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A state space representation of VAR models with sparse learning for dynamic gene networks. 基于稀疏学习的动态基因网络VAR模型的状态空间表示。
Pub Date : 2010-01-01 DOI: 10.1142/9781848165786_0006
Kaname Kojima, R. Yamaguchi, S. Imoto, Mai Yamauchi, Masao Nagasaki, Ryo Yoshida, Teppei Shimamura, Kazuko Ueno, T. Higuchi, N. Gotoh, S. Miyano
We propose a state space representation of vector autoregressive model and its sparse learning based on L1 regularization to achieve efficient estimation of dynamic gene networks based on time course microarray data. The proposed method can overcome drawbacks of the vector autoregressive model and state space model; the assumption of equal time interval and lack of separation ability of observation and systems noises in the former method and the assumption of modularity of network structure in the latter method. However, in a simple implementation the proposed model requires the calculation of large inverse matrices in a large number of times during parameter estimation process based on EM algorithm. This limits the applicability of the proposed method to a relatively small gene set. We thus introduce a new calculation technique for EM algorithm that does not require the calculation of inverse matrices. The proposed method is applied to time course microarray data of lung cells treated by stimulating EGF receptors and dosing an anticancer drug, Gefitinib. By comparing the estimated network with the control network estimated using non-treated lung cells, perturbed genes by the anticancer drug could be found, whose up- and down-stream genes in the estimated networks may be related to side effects of the anticancer drug.
提出了一种基于L1正则化的向量自回归模型的状态空间表示及其稀疏学习方法,以实现基于时程微阵列数据的动态基因网络的高效估计。该方法克服了矢量自回归模型和状态空间模型的不足;前一种方法采用等时间间隔假设,缺乏观测噪声与系统噪声的分离能力,后一种方法采用网络结构模块化假设。然而,在简单实现中,该模型需要在基于EM算法的参数估计过程中计算大量的逆矩阵。这限制了所提出的方法对相对较小的基因集的适用性。因此,我们为EM算法引入了一种不需要计算逆矩阵的新计算技术。该方法应用于通过刺激EGF受体和服用抗癌药物吉非替尼处理的肺细胞的时程微阵列数据。通过将估计的网络与未处理的肺细胞估计的控制网络进行比较,可以发现被抗癌药物干扰的基因,其在估计网络中的上下游基因可能与抗癌药物的副作用有关。
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引用次数: 32
Characterization and classification of adverse drug interactions. 药物不良反应的特征和分类。
Pub Date : 2010-01-01 DOI: 10.1142/9781848165786_0014
Masataka Takarabe, D. Shigemizu, Masaaki Kotera, S. Goto, M. Kanehisa
Drug interactions which may cause harmful events are important for our health and new drag development. In the previous work, we extracted the drug interaction data from Japanese drug package inserts and generated the drug interaction network. The network contains a large number of drugs densely connected to each other, where drug targets and drug-metabolizing enzymes were shared in the drug interactions. In this study, we further analyzed the obtained drug interaction network by merging drugs into drug categories based on the Anatomical Therapeutic Chemical (ATC) classification. The merged data of drug interactions indicated drug properties that are related to drug interaction mechanisms or symptoms. We investigated the relationships between the drug groups and drug interaction mechanisms or symptoms.
药物相互作用对我们的健康和新药开发具有重要的意义。在之前的工作中,我们从日本药品说明书中提取药物相互作用数据,并生成药物相互作用网络。该网络包含大量相互紧密连接的药物,其中药物靶点和药物代谢酶在药物相互作用中是共享的。在本研究中,我们进一步分析了获得的药物相互作用网络,将药物合并到基于解剖治疗化学(ATC)分类的药物类别中。药物相互作用的合并数据表明与药物相互作用机制或症状相关的药物特性。我们调查了药物组与药物相互作用机制或症状之间的关系。
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引用次数: 5
A dynamic programming algorithm to predict synthesis processes of tree-structured compounds with graph grammar. 基于图语法的树状化合物合成过程预测的动态规划算法。
Pub Date : 2010-01-01 DOI: 10.1142/9781848166585_0018
Yang Zhao, Takeyuki Tamura, M. Hayashida, T. Akutsu
For several decades, many methods have been developed for predicting organic synthesis paths. However these methods have non-polynomial computational time. In this paper, we propose a bottom-up dynamic programming algorithm to predict synthesis paths of target tree-structured compounds. In this approach, we transform the synthesis problem of tree-structured compounds to the generation problem of unordered trees by regarding tree-structured compounds and chemical reactions as unordered trees and rules, respectively. In order to represent rules corresponding to chemical reactions, we employ a subclass of NLC (Node Label Controlled) grammars. We also give some computational results on this algorithm.
几十年来,人们开发了许多预测有机合成路径的方法。然而,这些方法的计算时间都是非多项式的。本文提出了一种自下而上的动态规划算法来预测目标树状结构化合物的合成路径。在这种方法中,我们将树状结构化合物和化学反应分别视为无序树和规则,将树状结构化合物的合成问题转化为无序树的生成问题。为了表示与化学反应相对应的规则,我们使用了NLC(节点标签控制)语法的一个子类。最后给出了该算法的一些计算结果。
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引用次数: 0
Comparison of gene expression profiles produced by CAGE, illumina microarray and real time RT-PCR. CAGE、illumina芯片和实时RT-PCR基因表达谱的比较。
André Fujita, Masao Nagasaki, Seiya Imoto, Ayumu Saito, Emi Ikeda, Teppei Shimamura, Rui Yamaguchi, Yoshihide Hayashizaki, Satoru Miyano

