null, "evidence": null}, {"key": "publication", "status": "pending", "reason": null, "evidence": null}], "gaps": ["review.human_critique", "review.machine_critique.blocked"]}, "execution": {"state": "absent", "status": "not_run", "mode": null, "runs": [], "gaps": ["execution.not_run"]}, "provenance": {"entities": [{"id": "package:4cd4317a9e329b3b354ce6ffbc43ead8b49c5cdc4918fe31b4b5d1ccd166962f", "type": "sep_package", "label": "SEP v1 package for pmid:40741411"}], "activities": [{"id": "activity:conversion:pmid:40741411", "type": "conversion", "used": ["package:4cd4317a9e329b3b354ce6ffbc43ead8b49c5cdc4918fe31b4b5d1ccd166962f"], "agent": "agent:corpus-assay-engine"}], "agents": [{"id": "agent:minimax", "type": "model", "label": "minimax"}, {"id": "agent:minimax_alt", "type": "model", "label": "minimax_alt"}, {"id": "agent:corpus-assay-engine", "type": "software", "label": "Corpus assay engine"}], "source_run_id": "run-20261023T122449232913", "dsl_catalogue_fingerprint": "343fb30756ba6ec3", "capability_table_fingerprint": "2cb3e42f047d2ecf", "snapshot_id": "ba34b49490d9bfaf"}, "lineage": {"parent_id": "pmid:40741411", "parent_hash": "sha256:99d1a6ff1ea6790782b8ebfb40c7c75b1a3f6539c124f0dc18c0e1905bf02c80", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:40741411 not verified", "authors", "capability", "corpus_record_absent", "execution.not_run", "method", "review.human_critique", "review.machine_critique.blocked", "step:obtain_source_data blocked on data:not_downloaded", "step:run_analysis blocked on no owned computational capability is bound to this experiment", "step:run_analysis input 'materials:the source data behind the published result in pmid:40741411' does not resolve to a declared asset", "targets"]}