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pmid:33116619
Gene Expression Along with Genomic Copy Number Variation and Mutational Analysis Were Used to Develop a 9-Gene Signature for Estimating Prognosis of COAD.
Yiping Lu · Si Wu · Changwan Cui · Miao Yu · Shuang Wang · Yuanyi Yue · Miao Liu · Zhengrong Sun
OncoTargets and therapy · 2020 doi:10.2147/OTT.S255590
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Complete file
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Univariate Cox analysis was used to select genes which significantly related to the overall survival. GISTIC 2.0 software was used to identify significant amplification or deletion. Mutsig 2.0 software was used to identify significant mutation genes. The 9-gene signature was screened by random forest algorithm and Cox regression analysis. GSE17538 dataset was used as an external dataset to verify the predictive ability of 9-gene signature. qPCR was used to detect the expression of 9 genes in clinical specimens.\nRESULTS: A total of 71 candidate genes are obtained by integrating genomic variation, mutation and prognostic data. Then, 9-gene signature was established, which includes HOXD12, RNF25, CBLN3, DOCK3, DNAJB13, PYGO2, CTNNA1, PTPRK, and NAT1. The 9-gene signature is an independent prognostic risk factor for COAD patients. In addition, the signature shows good predicting performance and clinical practicality in training set, testing set and external verification set. The results of qPCR based on clinical samples showed that the expression of HOXD12, RNF25, CBLN3, DOCK3, DNAJB13, and PYGO2 was increased in colon cancer tissues and the expression of CTNNA1, PTPRK, NAT1 was decreased in colon cancer tissues.\nCONCLUSION: In this study, 9-gene signature is constructed as a new prognostic marker to predict the survival of COAD patients.", "claims": [{"id": "claim-data-access", "statement": "Level-3 RNA-sequencing data, the clinicopathological、 SNP 、 copy number segments and survival data of patients with COAD were downloaded from the UCSC Xena browser (https://xenabrowser.net/).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:33116619", "locator": "sections[3] \"Data Acquisition and Processing\" paragraph 2", "quote": "Level-3 RNA-sequencing data, the clinicopathological、 SNP 、 copy number segments and survival data of patients with COAD were downloaded from the UCSC Xena browser (https://xenabrowser.net/)."}], "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:33116619"], "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. 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