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A novel discretization method for processing digital gene expression profiles 一种处理数字基因表达谱的离散化方法
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623808
Jibin Qu, Jinxia Zhang, Chenyang Huang, Baogui Xie, Yong Wang, Xiang-Sun Zhang
{"title":"A novel discretization method for processing digital gene expression profiles","authors":"Jibin Qu, Jinxia Zhang, Chenyang Huang, Baogui Xie, Yong Wang, Xiang-Sun Zhang","doi":"10.1109/ISB.2013.6623808","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623808","url":null,"abstract":"Discretization serves as an important preprocessing step for analyzing gene expression data and many algorithms have been proposed. However, most of the discretization methods were designed for microarrays. As a new technology, digital gene expression (DGE) profiles can overcome the limitation of microarrays and were applied in a widely range. In this paper, we proposed a novel discretization method for DGE data and the validations in a time-series gene expression dataset proved the efficiency of our method.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"27 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134305591","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Construction of human tissue-specific phosphorylation networks with protein expression data 用蛋白表达数据构建人组织特异性磷酸化网络
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623807
Yin-Ying Wang, Chenglei Sun, Luonan Chen, Xingming Zhao
{"title":"Construction of human tissue-specific phosphorylation networks with protein expression data","authors":"Yin-Ying Wang, Chenglei Sun, Luonan Chen, Xingming Zhao","doi":"10.1109/ISB.2013.6623807","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623807","url":null,"abstract":"Phosphorylation is a post-translational modification process mediated by kinases through the addition of a covalently bound phosphate group, which plays important roles in a wide range of cellular progresses, such as signaling cascades and development. Over the past years, despite many phosphorylation sites have been determined with mass spectrometry techniques, it is not clear which kinase phosphorylates which proteins. Under the circumstance, we propose a new probabilistic model to identify the substrates phosphorylated by certain kinases. Furthermore, we construct three tissue-specific phosphorylation networks based on protein expression data. Investigating the constructed tissue-specific networks, we find they are functionally consistent with the corresponding tissues, implying the effectiveness and biological significance of our proposed approach.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"130019953","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Towards kinetic modeling of metabolic networks with incomplete parameters 不完全参数代谢网络动力学建模研究
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623801
W. Zheng, Xiaomei Zhu, Yong-Cong Chen, Paohung Lin, P. Ao
{"title":"Towards kinetic modeling of metabolic networks with incomplete parameters","authors":"W. Zheng, Xiaomei Zhu, Yong-Cong Chen, Paohung Lin, P. Ao","doi":"10.1109/ISB.2013.6623801","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623801","url":null,"abstract":"Modeling is an important direction in systems biology. The target towards kinetic modeling for metabolic network is to develop a practical computational method which can handle incomplete parameters. In principle, we could start with a set of randomly chosen parameters; calculating fluxes and metabolites concentration and comparing with experiments; iterating until the best parameters are found. But the large parametric space may require billions of times of iterations. In order to overcome such a difficulty, we develop a method to obtain the structure of parametric space. We are able to discover the correlation between parameters and variables, which is helpful for us to estimate the possible value of parameters. Differ from previous method, the implicit relationship between parameter and variable are also provided directly by our method, which provides a potential for us to analyze the feature of metabolic network.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123357550","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 2
Dynamical complexity in a predator-prey eco-epidemical system 捕食者-猎物生态流行病系统的动态复杂性
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623784
Min Su, Zhen-shan Lin
