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Kurubanjerdjit N, Ng KL. A database of integrated molecular and phytochemical interactions of the foxm1 pathway for lung cancer. J Biomol Struct Dyn 2020; 40:177-189. [PMID: 32835615 DOI: 10.1080/07391102.2020.1810777] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The FoxM1 pathway is an oncogenic signaling pathway involved in essential mechanisms including control cell-cycle progression, apoptosis and cell growth which are the common hallmarks of various cancers. Although its biological functions in the tumor development and progression are known, the mechanism by which it participates in those processes is not understood. The present work reveals images of the oncogenic FoxM1 pathway controlling the cell cycle process with alternative treatment options via phytochemical substances in the lung cancer study. The downstream significant protein modules of the FoxM1 pathway were extracted by the Molecular Complex Detection (MCODE) and the maximal clique (Mclique) algorithms. Furthermore, the effects of post-transcriptional modification by microRNA, transcription factor binding and the phytochemical compounds are observed through their interactions with the lung cancer protein modules. We provided two case studies to demonstrate the usefulness of our database. Our results suggested that the combination of various phytochemicals is effective in the treatment of lung cancer. The ultimate goal of the present work is to partly support the discovery of plant-derived compounds in combination treatment of classical chemotherapeutic agents to increase the efficacy of lung cancer method probably with minor side effects. Furthermore, a web-based system displaying results of the present work is set up for investigators posing queries at http://sit.mfu.ac.th/lcgdb/index_FoxM1.php.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
| | - Ka-Lok Ng
- Department of Bioinformatics and Medical Engineering, Asia University, Taichung, Taiwan.,Department of Medical Research, China Medical University Hospital, China Medical University, Taichung, Taiwan
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Li X, Li D, Dong Z, Hu Y, Liu C. Efficient Deployment of Key Nodes for Optimal Coverage of Industrial Mobile Wireless Networks. Sensors (Basel) 2018; 18:s18020545. [PMID: 29439439 PMCID: PMC5856136 DOI: 10.3390/s18020545] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 02/06/2018] [Accepted: 02/08/2018] [Indexed: 12/04/2022]
Abstract
In recent years, industrial wireless networks (IWNs) have been transformed by the introduction of mobile nodes, and they now offer increased extensibility, mobility, and flexibility. Nevertheless, mobile nodes pose efficiency and reliability challenges. Efficient node deployment and management of channel interference directly affect network system performance, particularly for key node placement in clustered wireless networks. This study analyzes this system model, considering both industrial properties of wireless networks and their mobility. Then, static and mobile node coverage problems are unified and simplified to target coverage problems. We propose a novel strategy for the deployment of clustered heads in grouped industrial mobile wireless networks (IMWNs) based on the improved maximal clique model and the iterative computation of new candidate cluster head positions. The maximal cliques are obtained via a double-layer Tabu search. Each cluster head updates its new position via an improved virtual force while moving with full coverage to find the minimal inter-cluster interference. Finally, we develop a simulation environment. The simulation results, based on a performance comparison, show the efficacy of the proposed strategies and their superiority over current approaches.
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Affiliation(s)
- Xiaomin Li
- School of Mechanical and Automotive Engineering, South China University of Technology, Guangzhou 510640, China.
| | - Di Li
- School of Mechanical and Automotive Engineering, South China University of Technology, Guangzhou 510640, China.
| | - Zhijie Dong
- School of Mechanical and Automotive Engineering, South China University of Technology, Guangzhou 510640, China.
| | - Yage Hu
- Super Micro Computer, Inc., San Jose 95131, CA, USA.
| | - Chengliang Liu
- School of Mechanical Engineering, Shanghai Jiao Tong University, Shanghai 200240, China.
