The role of multiple metabolic genes in predicting the overall survival of colorectal cancer: A study based on TCGA and GEO databases
The recent advances in gene chip technology have led to the identification of multiple metabolism-related genes that are closely associated with colorectal cancer (CRC). Nevertheless, none of these genes could accurately diagnose or predict CRC. The prognosis of CRC has been made by previous prognos...
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| description | The recent advances in gene chip technology have led to the identification of multiple metabolism-related genes that are closely associated with colorectal cancer (CRC). Nevertheless, none of these genes could accurately diagnose or predict CRC. The prognosis of CRC has been made by previous prognostic models constructed by using multiple genes, however, the predictive function of multi-gene prognostic models using metabolic genes for the CRC prognosis remains unexplored. In this study, we used the TCGA-CRC cohort as the test dataset and the GSE39582 cohort as the experimental dataset. Firstly, we constructed a prognostic model using metabolic genes from the TCGA-CRC cohort, which were also associated with CRC prognosis. We analyzed the advantages of the prognostic model in the prognosis of CRC and its regulatory mechanism of the genes associated with the model. Secondly, the outcome of the TCGA-CRC cohort analysis was validated using the GSE39582 cohort. We found that the prognostic model can be employed as an independent prognostic risk factor for estimating the CRC survival rate. Besides, compared with traditional clinical pathology, it can precisely predict CRC prognosis as well. The high-risk group of the prognostic model showed a substantially lower survival rate as compared to the low-risk group. In addition, gene enrichment analysis of metabolic genes showed that genes in the prognostic model are enriched in metabolism and cancer-related pathways, which may explain its underlying mechanism. Our study identified a novel metabolic profile containing 11 genes for prognostic prediction of CRC. The prognostic model may unravel the imbalanced metabolic microenvironment, and it might promote the development of biomarkers for predicting treatment response and streamlining metabolic therapy in CRC. |
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Nevertheless, none of these genes could accurately diagnose or predict CRC. The prognosis of CRC has been made by previous prognostic models constructed by using multiple genes, however, the predictive function of multi-gene prognostic models using metabolic genes for the CRC prognosis remains unexplored. In this study, we used the TCGA-CRC cohort as the test dataset and the GSE39582 cohort as the experimental dataset. Firstly, we constructed a prognostic model using metabolic genes from the TCGA-CRC cohort, which were also associated with CRC prognosis. We analyzed the advantages of the prognostic model in the prognosis of CRC and its regulatory mechanism of the genes associated with the model. Secondly, the outcome of the TCGA-CRC cohort analysis was validated using the GSE39582 cohort. We found that the prognostic model can be employed as an independent prognostic risk factor for estimating the CRC survival rate. Besides, compared with traditional clinical pathology, it can precisely predict CRC prognosis as well. The high-risk group of the prognostic model showed a substantially lower survival rate as compared to the low-risk group. In addition, gene enrichment analysis of metabolic genes showed that genes in the prognostic model are enriched in metabolism and cancer-related pathways, which may explain its underlying mechanism. Our study identified a novel metabolic profile containing 11 genes for prognostic prediction of CRC. The prognostic model may unravel the imbalanced metabolic microenvironment, and it might promote the development of biomarkers for predicting treatment response and streamlining metabolic therapy in CRC.