Several technologies are currently used for gene expression profiling, such as Real Time RT-PCR, microarray and CAGE (Cap Analysis of Gene Expression). CAGE is a recently developed method for constructing transcriptome maps and it has been successfully applied to analyzing gene expressions in diverse biological studies. The principle of CAGE has been developed to address specific issues such as determination of transcriptional starting sites, the study of promoter regions and identification of new transcripts. Here, we present both quantitative and qualitative comparisons among three major gene expression quantification techniques, namely: CAGE, illumina microarray and Real Time RT-PCR, by showing that the quantitative values of each method are not interchangeable, however, each of them has unique characteristics which render all of them essential and complementary. Understanding the advantages and disadvantages of each technology will be useful in selecting the most appropriate technique for a determined purpose.

目前有几种技术用于基因表达谱分析,如实时RT-PCR、微阵列和CAGE(基因表达帽分析)。CAGE是最近发展起来的一种构建转录组图谱的方法,它已成功地应用于多种生物学研究中的基因表达分析。CAGE的原理已经发展到解决特定的问题,如转录起始位点的确定、启动子区域的研究和新转录物的鉴定。在这里,我们对CAGE、illumina microarray和Real Time RT-PCR这三种主要的基因表达定量技术进行了定量和定性比较,表明每种方法的定量值是不可互换的,但每种方法都有其独特的特点,使它们都是必要的和互补的。了解每种技术的优点和缺点将有助于为确定的目的选择最合适的技术。
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引用次数: 0
Annotating gene functions with integrative spectral clustering on microarray expressions and sequences. 利用微阵列表达和序列的整合谱聚类来注释基因功能。
Limin Li, Motoki Shiga, Wai-Ki Ching, Hiroshi Mamitsuka

Annotating genes is a fundamental issue in the post-genomic era. A typical procedure for this issue is first clustering genes by their features and then assigning functions of unknown genes by using known genes in the same cluster. A lot of genomic information are available for this issue, but two major types of data which can be measured for any gene are microarray expressions and sequences, both of which however have their own flaws. Thus a natural and promising approach for gene annotation is to integrate these two data sources, especially in terms of their costs to be optimized in clustering. We develop an efficient gene annotation method with three steps containing spectral clustering over the integrated cost, based on the idea of network modularity. We rigorously examined the performance of our proposed method from three different viewpoints. All experimental results indicate the performance advantage of our method over possible clustering/classification-based approaches of gene function annotation, using expressions and/or sequences.

基因注释是后基因组时代的一个基本问题。一个典型的方法是首先根据基因的特征进行聚类,然后在同一聚类中使用已知基因来分配未知基因的功能。大量的基因组信息可用于这个问题,但可以测量任何基因的两种主要类型的数据是微阵列表达和序列,但两者都有自己的缺陷。因此,整合这两个数据源是一种自然而有前途的基因注释方法,特别是考虑到它们在聚类中优化的成本。基于网络模块化的思想,提出了一种基于集成代价的谱聚类的三步基因注释方法。我们从三个不同的角度严格检查了我们提出的方法的性能。所有的实验结果表明,我们的方法优于可能的基于聚类/分类的基因功能注释方法,使用表达式和/或序列。
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引用次数: 0
New kernel methods for phenotype prediction from genotype data. 从基因型数据预测表型的新核心方法。
Ritsuko Onuki, Tetsuo Shibuya, Minoru Kanehisa

Phenotype prediction from genotype data is one of the most important issues in computational genetics. In this work, we propose a new kernel (i.e., an SVM: Support Vector Machine) method for phenotype prediction from genotype data. In our method, we first infer multiple suboptimal haplotype candidates from each genotype by using the HMM (Hidden Markov Model), and the kernel matrix is computed based on the predicted haplotype candidates and their emission probabilities from the HMM. We validated the performance of our method through experiments on several datasets: One is an artificially constructed dataset via a program GeneArtisan, others are a real dataset of the NAT2 gene from the international HapMap project, and a real dataset of genotypes of diseased individuals. The experiments show that our method is superior to ordinary naive kernel methods (i.e., not based on haplotype prediction), especially in cases of strong LD (linkage disequilibrium).

