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Constructing Support Vector Machine Ensembles for Cancer Classification Based on Proteomic Profiling 被引量:1
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作者 Yong Mao Xiao-Bo Zhou +1 位作者 Dao-Ying Pi You-Xian Sun 《Genomics, Proteomics & Bioinformatics》 SCIE CAS CSCD 2005年第4期238-241,共4页
In this study, we present a constructive algorithm for training cooperative support vector machine ensembles (CSVMEs). CSVME combines ensemble architecture design with cooperative training for individual SVMs in ens... In this study, we present a constructive algorithm for training cooperative support vector machine ensembles (CSVMEs). CSVME combines ensemble architecture design with cooperative training for individual SVMs in ensembles. Unlike most previous studies on training ensembles, CSVME puts emphasis on both accuracy and collaboration among individual SVMs in an ensemble. A group of SVMs selected on the basis of recursive classifier elimination is used in CSVME, and the number of the individual SVMs selected to construct CSVME is determined by 10-fold cross-validation. This kind of SVME has been tested on two ovarian cancer datasets previously obtained by proteomic mass spectrometry. By combining several individual SVMs, the proposed method achieves better performance than the SVME of all base SVMs. 展开更多
关键词 support vector machine ensemble (SVME) design constructive approach proteomic profiling cancer diagnosis
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Cold exposure alters proteomic profiles of the hypothalamus and pituitary in female rats
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作者 Xiangyu Bian Xi Li +8 位作者 Tong Xu Li Zhang Yongqiang Zhang Shuai Wu Renren Yang Weiyun Dong Changjiang Guo Danfeng Yang Weina Gao 《Frigid Zone Medicine》 2023年第2期114-125,共12页
Objective:Studies have shown that both short-term and long-term cold exposures disturb the biological process.The aim of the present study is to investigate the effects of intermittent cold exposure on proteomic profi... Objective:Studies have shown that both short-term and long-term cold exposures disturb the biological process.The aim of the present study is to investigate the effects of intermittent cold exposure on proteomic profiles in the hypothalamus and pituitary of female Sprague-Dawley(SD)rats.Materials and methods:The rats were exposed to-10°C in a cabin for 4 h per day,and the treatment lasted for 14 days.The comparative label-free LC-MS/MS analysis was performed to investigate the changes of proteomic profiles in the hypothalamus and pituitary.ELISA analysis was used to validate the expression of differential proteins.Results:22 differential proteins in the hypothalamus and 75 differential proteins in the pituitary were identified by the label-free proteomic analysis.Gene ontology annotation and enrichment analysis indicated that cold exposure disrupted protein phosphorylation,filopodium assembly,intracellular protein transport,peripheral nervous system neuron axonogenesis,spinal cord development,Golgi organization,positive regulation of pseudopodium assembly,and cell-cell adhesion.Three proteins(Cdc42,Ptprs,and Setd7)were down-regulated in the cold exposure group.Conclusion:The results indicate that intermittent cold exposure alters the proteomic profiles of hypothalamus and pituitary in female rats. 展开更多
关键词 cold exposure proteomic profile HYPOTHALAMUS PITUITARY
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Comparison of biliary protein spectrum in gallstone patients with obesity and those with normal body weight
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作者 Min-Zhi Chen Ping Xie +4 位作者 Xiao-Chang Wu Zhen-Hua Tan Hai Qian Zhi-Hong Ma Xing Yao 《Hepatobiliary & Pancreatic Diseases International》 SCIE CAS CSCD 2024年第4期385-392,共8页
Background: Obesity is a common public health issue and is currently deemed a disease. Research has shown that the risk of gallstones in individuals with obesity is elevated. This study aimed to explore the bile prote... Background: Obesity is a common public health issue and is currently deemed a disease. Research has shown that the risk of gallstones in individuals with obesity is elevated. This study aimed to explore the bile proteomics differences between cholelithiasis patients with obesity and normal body weight. Methods: Bile samples from 20 patients(10 with obesity and 10 with normal body weight) who underwent laparoscopic cholecystectomy at our center were subjected to tandem mass tag labeling(TMT) and liquid chromatography-tandem mass spectrometry(LC-MS/MS), followed by further bioinformatic analysis. Results: Among the differentially expressed proteins, 23 were upregulated and 67 were downregulated. Bioinformatic analysis indicated that these differentially expressed proteins were mainly involved in cell development, inflammatory responses, glycerolipid metabolic processes, and protein activation cascades. In addition, the activity of the peroxisome proliferator-activated receptor(PPAR, a subfamily of nuclear receptors) signaling pathway was decreased in the Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment analysis. Two downregulated proteins in the PPAR signaling pathway, APO A-Ⅰ and APO A-Ⅱ, were confirmed using enzyme-linked immunosorbent assay. Conclusions: The PPAR signaling pathway may play a crucial role in the development of cholelithiasis among patients with obesity. Furthermore, biliary proteomics profiling of gallstones patients with obesity is revealed, providing a reference for future research. 展开更多
