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→完善的模体及其功能
==Well-established motifs and their functions==
Much experimental work has been devoted to understanding network motifs in [[gene regulatory networks]]. These networks control which genes are expressed in the cell in response to biological signals. The network is defined such that genes are nodes, and directed edges represent the control of one gene by a transcription factor (regulatory protein that binds DNA) encoded by another gene. Thus, network motifs are patterns of genes regulating each other's transcription rate. When analyzing transcription networks, it is seen that the same network motifs appear again and again in diverse organisms from bacteria to human. The transcription network of ''[[Escherichia coli|E. coli]]'' and yeast, for example, is made of three main motif families, that make up almost the entire network. The leading hypothesis is that the network motif were independently selected by evolutionary processes in a converging manner,<ref name="bab1">{{cite journal |vauthors=Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA |title=Structure and evolution of transcriptional regulatory networks |journal=Current Opinion in Structural Biology |volume=14 |issue=3 |pages=283–91 |date=June 2004 |pmid=15193307 |doi=10.1016/j.sbi.2004.05.004 |citeseerx=10.1.1.471.9692 }}</ref><ref name="con1">{{cite journal |vauthors=Conant GC, Wagner A |title=Convergent evolution of gene circuits |journal=Nat. Genet. |volume=34 |issue=3 |pages=264–6 |date=July 2003 |pmid=12819781 |doi=10.1038/ng1181}}</ref> since the creation or elimination of regulatory interactions is fast on evolutionary time scale, relative to the rate at which genes change,<ref name="bab1"/><ref name="con1"/><ref name="dek1">{{cite journal |vauthors=Dekel E, Alon U |title=Optimality and evolutionary tuning of the expression level of a protein |journal=Nature |volume=436 |issue=7050 |pages=588–92 |date=July 2005 |pmid=16049495 |doi=10.1038/nature03842 |bibcode=2005Natur.436..588D }}</ref> Furthermore, experiments on the dynamics generated by network motifs in living cells indicate that they have characteristic dynamical functions. This suggests that the network motif serve as building blocks in gene regulatory networks that are beneficial to the organism.
The functions associated with common network motifs in transcription networks were explored and demonstrated by several research projects both theoretically and experimentally. Below are some of the most common network motifs and their associated function.
==完善的模体及其功能==
==完善的模体及其功能==
许多实验工作致力于理解[[基因调控网络]]中的网络模体。在响应生物信号的过程中，这些网络控制细胞中的哪些基因来表达。这样的网络以基因作为节点，有向边代表对某个基因的调控，基因调控通过其他基因编码的转录因[[结合在DNA上的调控蛋白]]子来实现。因此，网络模体是基因之间相互调控转录速率的模式。在分析转录调控网络的时候，人们发现相同的网络模体在不同的物种中不断地出现，从细菌到人类。例如，''[[大肠杆菌]]''和酵母的转录网络由三种主要的网络模体家族组成，它们可以构建几乎整个网络。主要的假设是在进化的过程中，网络模体是被以收敛的方式独立选择出来的。<ref name="bab1">{{cite journal |vauthors=Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA |title=Structure and evolution of transcriptional regulatory networks |journal=Current Opinion in Structural Biology |volume=14 |issue=3 |pages=283–91 |date=June 2004 |pmid=15193307 |doi=10.1016/j.sbi.2004.05.004 |citeseerx=10.1.1.471.9692 }}</ref><ref name="con1">{{cite journal |vauthors=Conant GC, Wagner A |title=Convergent evolution of gene circuits |journal=Nat. Genet. |volume=34 |issue=3 |pages=264–6 |date=July 2003 |pmid=12819781 |doi=10.1038/ng1181}}</ref> 因为相对于基因改变的速率，转录相互作用产生和消失的时间尺度在进化上是很快的。<ref name="bab1"/><ref name="con1"/><ref name="dek1">{{cite journal |vauthors=Dekel E, Alon U |title=Optimality and evolutionary tuning of the expression level of a protein |journal=Nature |volume=436 |issue=7050 |pages=588–92 |date=July 2005 |pmid=16049495 |doi=10.1038/nature03842 |bibcode=2005Natur.436..588D }}</ref> 此外，对活细胞中网络模体所产生的动力学行为的实验表明，它们具有典型的动力学功能。这表明，网络模体是基因调控网络中对生物体有益的基本单元。
许多实验工作致力于理解[[基因调控网络]]中的网络模体。在响应生物信号的过程中，这些网络控制细胞中的哪些基因来表达。这样的网络以基因作为节点，有向边代表对某个基因的调控，基因调控通过其他基因编码的转录因[[结合在DNA上的调控蛋白]]子来实现。因此，网络模体是基因之间相互调控转录速率的模式。在分析转录调控网络的时候，人们发现相同的网络模体在不同的物种中不断地出现，从细菌到人类。例如，''[[大肠杆菌]]''和酵母的转录网络由三种主要的网络模体家族组成，它们可以构建几乎整个网络。主要的假设是在进化的过程中，网络模体是被以收敛的方式独立选择出来的。<ref name="bab1">{{cite journal |vauthors=Babu MM, Luscombe NM, Aravind L, Gerstein M, Teichmann SA |title=Structure and evolution of transcriptional regulatory networks |journal=Current Opinion in Structural Biology |volume=14 |issue=3 |pages=283–91 |date=June 2004 |pmid=15193307 |doi=10.1016/j.sbi.2004.05.004 |citeseerx=10.1.1.471.9692 }}</ref><ref name="con1">{{cite journal |vauthors=Conant GC, Wagner A |title=Convergent evolution of gene circuits |journal=Nat. Genet. |volume=34 |issue=3 |pages=264–6 |date=July 2003 |pmid=12819781 |doi=10.1038/ng1181}}</ref> 因为相对于基因改变的速率，转录相互作用产生和消失的时间尺度在进化上是很快的。<ref name="bab1"/><ref name="con1"/><ref name="dek1">{{cite journal |vauthors=Dekel E, Alon U |title=Optimality and evolutionary tuning of the expression level of a protein |journal=Nature |volume=436 |issue=7050 |pages=588–92 |date=July 2005 |pmid=16049495 |doi=10.1038/nature03842 |bibcode=2005Natur.436..588D }}</ref> 此外，对活细胞中网络模体所产生的动力学行为的实验表明，它们具有典型的动力学功能。这表明，网络模体是基因调控网络中对生物体有益的基本单元。