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pmid:32021241
Potential Prognostic and Diagnostic Values of CDC6, CDC45, ORC6 and SNHG7 in Colorectal Cancer.
Yang Hu · Liping Wang · Zhixing Li · Zirui Wan · Mingjie Shao · Shaobin Wu · Guo Wang
OncoTargets and therapy · 2019 doi:10.2147/OTT.S231941
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Experiment
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Complete file
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The aims of this study are to investigate the gene expression profile of CRC and to explore potential strategy for CRC diagnosis, therapy and prognosis.\nMETHODS: We use affy and Limma package of Bioconductor R to do differential expression genes (DEGs) and differential expression lncRNAs (DELs) analysis from the gene datasets (GSE8671, GSE21510, GSE32323, GSE39582 and TCGA) respectively. Then, DEGs were analyzed by GO and KEGG pathway and Kaplan-Meier survival curve and Cox regression analyses were used to find aberrantly expressed genes associated with survival outcome of CRC patients. Real-time PCR assay was used to verify the aberrantly expressed genes expression in CRC samples.\nRESULTS: 306 up-regulation and 213 down-regulation common DEGs were found. A total of 485 DELs were identified, of which 241 up-regulated and 244 down-regulated. Then, GO and KEGG pathway analyses showed that DEGs were involved in cell cycle, mineral absorption, DNA replication, and Nitrogen metabolism. Among them, Kaplan-Meier survival curve and Cox regression analyses revealed that CDC6, CDC45, ORC6 and SNHG7 levels were significantly associated with survival outcome of CRC patients. Finally, real-time PCR assay was used to verify that the CDC6, CDC45, ORC6 and SNHG7 expression were up-regulated in 198 CRC samples compared with the expression levels in individual-matched adjacent mucosa samples.\nCONCLUSION: CDC6, CDC45, ORC6 and SNHG7 are implicated in CRC initiation and progression and could be explored as potential diagnosis, therapy and prognosis targets for CRC.", "claims": [{"id": "claim-method", "statement": "The DEG analysis between tumor and non-tumor samples of the GSE8671, GSE21510, GSE32323, and GSE39582 datasets and the DELs between tumor and non-tumor of TCGA dataset were performed with the Limma package of Bioconductor R (http://www.bioconductor.org/packages/release/bioc/html/limma.html).", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32021241", "locator": "sections[4] \"Identification of DEGs\" paragraph 2", "quote": "The DEG analysis between tumor and non-tumor samples of the GSE8671, GSE21510, GSE32323, and GSE39582 datasets and the DELs between tumor and non-tumor of TCGA dataset were performed with the Limma package of Bioconductor R (http://www.bioconductor.org/packages/release/bioc/html/limma.html)."}], "state": "complete"}, {"id": "claim-data-access", "statement": "The discovery datasets GSE8671,9 GSE21510,10 GSE3232311 and GSE3958212 were downloaded from the GEO.", "kind": "methodological", "target": null, "evidence": [{"asset": "source:pmid:32021241", "locator": "sections[3] \"Colorectal Cancer Datasets\" paragraph 2", "quote": "The discovery datasets GSE8671,9 GSE21510,10 GSE3232311 and GSE3958212 were downloaded from the GEO."}], "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:32021241"], "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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