关键词 Proteome profiling GALLSTONES Obesity-associated gallstones Tandem mass tag labeling PPAR signaling
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Multiple inducible thermogenic mechanisms in the development of cold acclimatization
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作者 Huanyu Lu Wenjing Luo 《Frigid Zone Medicine》 2023年第2期83-91,共9页
Extreme cold environment can threaten human health and life through increasing the risk of myocardial infarction,stroke,frostbite,and hypothermia.Insufficient heat production to maintain core body temperature is a maj... Extreme cold environment can threaten human health and life through increasing the risk of myocardial infarction,stroke,frostbite,and hypothermia.Insufficient heat production to maintain core body temperature is a major cause of cold injury.To cope with cold stress,human and other mammals have developed the capacity of cold acclimatization to adapt to such a harsh environment.Adaptive non-shivering thermogenesis is a ubiquitous form of cold acclimatization.This review article systematically summarizes the role of three inducible thermogenic forms,including food intake,circadian rhythms,and cold exposure in mediating non-shivering thermogenesis under cold exposure and presents the potential interventions for minimizing the adverse health consequences of cold temperature. 展开更多
关键词 cold exposure proteomic profile HYPOTHALAMUS PITUITARY
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Identification of commonly regulated protein targets and molecular pathways in PC-3 and DU145 androgen-independent human prostate cancer cells treated with the curcumin analogue 1,5-bis(2-hydroxyphenyl)-1,4-pentadiene-3-one 被引量:2
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作者 Kamini Citalingam Faridah Abas +2 位作者 Nordin H.Lajis Iekhsan Othman Rakesh Naidu 《Asian Pacific Journal of Tropical Biomedicine》 SCIE CAS 2018年第9期436-445,共10页
Objective: To identify mutually regulated proteins in PC-3 and DU145 androgen-independent prostate cancer cell lines treated with 1,5-bis(2-hydroxyphenyl)-1,4-pentadiene-3-one(MS17), and to study the molecular pathway... Objective: To identify mutually regulated proteins in PC-3 and DU145 androgen-independent prostate cancer cell lines treated with 1,5-bis(2-hydroxyphenyl)-1,4-pentadiene-3-one(MS17), and to study the molecular pathways that contributed to the anticancer activity of MS17.Methods: PC-3 and DU145 cells were treated with 3 × EC_(50)(15 μM) concentration of MS17 for 24 h and were subjected to protein expression profiling using two-dimensional gel electrophoresis and protein identification by mass spectrometry.Selected differentially expressed proteins with significant P-value of P<0.05 and fold change over 1.5-folds were filtered through and ontologically classified.Mutually regulated proteins were ranked by fold change and identified as common protein targets of MS17.Results: Profiling data revealed that, the mutually down-regulated proteins included ACTB and ACTG associated with structural molecule activity, ACTN1 with cell cycle, ACTN4 with cell migration, HNRPK with apoptosis, PLST with morphogenesis and TERA with proteolysis.However, the expressions of CH60 and HS71 A respectively associated with response to unfolded protein demonstrated opposing regulation in PC-3 and DU145 cells.Pathway analysis of the differentially expressed proteins in PC-3 cells demonstrated the modulation of top pathways associated with cell-cell adhesion and cytoskeletal organization while in DU145 cells the pathways were associated with proteosomal degradation, regulation of electrolytes and water, regulation control of germ cells and organization of filament assembly/disassembly.Conclusions: The findings of the present study provide an understanding on the anti-tumorigenic activity of MS17 at the proteome level and warrant further research for its potential application for the management and treatment of androgen-independent prostate cancer. 展开更多
关键词 Androgen-independent prostate cancer Diarylpentanoid proteomics profiling Mass spectrometry Pathway analysis
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Proteomic dissection of biological pathways/processes through profiling protein-protein interaction networks 被引量:2
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作者 CHEN Xian Institutes for Biomedical Sciences, Fudan University, Shanghai 200433, China Department of Biochemistry & Biophysics, School of Medicine, University of North Carolina-Chapel Hill, USA 《Science China Chemistry》 SCIE EI CAS 2010年第4期737-746,共10页
