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dc.contributor.authorLi, Haoyang
dc.contributor.authorZhou, Juexiao
dc.contributor.authorSun, Huiyan
dc.contributor.authorQiu, Zhaowen
dc.contributor.authorGao, Xin
dc.contributor.authorXu, Ying
dc.date.accessioned2020-03-15T13:14:30Z
dc.date.available2020-03-15T13:14:30Z
dc.date.issued2020-02-25
dc.date.submitted2-10-12-10
dc.identifier.citationLi, H., Zhou, J., Sun, H., Qiu, Z., Gao, X., & Xu, Y. (2020). CaMeRe: A Novel Tool for Inference of Cancer Metabolic Reprogramming. Frontiers in Oncology, 10. doi:10.3389/fonc.2020.00207
dc.identifier.doi10.3389/fonc.2020.00207
dc.identifier.urihttp://hdl.handle.net/10754/662144
dc.description.abstractMetabolic reprogramming is prevalent in cancer, largely due to its altered chemical environments such as the distinct intracellular concentrations of O2, H2O2 and H+, compared to those in normal tissue cells. The reprogrammed metabolisms are believed to play essential roles in cancer formation and progression. However, it is highly challenging to elucidate how individual normal metabolisms are altered in a cancer-promoting environment; hence for many metabolisms, our knowledge about how they are changed is limited. We present a novel method, CaMeRe (CAncer MEtabolic REprogramming), for identifying metabolic pathways in cancer tissues. Based on the specified starting and ending compounds, along with gene expression data of given cancer tissue samples, CaMeRe identifies metabolic pathways connecting the two compounds via collection of compatible enzymes, which are most consistent with the provided gene-expression data. In addition, cancer-specific knowledge, such as the expression level of bottleneck enzymes in the pathways, is incorporated into the search process, to enable accurate inference of cancer-specific metabolic pathways. We have applied this tool to predict the altered sugar-energy metabolism in cancer, referred to as the Warburg effect, and found the prediction result is highly accurate by checking the appearance and ranking of those key pathways in the results of CaMeRe. Computational evaluation indicates that the tool is fast and capable of handling large metabolic network inference in cancer tissues. Hence, we believe that CaMeRe offers a powerful tool to cancer researchers for their discovery of reprogrammed metabolisms in cancer. The URL of CaMeRe is http://csbl.bmb.uga.edu/CaMeRe/.
dc.description.sponsorshipThe research reported in this publication was supported by funding from King Abdullah University of Science and Technology (KAUST), under award number FCC/1/1976-18-01, FCC/1/1976-23-01, FCC/1/1976-25-01, FCC/1/1976-26-01, URF/1/3450-01-01, URF/1/3454-01-01 and the National Natural Science Foundation of China (No. 61902144).
dc.publisherFrontiers Media SA
dc.relation.urlhttps://www.frontiersin.org/article/10.3389/fonc.2020.00207/full
dc.rightsArchived with thanks to Frontiers in oncology
dc.titleCaMeRe: A Novel Tool for Inference of Cancer Metabolic Reprogramming.
dc.typeArticle
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentStructural and Functional Bioinformatics Group
dc.identifier.journalFrontiers in oncology
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionKey Laboratory of Symbol Computation and Knowledge Engineering of Ministry of Education, College of Computer Science and Technology, Jilin University, Changchun, China
dc.contributor.institutionCancer Systems Biology Center, The China-Japan Union Hospital, Jilin University, Changchun, China
dc.contributor.institutionDepartment of Biology, Southern University of Science and Technology, Shenzhen, China
dc.contributor.institutionSchool of Artificial Intelligence, Jilin University, Changchun, China
dc.contributor.institutionInstitute of Information and Computer Engineering, North East Forestry University, Harbin, China
dc.contributor.institutionComputational Systems Biology Lab, Department of Biochemistry and Molecular Biology, Institute of Bioinformatics, University of Georgia, Athens, GA, United States
kaust.personGao, Xin
kaust.grant.numberFCC/1/1976-18-01
kaust.grant.numberFCC/1/1976-23-01
kaust.grant.numberFCC/1/1976-25-01
kaust.grant.numberFCC/1/1976-26-01
kaust.grant.numberURF/1/3450-01-01
kaust.grant.numberURF/1/3454-01-01
dc.date.accepted2020-02-06
refterms.dateFOA2020-03-15T13:15:46Z


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