从基因型数据预测表型是计算遗传学中最重要的问题之一。在这项工作中,我们提出了一种新的核(即SVM:支持向量机)方法,用于从基因型数据中预测表型。该方法首先利用隐马尔可夫模型(HMM)从每个基因型中推断出多个次优候选单倍型,然后根据预测的候选单倍型及其在隐马尔可夫模型中的发射概率计算核矩阵。我们通过几个数据集的实验验证了我们方法的性能:一个是通过GeneArtisan程序人工构建的数据集,另一个是来自国际HapMap项目的NAT2基因的真实数据集,以及患病个体的真实基因型数据集。实验表明,我们的方法优于普通的朴素核方法(即不基于单倍型预测),特别是在强LD(连锁不平衡)的情况下。
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引用次数: 0
A state space representation of VAR models with sparse learning for dynamic gene networks. 基于稀疏学习的动态基因网络VAR模型的状态空间表示。
Kaname Kojima, Rui Yamaguchi, Seiya Imoto, Mai Yamauchi, Masao Nagasaki, Ryo Yoshida, Teppei Shimamura, Kazuko Ueno, Tomoyuki Higuchi, Noriko Gotoh, Satoru Miyano

We propose a state space representation of vector autoregressive model and its sparse learning based on L1 regularization to achieve efficient estimation of dynamic gene networks based on time course microarray data. The proposed method can overcome drawbacks of the vector autoregressive model and state space model; the assumption of equal time interval and lack of separation ability of observation and systems noises in the former method and the assumption of modularity of network structure in the latter method. However, in a simple implementation the proposed model requires the calculation of large inverse matrices in a large number of times during parameter estimation process based on EM algorithm. This limits the applicability of the proposed method to a relatively small gene set. We thus introduce a new calculation technique for EM algorithm that does not require the calculation of inverse matrices. The proposed method is applied to time course microarray data of lung cells treated by stimulating EGF receptors and dosing an anticancer drug, Gefitinib. By comparing the estimated network with the control network estimated using non-treated lung cells, perturbed genes by the anticancer drug could be found, whose up- and down-stream genes in the estimated networks may be related to side effects of the anticancer drug.

提出了一种基于L1正则化的向量自回归模型的状态空间表示及其稀疏学习方法,以实现基于时程微阵列数据的动态基因网络的高效估计。该方法克服了矢量自回归模型和状态空间模型的不足;前一种方法采用等时间间隔假设,缺乏观测噪声与系统噪声的分离能力,后一种方法采用网络结构模块化假设。然而,在简单实现中,该模型需要在基于EM算法的参数估计过程中计算大量的逆矩阵。这限制了所提出的方法对相对较小的基因集的适用性。因此,我们为EM算法引入了一种不需要计算逆矩阵的新计算技术。该方法应用于通过刺激EGF受体和服用抗癌药物吉非替尼处理的肺细胞的时程微阵列数据。通过将估计的网络与未处理的肺细胞估计的控制网络进行比较,可以发现被抗癌药物干扰的基因,其在估计网络中的上下游基因可能与抗癌药物的副作用有关。
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引用次数: 0
Formal representation of the high osmolarity glycerol pathway in yeast. 酵母中高渗透压甘油途径的形式表示。
Pub Date : 2010-01-01 DOI: 10.1142/9781848165786_0007
C. Kühn, K. V. S. Prasad, E. Klipp, P. Gennemark
The high osmolarity glycerol (HOG) signalling system in yeast belongs to the class of Mitogen Activated Protein Kinase (MAPK) pathways that are found in all eukaryotic organisms. It includes at least three scaffold proteins that form complexes, and involves reactions that are strictly dependent on the set of species bound to a certain complex. The scaffold proteins lead to a combinatorial increase in the number of possible states. To date, representations of the HOG pathway have used simplifying assumptions to avoid this combinatorial problem. Such assumptions are hard to make and may obscure or remove essential properties of the system. This paper presents a detailed generic formal representation of the HOG system without such assumptions, showing the molecular interactions known from the literature. The model takes complexes into account, and summarises existing knowledge in an unambiguous and detailed representation. It can thus be used to anchor discussions about the HOG system. In the commonly used Systems Biology Markup Language (SBML), such a model would need to explicitly enumerate all state variables. The Kappa modelling language which we use supports representation of complexes without such enumeration. To conclude, we compare Kappa with a few other modelling languages and software tools that could also be used to represent and model the HOG system.
酵母中的高渗透压甘油(HOG)信号系统属于丝裂原活化蛋白激酶(MAPK)途径,在所有真核生物中都有发现。它包括至少三种形成复合物的支架蛋白,并涉及严格依赖于与特定复合物结合的物种集的反应。支架蛋白导致可能状态数量的组合增加。迄今为止,HOG途径的表示已经使用简化的假设来避免这种组合问题。这样的假设很难做出,可能会模糊或删除系统的基本属性。本文给出了没有这些假设的HOG系统的详细的一般形式表示,显示了从文献中已知的分子相互作用。该模型考虑了复杂性,并以明确和详细的表示总结了现有知识。因此,它可以用来锚定关于HOG系统的讨论。在常用的系统生物学标记语言(SBML)中,这样的模型需要显式地枚举所有状态变量。我们使用的Kappa建模语言支持没有这种枚举的复合体的表示。最后,我们将Kappa与其他一些建模语言和软件工具进行了比较,这些语言和软件工具也可用于表示和建模HOG系统。
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引用次数: 15
Evaluation of DNA intramolecular interactions for nucleosome positioning in yeast. 酵母核小体定位中DNA分子内相互作用的评价。
Michael Fernandez, Satoshi Fujii, Hidetoshi Kono, Akinori Sarai