{"title":"Dynamical complexity in a predator-prey eco-epidemical system","authors":"Min Su, Zhen-shan Lin","doi":"10.1109/ISB.2013.6623784","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623784","url":null,"abstract":"Effects of the relationship between species and environment on an eco-epidemiological system are investigated. And periodic variation is also added to the disharmony parameter. The dynamic behaviors of the system are simulated numerically. A variety of complex population dynamics including stable state, periodic resonance and chaos are obtained. The most important result is that harmony relationship between prey species and environment is benefit for the controlling of disease. Our result reinforces the conjecture that the relationship between species and environment is crucial to transmission of infectious disease.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"44 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124542249","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Pharmacophores generation of multiple anti-inflammatory targets and identification of active compounds in Chinese herbs 中药多种抗炎靶点的药效团生成及活性成分的鉴定
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623787
Yanling Zhang, Yuanming Wang, Yanjiang Qiao
{"title":"Pharmacophores generation of multiple anti-inflammatory targets and identification of active compounds in Chinese herbs","authors":"Yanling Zhang, Yuanming Wang, Yanjiang Qiao","doi":"10.1109/ISB.2013.6623787","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623787","url":null,"abstract":"Chinese herbs always have activity on multiple targets. For the identification of potential anti-inflammatory compounds from Chinese herbs, six targets, which are mostly associated with inflammatory, were selected as following: Cox-2 (cyclooxygenase 2), PDE4B (phosphodiesterase 4B), p38α MAPK (p38α mitogen-activated protein kinase), JNK3 (c-Jun N-terminal kinases 3), ICE (interlenkin-1β converting enzyme) and iNOS (inducible type of nitric oxide synthase). Structure-based pharmacophore models of the inhibitors of each target were generated by LigandScout based on complexes from the PDB (Protein Data Bank). Based on the screening results of MDDR (MDL Drug Data Report database) and a new metric CAI (comprehensive appraisal index), the best models for each target were defined and used to identify the potential anti-inflammatory compounds from Chinese herbs. Six compounds and sixteen herbs were obtained that can act on multiple targets. The traditional function of the most hit herbs was `heat-clearing and detoxifying', which has been experimentally demonstrated to have anti-inflammatory activity.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129829285","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
A novel HMM for analyzing chromosomal aberrations in heterogeneous tumor samples 一种分析异质肿瘤样本染色体畸变的新型HMM
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623800
Hong Xia, Yuanning Liu, Minghui Wang, Huanqing Feng, Ao Li
{"title":"A novel HMM for analyzing chromosomal aberrations in heterogeneous tumor samples","authors":"Hong Xia, Yuanning Liu, Minghui Wang, Huanqing Feng, Ao Li","doi":"10.1109/ISB.2013.6623800","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623800","url":null,"abstract":"Comprehensive detection and identification of copy number and LOH of chromosomal aberration is required to provide an accurate therapy of human cancer. As a cost-saving and high-throughput tool, SNP arrays facilitate analysis of chromosomal aberration throughout the whole genome. The performance of previous approaches has been limited to several critical issues such as normal cell contamination, aneuploidy and tumor heterogeneity. For these reasons we present a Hidden Markov Model (HMM) based approach called TH-HMM (Tumor Heterogeneity HMM), for simultaneous detection of copy number and LOH in heterogeneous tumor samples using data from Illumina SNP arrays. Through adopting an efficient EM algorithm, our method can correctly detect chromosomal aberration events in tumor subclones. Evaluation on simulated data series indicated that TH-HMM could accurately estimate both normal cell and subclone proportions, and finally recovery the aberration profiles for each clones.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"19 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134323655","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 1
Genetic analysis of leaf expansion trait in Brassica rapa L. ssp. chinensis (L.) Hanelt 油菜叶片膨大性状的遗传分析。对(l)Hanelt
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623783
Jian-Ming Han, Rui-ling Wang, Y. Cheng, Xue Li, Chao-jun He
