Topological characterization of neuronal arbor morphology via sequence representation: II--global alignment.
Topological characterization of neuronal arbor morphology via sequence representation: II--global alignment.
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DOI：
10.1186/s12859-015-0605-1
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发表时间：
2015-07-04
影响因子：
3
通讯作者：
Ascoli GA
中科院分区：
文献类型：
--
作者：
Gillette TA;Hosseini P;Ascoli GA
越来越丰富的神经形态学数据提供了机会和挑战，以比较大量的神经元从广泛的多样性来源有效和有效。我们实现了一个修改后的全局对齐算法，轴突和树突分叉字符串。序列比对通过识别树之间的分支水平对应来量化神经元的相似性。从成对的相似性产生的空间是能够分类神经元乔木类型以及，或更好地比，传统的拓扑度量。无监督聚类分析产生与轴突、树突和锥体顶端树突的已知细胞类别显著对应的组。此外，由一组神经元的多序列比对产生的独特的共有拓扑结构揭示了它们共享的分支蓝图。有趣的是，树突靶向中间神经元的轴突在啮齿类动物皮层与锥体轴突，但除了（拓扑对称）轴突周围靶向中间神经元。神经突拓扑结构的全局成对和多序列比对使神经突的详细比较和保守的拓扑特征的识别在神经突定义的集群。提出的方法还提供了一个框架，将额外的分支级形态特征。此外，多重比对与模体分析的比较表明，这两种技术提供了互补的信息，分别揭示全局和局部特征。本文的在线版本（doi：10.1186/s12859-015-0605-1）包含补充材料，可供授权用户使用。
The increasing abundance of neuromorphological data provides both the opportunity and the challenge to compare massive numbers of neurons from a wide diversity of sources efficiently and effectively. We implemented a modified global alignment algorithm representing axonal and dendritic bifurcations as strings of characters. Sequence alignment quantifies neuronal similarity by identifying branch-level correspondences between trees. The space generated from pairwise similarities is capable of classifying neuronal arbor types as well as, or better than, traditional topological metrics. Unsupervised cluster analysis produces groups that significantly correspond with known cell classes for axons, dendrites, and pyramidal apical dendrites. Furthermore, the distinguishing consensus topology generated by multiple sequence alignment of a group of neurons reveals their shared branching blueprint. Interestingly, the axons of dendritic-targeting interneurons in the rodent cortex associates with pyramidal axons but apart from the (more topologically symmetric) axons of perisomatic-targeting interneurons. Global pairwise and multiple sequence alignment of neurite topologies enables detailed comparison of neurites and identification of conserved topological features in alignment-defined clusters. The methods presented also provide a framework for incorporation of additional branch-level morphological features. Moreover, comparison of multiple alignment with motif analysis shows that the two techniques provide complementary information respectively revealing global and local features. The online version of this article (doi:10.1186/s12859-015-0605-1) contains supplementary material, which is available to authorized users.
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影响因子：
1.1
作者：
Bille, P
通讯作者：
Bille, P
影响因子：
9.2
作者：
Chiang, Ann-Shyn;Lin, Chih-Yung;Hwang, Jenn-Kang
通讯作者：
Hwang, Jenn-Kang
DOI：
10.1073/pnas.1200430109
发表时间：
2012-07-03
影响因子：
11.1
作者：
Cuntz, Hermann;Mathy, Alexandre;Haeusser, Michael
通讯作者：
Haeusser, Michael
DOI：
10.1111/j.2517-6161.1977.tb01600.x
发表时间：
1977-01-01
期刊：
JOURNAL OF THE ROYAL STATISTICAL SOCIETY SERIES B-METHODOLOGICAL
影响因子：
--
作者：
DEMPSTER, AP;LAIRD, NM;RUBIN, DB
通讯作者：
RUBIN, DB
影响因子：
5.3
作者：
Ascoli, Giorgio A.;Donohue, Duncan E.;Halavi, Maryam
通讯作者：
Halavi, Maryam