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pmid:34035992
Identification of Vitamin D-related gene signature to predict colorectal cancer prognosis.
Luping Bu · Fengxing Huang · Mengting Li · Yanan Peng · Haizhou Wang · Meng Zhang · Liqun Peng · Lan Liu · Qiu Zhao
PeerJ · 2021 doi:10.7717/peerj.11430
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Experiment
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Complete file
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Previous experiments and epidemiological studies have shown that vitamin D and vitamin D-related genes play a vital role in CRC. Therefore, we aimed to construct a vitamin D-related gene signature to predict prognosis in CRC. The CRC data from The Cancer Genome Atlas (TCGA) was performed as the training set. A total of 173 vitamin D-related genes in the TCGA CRC dataset were screened, and 17 genes associated with CRC prognosis were identified from them. Then, a vitamin D-related gene signature consisting of those 17 genes was established by univariate and multivariate Cox analyses. Moreover, four external datasets (GSE17536, GSE103479, GSE39582, and GSE17537) were used as testing set to validate the stability of this signature. The high-risk group presented a significantly poorer overall survival than low-risk group in both of training set and testing sets. Besides, the areas under the curve (AUCs) for signature on OS in training set at 1, 3, and 5 years were 0.710, 0.708, 0.710 respectively. The AUCs of the ROC curve in GSE17536 for 1, 3, and 5 years were 0.649, 0.654, and 0.694. These results indicated the vitamin D-related gene signature model could effectively predict the survival status of CRC patients. This vitamin D-related gene signature was also correlated with TNM stage in CRC clinical parameters, and the higher risk score from this model was companied with higher clinical stage. Furthermore, the high accuracy of this prognostic signature was validated and confirmed by nomogram model. 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"44(22.0%)", "61(31.6%)", ""], ["IV", "64(16.3%)", "20(10.0%)", "44(22.8%)", ""], ["T classification", "", "", "", ""], ["T1", "9(2.3%)", "8(4.0%)", "1(0.5%)", "0.0006668"], ["T2", "66(16.8%)", "40(20%)", "26(13.5%)", ""], ["T3", "272(69.2%)", "139(69.5%)", "133(68.9%)", ""], ["T4", "46(11.7%)", "13(6.5%)", "33(17.1%)", ""], ["N classification", "", "", "", ""], ["N0", "233(59.3%)", "139(69.5%)", "94(48.7%)", "0.00001556"], ["N1", "90(22.9%)", "41(20.5%)", "49(25.4%)", ""], ["N2", "70(17.8%)", "20(10.0%)", "50(25.9%)", ""], ["M classification", "", "", "", ""], ["M0", "329(83.7%)", "180(90%)", "149(77.2%)", "0.0009721"], ["M1", "64(16.3%)", "20(10.0%)", "44(22.8%)", ""]], "row_count": 24, "column_count": 5, "numeric_cells": 62, "header_rows": 1, "locator": "section[11]/table-wrap[1]#table-2"}}, {"id": "asset:table:pmid:34035992:3", "role": "table", "format": "jats-table", "media_type": "application/vnd.jats.table+json", "uri": null, "sha256": 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"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": ["logrank_test"], "missing_operations": [], "basis": "The paper names the method it used and the corpus's method extractor maps it onto the DSL catalogue: log_rank_test."}, "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": ["GSE17536", "GSE103479", "GSE39582", "GSE17537"], "resolved_accessions": ["GSE17536", "GSE103479", "GSE39582", "GSE17537"], "statements": ["The following information was supplied regarding data availability:\nData is available at TCGA-COAD and NCBI GEO: GSE17536, GSE103479, GSE39582, and GSE17537.\nhttps://portal.gdc.cancer.gov/projects/TCGA-COAD."], "basis": "The paper names GSE17536, GSE103479, GSE39582, GSE17537 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": ["logrank_test"], "assets": ["source:pmid:34035992", "data:geo:GSE103479", "asset:table:pmid:34035992:1", "asset:table:pmid:34035992:2", "asset:table:pmid:34035992:3"], "steps": ["run_analysis"]}, "must_build": {"dsl_operations": [], "converters": [], "readers": [], "capabilities": [], "data_gaps": ["data:geo:GSE103479"]}, "gaps": []}, "review": {"state": "partial", "machine_critique": {"kind": "extraction_review", "reader": {"model": "MiniMax-M3.1-Flash", "provider": "minimax", "provider_family": "minimax", "read_at": "2026-10-31T19:35:22Z", "independence": "single_reader"}, "evidence_check": {"method": "absent", "availability": "verbatim"}, "calls": 3, "usage": {"prompt_tokens": 41061, "completion_tokens": 1936, "cached_tokens": 784}}, "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:34035992", "type": "paper", "label": "pmid:34035992"}, {"id": "source:pmid:34035992", "type": "manuscript", "label": "PMID 34035992 full text"}, {"id": "data:geo:GSE103479", "type": "dataset", "label": "GEO GSE103479"}], "activities": [{"id": "activity-reading-sci-2026-11-01", "type": "classification", "used": [{"id": "pmid:34035992", "type": "paper", "label": "pmid:34035992"}, {"id": "source:pmid:34035992", "type": "manuscript", "label": "PMID 34035992 full text"}, {"id": "data:geo:GSE103479", "type": "dataset", "label": "GEO GSE103479"}], "agent": "agent:corpus-assay-engine"}, {"id": "activity-read-34035992", "type": "extraction", "used": ["source:pmid:34035992"], "agent": "agent:minimax-reader"}, {"id": "activity-resolve-GSE103479", "type": "accession_resolution", "used": ["data:geo:GSE103479"], "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:34035992", "parent_hash": "sha256:d11680f9650c5a03e3fc70ce981d7018eed33d6b07f52f9b94e66e076e52823a", "fork_of": null, "generation": 6}, "gaps": ["asset:data:geo:GSE103479 licence not read", "asset:data:geo:GSE103479 not downloaded", "asset:data:geo:GSE17536 licence not read", "asset:data:geo:GSE17536 not downloaded", "asset:data:geo:GSE17537 licence not read", "asset:data:geo:GSE17537 not downloaded", "asset:data:geo:GSE39582 licence not read", "asset:data:geo:GSE39582 not downloaded", "execution.not_run", "review.human_critique", "review.independent_reader", "review.machine_critique"], "assays": [{"role": "analysis", "definition_id": "survival_analysis", "definition_version": "f2132e96ae6c7a4e", "definition_digest": null, "required_operations": ["logrank_test"], "support_state": "supported", "source_hashes": {"dsl_catalogue": "f2132e96ae6c7a4e"}, "confidence": 0.8, "evidence": ["log-rank"], "order_basis": "analysis_only", "id": "assay:1"}]}