Identification of ALDH7A1 as a DNA-methylation-driven gene in lung squamous cell carcinoma.

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"role": "manuscript", "format": "xml", "media_type": "application/xml", "uri": "https://doi.org/10.1080/07853890.2024.2442529", "sha256": "sha256:896eb03764785837245f01141d33584af3dd3ad78e007a9a8483f4326265eac9", "bytes": null, "access": "open", "state": "resolved", "reader": null, "reader_status": "reader_required", "identifier": "10.1080/07853890.2024.2442529", "version": null, "note": "Source read by the package builder: full_text.", "structure": {"access_state": "full_text"}}, {"id": "asset:table:pmid:39711312:1", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": "sha256:eb095c04e0d36887c9b868198acc1680e4be9e41da18eab715bd3180c9488d98", "bytes": 558, "access": "open", "state": "verified", "reader": "read_table", "reader_status": "available", "identifier": "section[19]/table-wrap[1]#t0001", "version": null, "note": "The multi-cox of the DNA-methylation-driven gene.", "structure": {"pmcid": "PMC11703541", "section_index": 19, "section_title": "Constructing and validating an MDG risk profile model", "row_count": 6, "column_count": 7}, "table": {"label": "Table 1.", "caption": "The multi-cox of the DNA-methylation-driven gene.", "rows": [["ID", "Gene", "Co-efficiency", "HR", "HR.95L", "HR.95H", "p-Value"], ["TCGA_LUSC", "TRIM61", "0.364", "1.438", "0.949", "2.180", "0.087"], ["SMIM22", "0.258", "1.294", "0.996", "1.681", "0.053"], ["ALDH7A1", "0.433", "1.542", "1.148", "2.072", "0.004"], ["GSE37745", "ZNF486", "−0.753", "0.471", "0.203", "1.093", "0.080"], ["GSE37745", "ALDH7A1", "0.689", "1.991", "1.025", "3.866", "0.042"]], "row_count": 6, "column_count": 7, "numeric_cells": 32, "header_rows": 1, "locator": "section[19]/table-wrap[1]#t0001"}}], "gaps": ["asset:source:pmid:39711312 not verified"]}, "analysis": {"state": "absent", "methods": [], "targets": [], "gaps": ["method", "targets"]}, "capability": {"state": "absent", "requirements": [], "gaps": ["capability"]}, "readiness": {"state": "partial", 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"5f1dcec4d464c47cc09ab34f6f86612845fc0b233f18ba59dacf92b42647e680", "source_hash": "896eb03764785837245f01141d33584af3dd3ad78e007a9a8483f4326265eac9", "raw_response_sha256": "sha256:3373875d78e7d8d9291b7d0ba942535dbe5d6a49ef98a1682bfed23189fd8544", "raw_response_chars": 53404}], "target_providers": [{"provider": "minimax", "model": "MiniMax-M3.1-Flash", "prompt_version": "replication-target-v2", "prompt_hash": "251621ab11feb7adb9ab040f6f6c4f7879a6d69793095b0c38cb49b18fc9a6cc", "source_hash": "896eb03764785837245f01141d33584af3dd3ad78e007a9a8483f4326265eac9", "raw_response": "{\"parent_value\":-0.655,\"unit\":\"COR\",\"evidence\":\"The expression of ALDH7A1 in LUSC was negatively correlated with its methylation status (COR = −0.655).\",\"target_result\":\"ALDH7A1 expression in LUSC was negatively correlated with its methylation status (COR = −0.655).\",\"number_stated\":true}", "reading": {"parent_value": -0.655, "unit": "COR", "evidence": "The expression of ALDH7A1 in LUSC was negatively correlated with its methylation status (COR = −0.655).", "target_result": "ALDH7A1 expression in LUSC was negatively correlated with its methylation status (COR = −0.655).", "number_stated": true, "source_locator": "chars 1204-1307 of source sha256 896eb03764785837245f01141d33584af3dd3ad78e007a9a8483f4326265eac9"}, "recorded_at": "2026-10-31T15:18:46.952588+00:00"}, {"provider": "minimax_alt", "model": "MiniMax-M3", "prompt_version": "replication-target-v2", "prompt_hash": "8d16f5fede5089284a3496cb12f7eda500e7710ab3d1a2dec42148f28d154531", "source_hash": "896eb03764785837245f01141d33584af3dd3ad78e007a9a8483f4326265eac9", "raw_response": "<think>We need answer JSON only extracting headline numerical result paper states for registered target \"headline numerical result the paper states for its main finding\". Need determine likely number is COR = −0.655? Source text has several numbers but main finding ALDH7A1 methylation-driven gene, expression negatively correlated with methylation status (COR = −0.655). Target vague. Need inspect instruction: \"Read supplied paper text and find the single numerical result that a replication of the registered target has to reproduce. Report the headline number only: the value the paper itself states for the registered target, not a value you calculated, converted, averaged or reconstructed. The unit must be the unit the paper prints. The evidence must be an exact, contiguous quotation from SOURCE TEXT that contains the number; do not shorten it, do not add an ellipsis and do not paraphrase it. Attribution may be carried by the text's own wording: a number may be attached to the target by a parenthetical list, by the word 'respectively', or by words that name the target directly. When that is how the text links them, quote the whole clause so a reader can check the attribution for themselves. If the text states no number for the registered target, set number_stated to false, leave parent_value at 0, leave unit and evidence empty, and say in target_result what the text does state instead. Never invent a source.\"\n\nWe need choose single numerical result headline. The paper abstract explicitly gives COR = −0.655. That is likely headline numerical result for main finding. Need evidence exact contiguous quote containing number: \"The expression of ALDH7A1 in LUSC was negatively correlated with its methylation status (COR = −0.655).