{"title":"Genetic analysis of leaf expansion trait in Brassica rapa L. ssp. chinensis (L.) Hanelt","authors":"Jian-Ming Han, Rui-ling Wang, Y. Cheng, Xue Li, Chao-jun He","doi":"10.1109/ISB.2013.6623783","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623783","url":null,"abstract":"Brassica rapa L. ssp. chinensis (L.) Hanelt is an important vegetable in eastern Asia. Its leaf area is one of main factor of influencing on the yield of individual plant. To reveal the mechanism of the leaf expansion, the joint segregation analysis of multiple generations (P<sub>1</sub>, P<sub>2</sub>, F<sub>1</sub>, B<sub>1</sub>, B<sub>2</sub> and F<sub>2</sub>) was used to analyze the genetics of leaf expansion trait in combination SW-13×L-118 of Brassica rapa L. ssp. chinensis (L.) Hanelt. In this paper, the results showed that the leaf expansion trait was controlled by one pair of additive-dominant major genes plus additive-dominant-epistatic polygene (D model). The additive effect of the major gene was -2.3061, the dominant effect was -1.4525. The heritability of major gene of leaf expansion was 2.56% in B<sub>1</sub> generation, 1.55% in B<sub>2</sub> generation and 12.12% in F<sub>2</sub> generation. The heritabilites of the polygene were 54.04% in B<sub>1</sub> generation, 25.11% in B<sub>2</sub> generation, and 62.60% in F<sub>2</sub> generation, respectively. It appeared that the polygene effects should be given prior to the improvement of leaf expansion trait of combination SW-13×L-118, and the selection was effective in later generation, and the negative additive effect and negative dominant effect of major gene were noticed.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129549900","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Tissue significances tests on DNA binding sequence motifs for human genes 人类基因DNA结合序列基序的组织意义试验
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623791
Hua Yu, X. Gong
{"title":"Tissue significances tests on DNA binding sequence motifs for human genes","authors":"Hua Yu, X. Gong","doi":"10.1109/ISB.2013.6623791","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623791","url":null,"abstract":"DNA binding sequence motifs are becoming increasingly important in the analysis of gene regulation, disease diagnosis and drug design. Although so far there are amount of tools available to discover these kinds of motifs, little was done to identify the biological functions, especially in tissue or cell type specific contributions, of those motifs. In this paper we used an integrated pipeline to discover sequences motifs for the promoter regions of human genes. Then we distinguished two types of motifs: tissue rich motifs (TRM) and tissue even motifs (TEM), using hypotheses test approaches including Bayesian hypothesis, Binomial distribution and traditional z-test.We finally got 233 overlapped TRMs and 56 TEMs. Most of those motifs are validated against JASPAR databases.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"3 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"134150914","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 0
Karyotype and evolution analysis of vulerable fish Onychostoma lini from China 中国易危鱼类马甲鱼核型及进化分析
2013 7th International Conference on Systems Biology (ISB) Pub Date : 2013-10-10 DOI: 10.1109/ISB.2013.6623793
Ying-gui Dai
{"title":"Karyotype and evolution analysis of vulerable fish Onychostoma lini from China","authors":"Ying-gui Dai","doi":"10.1109/ISB.2013.6623793","DOIUrl":"https://doi.org/10.1109/ISB.2013.6623793","url":null,"abstract":"The karyotype and chromosomal characteristics of the vulnerable species Onychostoma lini (Wu 1939) from China were studied by examining metaphase chromosome spreads obtained from kidney. According to the 200 metaphase spreads from 10 specimen of Onychostoma lini, captured from the Duliu river (located in the Pearl River system), China, the chromosome formula in the species might be described as 2n=50=12M+8SM+4ST+26T and FN=70. The mean values of chromosome lengths in Onychostoma lini ranged from 7.975 to 14.270 μm, and the haploid chromosome length of the species was 289.111±27.767 μm. This study provides first knowledge on karyotypes in Onychostoma lini which may facilitate aquaculture, conservation practices of the species. Also, the evolutionary level of Onychostoma lini is preliminarily analyzed based on the karyotype of the species in this paper.","PeriodicalId":151775,"journal":{"name":"2013 7th International Conference on Systems Biology (ISB)","volume":"28 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2013-10-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121256525","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
引用次数: 3
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