kegg(graphite)
kegg()所属R语言包：graphite
KEGG pathways
KEGG通路
译者：生物统计家园网 机器人LoveR
描述----------Description----------
A list with a pathway object for each KEGG pathway.
pathway每个KEGG通路的对象名单。
Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M. KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 1999 Jan 1;27(1):29-34.
绪方贞子Ĥ，转到S，佐藤钾，Fujibuchi W，波诺Ĥ，Kanehisa研究KEGG：京都基因和基因组百科全书。核酸研究。 1999年1月1日; 27（1）:29-34。
http://www.genome.jp/kegg/
通路的拓扑结构转换----------Pathway topology conversion----------
KEGG pathway were retrieved in KGML format from the KEGG ftp site.
KEGG通路在从KEGG FTP站点KGML格式检索。
KEGG database provides separate xml files, one for each pathway. A pathway is therefore define by all the reactions described within each file.
KEGG数据库提供单独的XML文件，为每个途径之一。因此，定义每个文件内所述的所有反应的一个途径。
Pathway nodes often correspond to multiple gene products. These can be divided into protein complexes (proteins linked by protein-protein interactions) and groups made of alternative members (genes with similar biochemical functions). Thus, when considering signal propagation these groups are considered differently. The first kind (hereafter group AND) should be expanded into a clique (all proteins connected to the others), while the second (hereafter group OR) should be expanded without connection among them. In the KGML format there are two ways of defining nodes with multiple elements: protein complexes (group AND defined by entry type=“group”) and groups with alternative members (group OR defined by entry type=“gene”).
通路节点往往对应多个基因产物。这些可分为蛋白复合物（蛋白质蛋白质相互作用链接）和替代成员（具有类似的生化功能的基因）的群体。因此，当考虑信号传播这些群体被认为是不同的。第一类（以下简称组）应扩大成集团（连接到其他所有的蛋白质），而第二个（以下简称集团或）应扩大没有它们之间的连接。在KGML格式定义多个元素的节点有两种方法：蛋白复合物（组定义条目类型=“本集团”）和替代成员的组（组或条目类型=“基因”的定义）。
Compound mediated interactions are interactions for which a compound acts as a bridge between two elements. Since chemical compounds are not usually measured with high-throughput technology, they should be removed from the network to analyse gene signals. However, the trivial elimination of the compounds, without signal propagation, will strongly bias the topology interrupting the signals that pass through them. If element 'A' is linked to compound 'c' and compound 'c' is linked to element 'B', element 'A' should be linked to element 'B'. Within the KGML format there are two different ways of describing a compound mediated interaction: i) direct interaction type=&ldquo Prel” ('A' interacts whit 'B' through compound 'c' ) and ii) indirect one type=&ldquoCrel” ('A' interacts to compound 'c' and 'c' interacts with 'B').
复合介导的相互作用是相互作用的化合物，其中两个元素之间的桥梁作用。由于化合物通常不高通量技术来衡量，他们应该被从网络分析基因信号。然而，化合物的琐碎消除无信号传播，会强烈偏见的拓扑中断，通过他们传递的信号。如果元素一挂c和C是复合元素“B”复合元素“A”应与元素“B”。内KGML格式有两种不同的方式描述化合物介导的互动：i）直接互动式=的“PPrel”（“A”交互通过复合白衣“B”“C”）和ii）间接一个类型=“ PCrel“（”A“交互复合c和C”B“）进行交互。
Not all compounds are considered for the propagation because some of them (for example: H2O, ATP, ADP) are highly frequent in map descriptions and the signal propagation through them would lead to chains too long. Compounds not considered for propagation are not characteristic of a specific reaction, but act as secondary substrates/products widely shared among different processes.
并非所有的化合物被认为是为传播，因为他们中的一些（例如：水，三磷酸腺苷，ADP）中是非常频繁的，在图上描述，并通过它们的信号传播，会导致链太长。不考虑繁殖的化合物不是一个特定的反应的特点，但作为辅助基板/产品广泛应用于不同的进程之间共享。
graphite allows the user to see the single/multiple relation types that characterized an edge. The type of edges have been kept as much as possible similar to those annotated in the original data format. Some new types have been introduced due to topological conversion needs.
石墨允许用户看到单一/多重关系类型特征的边缘。边一直维持在尽可能多的原始数据格式类似这些注释。由于拓扑转换的需要，相继出台了一些新的类型。
参见----------See Also----------
pathway-class.
pathway-class。
转载请注明:出自 生物统计家园网(http://www.biostatistic.net)。
注：
注1：为了方便大家学习，本文档为生物统计家园网机器人LoveR翻译而成，仅供个人R语言学习参考使用，生物统计家园保留版权。
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发表于 2012-2-25 21:02:53