\" Need unit as paper prints. No physical unit, COR correlation coefficient unitless. So unit \"\"? They demand unit paper prints. For a correlation coefficient, no unit. Could be \"COR\" perhaps unit should be empty string because unitless. Need decide likely expected unit: \"COR\" or \"\"? Schema unit string. We can set \"unit\":\"\" since none printed. But desired extraction tasks often unit should correspond printed unit, e.g. \"%\" etc. Here none so \"\". parent_value -0.655 numeric. target_result description \"ALDH7A1 expression in LUSC was negatively correlated with its methylation status (COR = −0.655).\" number_stated true.\n\nNeed consider maybe headline is \"Forty-five DNA-methylation-driven genes (MDGs) were obtained, and 3 genes (TRIM61, SMIM22, and ALDH7A1) were significantly associated with survival...\" But registered target says \"the headline numerical result the paper states for its main finding\". Main finding ALDH7A1 high expression independent risk factor; numerical result COR −0.655. Is target perhaps \"45 MDGs\" headline number? They explicitly main finding ALDH7A1 as DNA methylation-driven gene and key quantitative finding correlation. We need not overthink. Need respond only JSON with no markdown.\n\nWe should provide exact clause quote. Parent value -0.655. Unit likely \"\" as no unit. target_result maybe \"The paper reports that ALDH7A1 expression in LUSC was negatively correlated with its methylation status, with COR = −0.655.\" evidence exact \"The expression of ALDH7A1 in LUSC was negatively correlated with its methylation status (COR = −0.655).\" Unit \"\".\n\nBut perhaps unit \"correlation coefficient\" since that's metric? They say \"The unit must be the unit the paper prints.\" Paper prints COR = -0.655; no unit. In other tasks units expected e.g. \"COR\" as unit? Usually unit should be literal unit. If no unit, \"\". We should obey avoid invention. We can put unit \"COR\" though that's abbreviation for metric, not unit. It would be safest empty unit. Need say target_result concise no extrapolate. Output JSON valid unicode minus supported. All requested keys.\n\nLet's revisit wording number_stated false case: if no number for registered target, parent_value 0, unit and evidence empty and target_result say text does state instead. We have number. Good.\n\nPotential issue \"headline number only\" means don't include multiple numbers in evidence? Exact contiguous quote containing number includes only -0.655. Fine. Target_result maybe quote or description. Fine.\n\nWe'll output.</think>\n\n{\"parent_value\":-0.655,\"unit\":\"\",\"evidence\":\"The expression of ALDH7A1 in LUSC was negatively correlated with its methylation status (COR = −0.655).\",\"target_result\":\"The paper reports that ALDH7A1 expression in LUSC was negatively correlated with its methylation status, with COR = −0.655.\",\"number_stated\":true}", "reading": {"parent_value": -0.655, "unit": "", "evidence": "The expression of ALDH7A1 in LUSC was negatively correlated with its methylation status (COR = −0.655).", "target_result": "The paper reports that ALDH7A1 expression in LUSC was negatively correlated with its methylation status, with COR = −0.655.", "number_stated": true, "source_locator": "chars 1204-1307 of source sha256 896eb03764785837245f01141d33584af3dd3ad78e007a9a8483f4326265eac9"}, "recorded_at": "2026-10-31T15:18:55.697543+00:00"}], "agreement": false, "disagreements": {"physical_methods": {"minimax": ["In vitro cell experiments with ALDH7A1 silencing and overexpression", "Real-time fluorescence quantitative reverse transcription polymerase chain reaction (qRT-PCR)", "Western blot analysis"], "minimax_alt": ["In vitro ALDH7A1 silencing and overexpression cell experiments", "Real-time fluorescence quantitative reverse transcription polymerase chain reaction (qRT-PCR)", "Western blot analysis"], "decisive": false}, "analysis_methods": {"minimax": ["MethylMix algorithm", "Wilcoxon rank-sum tests based on a β-mixture model", "Linear regression", "Univariate Cox regression", "Multivariate Cox regression", "KM analysis", "Nomination plot analysis", "Gene Set Enrichment Analysis (GSEA)"], "minimax_alt": ["MethylMix algorithm", "Wilcoxon rank-sum tests based on a β-mixture model", "Linear regression models", "Univariate and multivariate Cox regression", "KM analysis", "Gene Set Enrichment Analysis (GSEA)", "2−ΔΔCt method"], "decisive": false}, "statistical_method": {"minimax": "Linear regression", "minimax_alt": "Linear regression models", "decisive": true}, "unit": {"minimax": "COR", "minimax_alt": "", "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:081b42d2ffd170af4c64ef17cbfd7bcd2356212e8d92ca3f0cf5f48481a394fb", "type": "sep_package", "label": "SEP v1 package for pmid:39711312"}], "activities": [{"id": "activity:conversion:pmid:39711312", "type": "conversion", "used": ["package:081b42d2ffd170af4c64ef17cbfd7bcd2356212e8d92ca3f0cf5f48481a394fb"], "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:39711312", "parent_hash": "sha256:6c057d64fc6571888634841d6f14541388b9ab7c073780e1443b71dc912e8b07", "fork_of": null, "generation": 2}, "gaps": ["abstract", "asset:source:pmid:39711312 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:39711312' does not resolve to a declared asset", "targets"]}