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pmid:39921793

Multivariate Cox regression analysis of prognostic genes and therapeutic mechanisms of gastric cancer.

Discover oncology · 2025 doi:10.1007/s12672-025-01907-7

Paper

partial

Experiment

partial

Data

partial

Analysis

absent

Execution

absent

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Record details sci_version · id · kind · revision · content_hash · schema · created_at · updated_at · generator
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pmid:39921793
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science-record
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2026-11-01T10:25:49Z
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2026-11-01T10:25:49Z
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sep_to_sci_v1
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paper object · 10 fields
state
partial
title
Multivariate Cox regression analysis of prognostic genes and therapeutic mechanisms of gastric cancer.
doi
10.1007/s12672-025-01907-7
pmid
39921793
authors
null
journal
Discover oncology
year
2025
abstract
null
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claim-1
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the headline numerical result the paper states for its main finding
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quantitative
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prognostic related genes
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null
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source:pmid:39921793
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quote
Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.
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[0]
abstract
[1]
authors
experiment object · 8 fields
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partial
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the headline numerical result the paper states for its main finding
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read_published_estimate
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1
name
Read the published estimate and its interval from the source
kind
other
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complete
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null
description
The number a replication must land on, and the sentence it came from.
parameters object · 0 fields
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[0]
source:pmid:39921793
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[0]
the published estimate, its unit and its interval
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[1] object · 13 fields
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Obtain the source data behind the published result
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The published result cannot be recomputed without the data the paper analysed.
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the source data with its provenance
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Run the analysis programme
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blocked
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no owned computational capability is bound to this experiment
description
Re-run the paper's analysis on the source data and produce the registered result. | SEP input not carried into the asset list: materials:the source data behind the published result in pmid:39921793
parameters object · 0 fields
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[0]
the registered result
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10.1007/s12672-025-01907-7
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Source read by the package builder: full_text.
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asset:source:pmid:39921793 not verified
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read_published_estimate
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source:pmid:39921793
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{"parent_value":74,"unit":"prognostic related genes","evidence":"Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.","target_result":"The paper states that 74 prognostic related genes (PRG) were screened out.","number_stated":true}
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74
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prognostic related genes
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Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.
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The paper states that 74 prognostic related genes (PRG) were screened out.
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true
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raw_response