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Chi C, Ajwad R, Kuang Q, Hu P. A Novel Graph-based Algorithm to Infer Recurrent Copy Number Variations in Cancer. Cancer Inform 2016; 15:43-50. [PMID: 27773988 PMCID: PMC5063805 DOI: 10.4137/cin.s39368] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2016] [Revised: 09/08/2016] [Accepted: 09/09/2016] [Indexed: 12/17/2022] Open
Abstract
Many cancers have been linked to copy number variations (CNVs) in the genomic DNA. Although there are existing methods to analyze CNVs from individual samples, cancer-causing genes are more frequently discovered in regions where CNVs are common among tumor samples, also known as recurrent CNVs. Integrating multiple samples and locating recurrent CNV regions remain a challenge, both computationally and conceptually. We propose a new graph-based algorithm for identifying recurrent CNVs using the maximal clique detection technique. The algorithm has an optimal solution, which means all maximal cliques can be identified, and guarantees that the identified CNV regions are the most frequent and that the minimal regions have been delineated among tumor samples. The algorithm has successfully been applied to analyze a large cohort of breast cancer samples and identified some breast cancer-associated genes and pathways.
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Affiliation(s)
- Chen Chi
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada; Centre for Healthcare Innovation, Winnipeg Regional Health Authority/University of Manitoba, Winnipeg, Canada
| | - Rasif Ajwad
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada; Department of Computer Science, University of Manitoba, Winnipeg, Canada
| | - Qin Kuang
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada
| | - Pingzhao Hu
- Department of Biochemistry and Medical Genetics, University of Manitoba, Winnipeg, Canada; Centre for Healthcare Innovation, Winnipeg Regional Health Authority/University of Manitoba, Winnipeg, Canada; Department of Electrical and Computer Engineering, University of Manitoba, Winnipeg, Canada
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Li H, Gordon SM, Zhu X, Deng J, Swertfeger DK, Davidson WS, Lu LJ. Network-Based Analysis on Orthogonal Separation of Human Plasma Uncovers Distinct High Density Lipoprotein Complexes. J Proteome Res 2015; 14:3082-94. [PMID: 26057100 DOI: 10.1021/acs.jproteome.5b00419] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
High density lipoprotein (HDL) particles are blood-borne complexes whose plasma levels have been associated with protection from cardiovascular disease (CVD). Recent studies have demonstrated the existence of distinct HDL subspecies; however, these have been difficult to isolate and characterize biochemically. Here, we present the first report that employs a network-based approach to systematically infer HDL subspecies. Healthy human plasma was separated into 58 fractions using our previously published three orthogonal chromatography techniques. Similar local migration patterns among HDL proteins were captured with a novel similarity score, and individual comigration networks were constructed for each fraction. By employing a graph mining algorithm, we identified 183 overlapped cliques, among which 38 were further selected as candidate HDL subparticles. Each of these 38 subparticles had at least two literature supports. In addition, GO function enrichment analysis showed that they were enriched with fundamental biological and CVD protective functions. Furthermore, gene knockout experiments in mouse model supported the validity of these subparticles related to three apolipoproteins. Finally, analysis of an apoA-I deficient human patient's plasma provided additional support for apoA-I related complexes. Further biochemical characterization of these putative subspecies may facilitate the mechanistic research of CVD and guide targeted therapeutics aimed at its mitigation.
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Affiliation(s)
- Hailong Li
- §Institute for Systems Biology, Jianghan University, Wuhan, Hubei, 430056, P.R. China.,†Division of Biomedical Informatics, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, MLC 7024, Cincinnati, Ohio 45229-3039, United States
| | - Scott M Gordon
- ‡Center for Lipid and Arteriosclerosis Science, Department of Pathology and Laboratory Medicine, University of Cincinnati, 2120 East Galbraith Road, Cincinnati, Ohio 45237-0507, United States
| | - Xiaoting Zhu
- †Division of Biomedical Informatics, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, MLC 7024, Cincinnati, Ohio 45229-3039, United States
| | - Jingyuan Deng
- †Division of Biomedical Informatics, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, MLC 7024, Cincinnati, Ohio 45229-3039, United States
| | - Debi K Swertfeger
- †Division of Biomedical Informatics, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, MLC 7024, Cincinnati, Ohio 45229-3039, United States
| | - W Sean Davidson
- ‡Center for Lipid and Arteriosclerosis Science, Department of Pathology and Laboratory Medicine, University of Cincinnati, 2120 East Galbraith Road, Cincinnati, Ohio 45237-0507, United States
| | - L Jason Lu
- †Division of Biomedical Informatics, Cincinnati Children's Hospital Research Foundation, 3333 Burnet Avenue, MLC 7024, Cincinnati, Ohio 45229-3039, United States
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