</description><identifier>ISSN: 1932-6203</identifier><identifier>EISSN: 1932-6203</identifier><identifier>DOI: 10.1371/journal.pone.0251323</identifier><identifier>PMID: 34398900</identifier><language>eng</language><publisher>San Francisco: Public Library of Science</publisher><subject>Analysis ; Antigens ; Biology and Life Sciences ; Biomarkers ; Cancer ; Cancer therapies ; Chemotherapy ; Colorectal cancer ; Colorectal carcinoma ; Computer and Information Sciences ; Datasets ; Engineering and Technology ; Gastroenterology ; Gene expression ; Genes ; Genetic aspects ; Genomes ; Health risks ; Hospitals ; Laboratories ; Life sciences ; Medical prognosis ; Medical research ; Medical schools ; Medicine and Health Sciences ; Metabolism ; Metabolites ; Metastasis ; Microenvironments ; Mutation ; Patient outcomes ; Patients ; Perl ; Prognosis ; Regression analysis ; Regulatory mechanisms (biology) ; Risk analysis ; Risk factors ; Risk groups ; Software ; Streamlining ; Survival ; Survival analysis</subject><ispartof>PloS one, 2021-08, Vol.16 (8), p.e0251323-e0251323</ispartof><rights>COPYRIGHT 2021 Public Library of Science</rights><rights>2021 Shi et al. This is an open access article distributed under the terms of the Creative Commons Attribution License: http://creativecommons.org/licenses/by/4.0/ (the “License”), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Notwithstanding the ProQuest Terms and Conditions, you may use this content in accordance with the terms of the License.</rights><rights>2021 Shi et al 2021 Shi et al</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c669t-503dd20384bca582e3358da4242b4835a01606d5a7ae6b29dadb063e842243893</citedby><cites>FETCH-LOGICAL-c669t-503dd20384bca582e3358da4242b4835a01606d5a7ae6b29dadb063e842243893</cites><orcidid>0000-0003-2655-5402</orcidid></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8367004/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC8367004/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,860,881,2096,2915,23845,27901,27902,53766,53768,79343,79344</link.rule.ids></links><search><creatorcontrib>Shi, Weijun</creatorcontrib><creatorcontrib>Li, Xincan</creatorcontrib><creatorcontrib>Su, Xu</creatorcontrib><creatorcontrib>Wen, Hexin</creatorcontrib><creatorcontrib>Chen, Tianwen</creatorcontrib><creatorcontrib>Wu, Huazhang</creatorcontrib><creatorcontrib>Liu, Mulin</creatorcontrib><title>The role of multiple metabolic genes in predicting the overall survival of colorectal cancer: A study based on TCGA and GEO databases</title><title>PloS one</title><description>The recent advances in gene chip technology have led to the identification of multiple metabolism-related genes that are closely associated with colorectal cancer (CRC). Nevertheless, none of these genes could accurately diagnose or predict CRC. The prognosis of CRC has been made by previous prognostic models constructed by using multiple genes, however, the predictive function of multi-gene prognostic models using metabolic genes for the CRC prognosis remains unexplored. In this study, we used the TCGA-CRC cohort as the test dataset and the GSE39582 cohort as the experimental dataset. Firstly, we constructed a prognostic model using metabolic genes from the TCGA-CRC cohort, which were also associated with CRC prognosis. We analyzed the advantages of the prognostic model in the prognosis of CRC and its regulatory mechanism of the genes associated with the model. Secondly, the outcome of the TCGA-CRC cohort analysis was validated using the GSE39582 cohort. We found that the prognostic model can be employed as an independent prognostic risk factor for estimating the CRC survival rate. Besides, compared with traditional clinical pathology, it can precisely predict CRC prognosis as well. The high-risk group of the prognostic model showed a substantially lower survival rate as compared to the low-risk group. In addition, gene enrichment analysis of metabolic genes showed that genes in the prognostic model are enriched in metabolism and cancer-related pathways, which may explain its underlying mechanism. Our study identified a novel metabolic profile containing 11 genes for prognostic prediction of CRC. The prognostic model may unravel the imbalanced metabolic microenvironment, and it might promote the development of biomarkers for predicting treatment response and streamlining metabolic therapy in CRC.</description><subject>Analysis</subject><subject>Antigens</subject><subject>Biology and Life Sciences</subject><subject>Biomarkers</subject><subject>Cancer</subject><subject>Cancer therapies</subject><subject>Chemotherapy</subject><subject>Colorectal cancer</subject><subject>Colorectal carcinoma</subject><subject>Computer and Information Sciences</subject><subject>Datasets</subject><subject>Engineering and Technology</subject><subject>Gastroenterology</subject><subject>Gene expression</subject><subject>Genes</subject><subject>Genetic aspects</subject><subject>Genomes</subject><subject>Health risks</subject><subject>Hospitals</subject><subject>Laboratories</subject><subject>Life sciences</subject><subject>Medical prognosis</subject><subject>Medical research</subject><subject>Medical schools</subject><subject>Medicine and Health Sciences</subject><subject>Metabolism</subject><subject>Metabolites</subject><subject>Metastasis</subject><subject>Microenvironments</subject><subject>Mutation</subject><subject>Patient