Cellular functions, either under the normal or pathological conditions or under different stresses, are the results of the coordinated action of multiple proteins interacting in macromolecular complexes or assemblies.... Cellular functions, either under the normal or pathological conditions or under different stresses, are the results of the coordinated action of multiple proteins interacting in macromolecular complexes or assemblies. The precise determination of the specific composition of protein complexes, especially using scalable and high-throughput methods, represents a systematic approach toward revealing particular cellular biological functions. In this regard, the direct profiling protein-protein interactions (PPIs) represent an efficient way to dissect functional pathways for revealing novel protein functions. In this review, we illustrate the technological evolution for the large-scale and precise identification of PPIs toward higher physiologically relevant accuracy. These techniques aim at improving the efficiency of complex pull-down, the signal specificity and accuracy in distinguishing specific PPIs, and the accuracy of identifying physiological relevant PPIs. A newly developed streamline proteomic approach for mapping the binary relationship of PPIs in a protein complex is introduced. 展开更多
关键词 CHEN proteomic dissection of biological pathways/processes through profiling protein-protein interaction networks
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Proteome Profiles of Longissimus and Biceps Femoris Porcine Muscles Related to Exercise and Resting
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作者 Marinus F.W. Te Pas Els Keuning +3 位作者 Dick J.M. Van De Wiel Jette F. Young Niels Oksbjerg Leo Kruijt 《Journal of Life Sciences》 2011年第8期598-608,共11页
Exercise affects muscle metabolism and composition in the untrained muscles. The proteome of muscle tissue will be affected by exercise and resting. This is of economic importance for pork quality where transportation... Exercise affects muscle metabolism and composition in the untrained muscles. The proteome of muscle tissue will be affected by exercise and resting. This is of economic importance for pork quality where transportation relates to exercise of untrained muscles. Rest reverses exercise effects. The objective of this research was to develop potential protein biomarkers that predict the optimal resting time after exercise related to optimal pork quality. Ten litters of four female pigs were within litter allocated to the four treatment groups: exercise by running on a treadmill for 27 minutes followed by rest for 0, 1, or 3 h; control pigs without exercise. Proteome profiles and biochemical traits measuring energy metabolism and meat quality traits expected to be related to exercise were determined in the Longissimus and the Biceps femoris of the pigs. The results indicated associations between protein abundances in muscles and exercise, resting, and biochemical traits. 展开更多
关键词 EXERCISE muscle tissue proteomics profiles Sus scrofa biochemical energy metabolism meat quality traits rest.
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The research of proteome profiling change of 1-bromopropane poisoning cases
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作者 缪荣明 《China Medical Abstracts(Internal Medicine)》 2017年第1期8-9,共2页
Objective This study was mainly focused on study of the proteome profile change between exposure to 1-Bromopropane(1-BP)and 1-BP poisoning.Methods The samples of serums from exposure to 1-BP and 1-BP poisoning were co... Objective This study was mainly focused on study of the proteome profile change between exposure to 1-Bromopropane(1-BP)and 1-BP poisoning.Methods The samples of serums from exposure to 1-BP and 1-BP poisoning were collected and analyzed through Label 展开更多
关键词 BP The research of proteome profiling change of 1-bromopropane poisoning cases
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Chemical Synthesis of diSUMO Photoaffinity Probes for the Identification of PolySUMO Chain-Specific Interacting Proteins 被引量:1
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作者 Yu Wang Chenchen Chen +7 位作者 Xianbin Meng Jian Fan Man Pan Jingnan Chen Haiteng Deng Jing Shi Lei Liu Yi-Ming Li 《CCS Chemistry》 CAS 2021年第4期1157-1168,共12页
Small ubiquitin-like modifiers(SUMOs)are protein modifiers that can form polymeric chains.They are important signals in cellular processes,and their study and profiling require the development of molecular tools.Herei... Small ubiquitin-like modifiers(SUMOs)are protein modifiers that can form polymeric chains.They are important signals in cellular processes,and their study and profiling require the development of molecular tools.Herein,the authors have reported an efficient chemical protein synthesis approach for the generation of dimeric SUMO-2-based photoaffinity probes through the ligation of four readily synthesizable peptides.Proteomic studies using this diSUMO-2 probe on HeLa cell nuclear lysate found it to capture a significantly different selection of proteins compared with its monoSUMO counterparts.This resulted in the identification of several previously unknown SUMO chain-specific interacting proteins such as 40S ribosomal protein S3,which showed a significantly higher affinity for polySUMO chains than monomeric SUMO.Collectively,these results emphasize the need to develop SUMO chain-based probes in other species,and to shed light on the important role of polySUMOylation in diseases. 展开更多
关键词 chemical protein synthesis small ubiquitin-like modifiers polySUMOylation photoaffinity probes proteomic profiling specific interactors
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