We calculated intramolecular interaction energies of DNA by threading DNA sequences around crystal structures of nucleosomes. The strength of the intramolecular energy oscillations at frequency approximately 10 bps for dinucleotides was in agreement with previous nucleosome models. The intramolecular energy calculated along yeast genome positively correlated with nucleosome positioning experimentally measured.

我们通过在核小体的晶体结构周围穿线DNA序列来计算DNA的分子内相互作用能。二核苷酸的分子内能量振荡频率约为10 bps,与先前的核小体模型一致。沿酵母基因组计算的分子内能量与实验测量的核小体定位呈正相关。
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引用次数: 0
Comparative analysis of aerobic and anaerobic prokaryotes to identify correlation between oxygen requirement and gene-gene functional association patterns. 好氧和厌氧原核生物的比较分析,以确定氧需求与基因-基因功能关联模式之间的相关性。
Yaming Lin, Hongwei Wu

Activities of prokaryotes are pivotal in shaping the environment, and are also greatly influenced by the environment. With the substantial progress in genome and metagenome sequencing and the about-to-be-standardized ecological context information, environment-centric comparative genomics will complement species-centric comparative genomics, illuminating how environments have shaped and maintained prokaryotic diversities. In this paper we report our preliminary studies on the association analysis of a particular duo of genomic and ecological traits of prokaryotes--gene-gene functional association patterns vs. oxygen requirement conditions. We first establish a stochastic model to describe gene arrangements on chromosomes, based on which the functional association between genes are quantified. The gene-gene functional association measures are validated using biological process ontology and KEGG pathway annotations. Student's t-tests are then performed on the aerobic and anaerobic organisms to identify those gene pairs that exhibit different functional association patterns in the two different oxygen requirement conditions. As it is difficult to design and conduct biological experiments to validate those genome-environment association relationships that have resulted from long-term accumulative genome-environment interactions, we finally conduct computational validations to determine whether the oxygen requirement condition of an organism is predictable based on gene-gene functional association patterns. The reported study demonstrates the existence and significance of the association relationships between certain gene-gene functional association patterns and oxygen requirement conditions of prokaryotes, as well as the effectiveness of the adopted methodology for such association analysis.

原核生物的活动是塑造环境的关键,也受环境的极大影响。随着基因组和宏基因组测序的实质性进展以及即将标准化的生态背景信息,以环境为中心的比较基因组学将补充以物种为中心的比较基因组学,阐明环境如何塑造和维持原核生物多样性。在本文中,我们报告了我们对原核生物基因组和生态性状的关联分析的初步研究——基因-基因功能关联模式与需氧量条件的关系。我们首先建立了一个随机模型来描述基因在染色体上的排列,并在此基础上量化了基因之间的功能关联。利用生物过程本体和KEGG通路注释验证了基因-基因功能关联测度。然后对有氧和厌氧生物进行学生t检验,以确定在两种不同的氧气需求条件下表现出不同功能关联模式的基因对。由于很难设计和实施生物学实验来验证那些由长期累积的基因组-环境相互作用产生的基因组-环境关联关系,我们最终进行计算验证,以确定基于基因-基因功能关联模式的生物体的需氧量条件是否可预测。本研究证明了某些基因-基因功能关联模式与原核生物的需氧量条件之间存在关联关系并具有重要意义,以及所采用的关联分析方法的有效性。
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引用次数: 0
期刊
Genome informatics. International Conference on Genome Informatics
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