outcomes</subject><subject>Patients</subject><subject>Perl</subject><subject>Prognosis</subject><subject>Regression analysis</subject><subject>Regulatory mechanisms (biology)</subject><subject>Risk analysis</subject><subject>Risk factors</subject><subject>Risk groups</subject><subject>Software</subject><subject>Streamlining</subject><subject>Survival</subject><subject>Survival 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role of multiple metabolic genes in predicting the overall survival of colorectal cancer: A study based on TCGA and GEO databases</title><author>Shi, Weijun ; Li, Xincan ; Su, Xu ; Wen, Hexin ; Chen, Tianwen ; Wu, Huazhang ; Liu, Mulin</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c669t-503dd20384bca582e3358da4242b4835a01606d5a7ae6b29dadb063e842243893</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>Analysis</topic><topic>Antigens</topic><topic>Biology and Life Sciences</topic><topic>Biomarkers</topic><topic>Cancer</topic><topic>Cancer therapies</topic><topic>Chemotherapy</topic><topic>Colorectal cancer</topic><topic>Colorectal carcinoma</topic><topic>Computer and Information Sciences</topic><topic>Datasets</topic><topic>Engineering and Technology</topic><topic>Gastroenterology</topic><topic>Gene expression</topic><topic>Genes</topic><topic>Genetic 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metabolic genes in predicting the overall survival of colorectal cancer: A study based on TCGA and GEO databases</atitle><jtitle>PloS one</jtitle><date>2021-08-16</date><risdate>2021</risdate><volume>16</volume><issue>8</issue><spage>e0251323</spage><epage>e0251323</epage><pages>e0251323-e0251323</pages><issn>1932-6203</issn><eissn>1932-6203</eissn><abstract>The recent advances in gene chip technology have led to the identification of multiple metabolism-related genes that are closely associated with colorectal cancer (CRC). Nevertheless, none of these genes could accurately diagnose or predict CRC. The prognosis of CRC has been made by previous prognostic models constructed by using multiple genes, however, the predictive function of multi-gene prognostic models using metabolic genes for the CRC prognosis remains unexplored. In this study, we used the TCGA-CRC cohort as the test dataset and the GSE39582 cohort as the experimental dataset. Firstly, we constructed a prognostic model using metabolic genes from the TCGA-CRC cohort, which were also associated with CRC prognosis. We analyzed the advantages of the prognostic model in the prognosis of CRC and its regulatory mechanism of the genes associated with the model. Secondly, the outcome of the TCGA-CRC cohort analysis was validated using the GSE39582 cohort. We found that the prognostic model can be employed as an independent prognostic risk factor for estimating the CRC survival rate. Besides, compared with traditional clinical pathology, it can precisely predict CRC prognosis as well. The high-risk group of the prognostic model showed a substantially lower survival rate as compared to the low-risk group. In addition, gene enrichment analysis of metabolic genes showed that genes in the prognostic model are enriched in metabolism and cancer-related pathways, which may explain its underlying mechanism. Our study identified a novel metabolic profile containing 11 genes for prognostic prediction of CRC. The prognostic model may unravel the imbalanced metabolic microenvironment, and it might promote the development of biomarkers for predicting treatment response and streamlining metabolic therapy in CRC.</abstract><cop>San Francisco</cop><pub>Public Library of Science</pub><pmid>34398900</pmid><doi>10.1371/journal.pone.0251323</doi><tpages>e0251323</tpages><orcidid>https://orcid.org/0000-0003-2655-5402</orcidid><oa>free_for_read</oa></addata></record> |
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| subjects | Analysis Antigens Biology and Life Sciences Biomarkers Cancer Cancer therapies Chemotherapy Colorectal cancer Colorectal carcinoma Computer and Information Sciences Datasets Engineering and Technology Gastroenterology Gene expression Genes Genetic aspects Genomes Health risks Hospitals Laboratories Life sciences Medical prognosis Medical research Medical schools Medicine and Health Sciences Metabolism Metabolites Metastasis Microenvironments Mutation Patient outcomes Patients Perl Prognosis Regression analysis Regulatory mechanisms (biology) Risk analysis Risk factors Risk groups Software Streamlining Survival Survival analysis |
| title | The role of multiple metabolic genes in predicting the overall survival of colorectal cancer: A study based on TCGA and GEO databases |
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