<think>We need answer JSON only. Need interpret registered target: headline numerical result paper states for main finding. Source says 74 prognostic related genes screened, identify four key genes. "headline numerical result" likely 74? Registered target main finding maybe headline numerical result perhaps number of PRGs. Need determine singular numerical result replication target. They ask value paper itself states for registered target. Target defined "the headline numerical result the paper states for its main finding". Main finding likely 74 prognostic related genes, perhaps abstract: "Through ... 74 prognostic related genes (PRG) were screened out." Is headline numerical result 74 genes. Need report headline number only and unit paper prints. Exact contiguous quote contains number, whole clause attribution. Unit should be printed unit? "74 prognostic related genes (PRG)" unit perhaps "prognostic related genes". Evidence exact quote whole clause: "Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out." parent_value 74, unit "prognostic related genes". target_result maybe "74 prognostic related genes (PRG) were screened out." number_stated true. But ambiguity: Main finding is four key genes? Yet those are named, numerical count four. User singular target says headline numerical result. Could be 74 in abstract is central sample/result. Let's inspect wording. Title. Abstract has findings. "Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out. A PPI network was established for PRG to identify four key genes..." Headline numerical result could be 74 prognostic genes. The prompt likely benchmark asks extract target result. Need perhaps infer "headline numerical result the paper states for its main finding" perhaps exact abstract key quantitative statement. There is no explicit registry elsewhere. Need return strongest numeric. 74 likely. Unit as paper prints: "prognostic related genes" perhaps "genes". User says unit must be unit paper prints. Could set "prognostic related genes" exact phrase. Evidence quote entire clause. target_result maybe state result. Ensure valid JSON.</think> {"parent_value":74,"unit":"prognostic related genes","evidence":"Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.","target_result":"74 prognostic related genes (PRG) were screened out.","number_stated":true}
reading object · 6 fields
parent_value
74
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prognostic related genes
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Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.
target_result
74 prognostic related genes (PRG) were screened out.
number_stated
true
source_locator
chars 460-587 of source sha256 ab9e8592e0e13bd0a8029e7f10dcb238b24460b80215723840a028e5da579b4d
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2026-10-31T15:23:16.182526+00:00
agreement
false
disagreements object · 3 fields
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minimax
74 prognostic related genes (PRG) were identified, with four key genes (LMOD1, CRYAB, VCL and MYL9); high expression of the key genes was associated with poor prognosis, and multivariate Cox regression analysis showed that the key genes were an independent prognostic factor.
minimax_alt
Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out. A PPI network was established for PRG to identify four key genes (KG), namely LMOD1, CRYAB, VCL and MYL9.
decisive
false
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[0]
Kaplan–meier analysis
[1]
univariate Cox regression analysis
[2]
multivariate Cox regression analysis
[3]
Wilcoxon rank sum test
[4]
Kruskal–Wallis H test
[5]
Gene Ontology functional enrichment analysis
[6]
KEGG pathway enrichment analysis
minimax_alt array · 8 items
[0]
Kaplan–meier analysis
[1]
univariate Cox regression analysis
[2]
multivariate Cox multiple regression analysis
[3]
Wilcoxon rank sum test
[4]
Kruskal–Wallis H test
[5]
PPI network analysis
[6]
Gene Ontology functional enrichment analysis
[7]
KEGG pathway enrichment analysis
decisive
false
statistical_method object · 3 fields
minimax
multivariate Cox regression analysis
minimax_alt
Kaplan–meier analysis, univariate Cox regression analysis and multivariate Cox multiple regression analysis for prognosis-related gene assessment; Wilcoxon rank sum test and Kruskal–Wallis H test for clinical-correlation comparisons
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true
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decisive_fields
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step:run_analysis input 'materials:the source data behind the published result in pmid:39921793' does not resolve to a declared asset
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targets
Complete file
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"minimax_alt", "model": "MiniMax-M3", "prompt_version": "full-text-reading-v1", "prompt_hash": "c02a59b0ba89429c7b6f85823264828425d22a8bc9eec2bdbbf010777675aa59", "source_hash": "ab9e8592e0e13bd0a8029e7f10dcb238b24460b80215723840a028e5da579b4d", "raw_response_sha256": "sha256:5dd37deb9435427f9147f3b62b1f013033b78e18c8e040e9b4064bda73c74ce5", "raw_response_chars": 53883}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "016a0913d1b5cd701b23a5775e8b76ee17189b7f8c0108ff85a46c40866a056c", "source_hash": "ab9e8592e0e13bd0a8029e7f10dcb238b24460b80215723840a028e5da579b4d", "raw_response": "{\"parent_value\":74,\"unit\":\"prognostic related genes\",\"evidence\":\"Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.\",\"target_result\":\"The paper states that 74 prognostic related genes (PRG) were screened out.\",\"number_stated\":true}", "reading": {"parent_value": 74, "unit": "prognostic related genes", "evidence": "Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.", "target_result": "The paper states that 74 prognostic related genes (PRG) were screened out.", "number_stated": true, "source_locator": "chars 460-587 of source sha256 ab9e8592e0e13bd0a8029e7f10dcb238b24460b80215723840a028e5da579b4d"}, "recorded_at": "2026-10-31T15:23:14.847239+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "784d0ed322f920717d28c05b4387c82ed9601e39898a496de001606f8e3b2d08", "source_hash": "ab9e8592e0e13bd0a8029e7f10dcb238b24460b80215723840a028e5da579b4d", "raw_response": "<think>We need answer JSON only. Need interpret registered target: headline numerical result paper states for main finding. Source says 74 prognostic related genes screened, identify four key genes. \"headline numerical result\" likely 74? Registered target main finding maybe headline numerical result perhaps number of PRGs. Need determine singular numerical result replication target. They ask value paper itself states for registered target. Target defined \"the headline numerical result the paper states for its main finding\". Main finding likely 74 prognostic related genes, perhaps abstract: \"Through ... 74 prognostic related genes (PRG) were screened out.\" Is headline numerical result 74 genes. Need report headline number only and unit paper prints. Exact contiguous quote contains number, whole clause attribution. Unit should be printed unit? \"74 prognostic related genes (PRG)\" unit perhaps \"prognostic related genes\". Evidence exact quote whole clause: \"Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.\" parent_value 74, unit \"prognostic related genes\". target_result maybe \"74 prognostic related genes (PRG) were screened out.\" number_stated true.\n\nBut ambiguity: Main finding is four key genes? Yet those are named, numerical count four. User singular target says headline numerical result. Could be 74 in abstract is central sample/result. Let's inspect wording. Title. Abstract has findings. \"Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out. A PPI network was established for PRG to identify four key genes...\" Headline numerical result could be 74 prognostic genes. The prompt likely benchmark asks extract target result. Need perhaps infer \"headline numerical result the paper states for its main finding\" perhaps exact abstract key quantitative statement. There is no explicit registry elsewhere. Need return strongest numeric. 74 likely. Unit as paper prints: \"prognostic related genes\" perhaps \"genes\". User says unit must be unit paper prints. Could set \"prognostic related genes\" exact phrase. Evidence quote entire clause. target_result maybe state result. Ensure valid JSON.</think>\n\n{\"parent_value\":74,\"unit\":\"prognostic related genes\",\"evidence\":\"Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.\",\"target_result\":\"74 prognostic related genes (PRG) were screened out.\",\"number_stated\":true}", "reading": {"parent_value": 74, "unit": "prognostic related genes", "evidence": "Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out.", "target_result": "74 prognostic related genes (PRG) were screened out.", "number_stated": true, "source_locator": "chars 460-587 of source sha256 ab9e8592e0e13bd0a8029e7f10dcb238b24460b80215723840a028e5da579b4d"}, "recorded_at": "2026-10-31T15:23:16.182526+00:00"}], "agreement": false, "disagreements": {"target_result": {"minimax": "74 prognostic related genes (PRG) were identified, with four key genes (LMOD1, CRYAB, VCL and MYL9); high expression of the key genes was associated with poor prognosis, and multivariate Cox regression analysis showed that the key genes were an independent prognostic factor.", "minimax_alt": "Through independent prognostic analysis and clinical correlation analysis, 74 prognostic related genes (PRG) were screened out. A PPI network was established for PRG to identify four key genes (KG), namely LMOD1, CRYAB, VCL and MYL9.", "decisive": false}, "analysis_methods": {"minimax": ["Kaplan–meier analysis", "univariate Cox regression analysis", "multivariate Cox regression analysis", "Wilcoxon rank sum test", "Kruskal–Wallis H test", "Gene Ontology functional enrichment analysis", "KEGG pathway enrichment analysis"], "minimax_alt": ["Kaplan–meier analysis", "univariate Cox regression analysis", "multivariate Cox multiple regression analysis", "Wilcoxon rank sum test", "Kruskal–Wallis H test", "PPI network analysis", "Gene Ontology functional enrichment analysis", "KEGG pathway enrichment analysis"], "decisive": false}, "statistical_method": {"minimax": "multivariate Cox regression analysis", "minimax_alt": "Kaplan–meier analysis, univariate Cox regression analysis and multivariate Cox multiple regression analysis for prognosis-related gene assessment; Wilcoxon rank sum test and Kruskal–Wallis H test for clinical-correlation comparisons", "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:f536f4aca50204d8eb6cafa86720bfacbdb913849bd06fd9d9046be63c4b4f46", "type": "sep_package", "label": "SEP v1 package for pmid:39921793"}], "activities": [{"id": "activity:conversion:pmid:39921793", "type": "conversion", "used": ["package:f536f4aca50204d8eb6cafa86720bfacbdb913849bd06fd9d9046be63c4b4f46"], "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": "973629b8-47e9-4046-86bf-6ef022603cae", "parent_hash": "f536f4aca50204d8eb6cafa86720bfacbdb913849bd06fd9d9046be63c4b4f46", "fork_of": null, "generation": 1}, "gaps": ["abstract", "asset:source:pmid:39921793 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:39921793' does not resolve to a declared asset", "targets"]}