Computational genetic neuroanatomy of the developing mouse brain: dimensionality reduction, visualization, and clustering.
Computational genetic neuroanatomy of the developing mouse brain: dimensionality reduction, visualization, and clustering.
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DOI：
10.1186/1471-2105-14-222
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发表时间：
2013-07-11
影响因子：
3
通讯作者：
Ji S
中科院分区：
文献类型：
--
作者：
Ji S
大脑中细胞的结构化组织在其功能效率中起着关键作用。这种微妙的组织是在发育过程中通过精确的时空基因表达控制逐渐建立的每个细胞的独特分子身份的结果。目前，对分子结构关联的研究开始揭示时空基因表达模式如何与细胞分化和结构发育相关。在这篇文章中，我们的目标是对发育中的小鼠大脑中基因表达与神经解剖学之间的关系进行全球性的数据驱动研究。为了使可视化的高维数据的探索，我们在原位杂交基因表达数据映射到一个二维空间，通过保留全局和局部结构。我们的研究结果表明，发育中的大脑解剖结构在很大程度上保留在减少的基因表达空间。为了提供定量分析，我们将减少的数据分组，并在多个级别上测量与神经解剖学的一致性。我们的研究结果表明，在低维空间中的集群是更符合神经解剖比那些在原始空间。基因表达模式和发育中的大脑解剖结构密切相关。视觉还原和视觉探索促进了这种关系的研究。
The structured organization of cells in the brain plays a key role in its functional efficiency. This delicate organization is the consequence of unique molecular identity of each cell gradually established by precise spatiotemporal gene expression control during development. Currently, studies on the molecular-structural association are beginning to reveal how the spatiotemporal gene expression patterns are related to cellular differentiation and structural development. In this article, we aim at a global, data-driven study of the relationship between gene expressions and neuroanatomy in the developing mouse brain. To enable visual explorations of the high-dimensional data, we map the in situ hybridization gene expression data to a two-dimensional space by preserving both the global and the local structures. Our results show that the developing brain anatomy is largely preserved in the reduced gene expression space. To provide a quantitative analysis, we cluster the reduced data into groups and measure the consistency with neuroanatomy at multiple levels. Our results show that the clusters in the low-dimensional space are more consistent with neuroanatomy than those in the original space. Gene expression patterns and developing brain anatomy are closely related. Dimensionality reduction and visual exploration facilitate the study of this relationship.
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影响因子：
32.8
作者：
Burges, Christopher J. C.
通讯作者：
Burges, Christopher J. C.
影响因子：
4.3
作者：
Bohland JW;Wu C;Barbas H;Bokil H;Bota M;Breiter HC;Cline HT;Doyle JC;Freed PJ;Greenspan RJ;Haber SN;Hawrylycz M;Herrera DG;Hilgetag CC;Huang ZJ;Jones A;Jones EG;Karten HJ;Kleinfeld D;Kötter R;Lester HA;Lin JM;Mensh BD;Mikula S;Panksepp J;Price JL;Safdieh J;Saper CB;Schiff ND;Schmahmann JD;Stillman BW;Svoboda K;Swanson LW;Toga AW;Van Essen DC;Watson JD;Mitra PP
通讯作者：
Mitra PP
影响因子：
4.8
作者：
Bohland, Jason W.;Bokil, Hemant;Mitra, Partha P.
通讯作者：
Mitra, Partha P.
影响因子：
--
作者：
Hidalgo-S치nchez, M;Millet, S;Alvarado-Mallart, RM
通讯作者：
Alvarado-Mallart, RM
影响因子：
64.8
作者：
Hawrylycz, Michael J.;Lein, Ed S.;Guillozet-Bongaarts, Angela L.;Shen, Elaine H.;Ng, Lydia;Miller, Jeremy A.;van de lagemaat, Louie N.;Smith, Kimberly A.;Ebbert, Amanda;Riley, Zackery L.;Abajian, Chris;Beckmann, Christian F.;Bernard, Amy;Bertagnolli, Darren;Boe, Andrew F.;Cartagena, Preston M.;Chakravarty, M. Mallar;Chapin, Mike;Chong, Jimmy;Dalley, Rachel A.;Daly, Barry David;Dang, Chinh;Datta, Suvro;Dee, Nick;Dolbeare, Tim A.;Faber, Vance;Feng, David;Fowler, David R.;Goldy, Jeff;Gregor, Benjamin W.;Haradon, Zeb;Haynor, David R.;Hohmann, John G.;Horvath, Steve;Howard, Robert E.;Jeromin, Andreas;Jochim, Jayson M.;Kinnunen, Marty;Lau, Christopher;Lazarz, Evan T.;Lee, Changkyu;Lemon, Tracy A.;Li, Ling;Li, Yang;Morris, John A.;Overly, Caroline C.;Parker, Patrick D.;Parry, Sheana E.;Reding, Melissa;Royall, Joshua J.;Schulkin, Jay;Sequeira, Pedro Adolfo;Slaughterbeck, Clifford R.;Smith, Simon C.;Sodt, Andy J.;Sunkin, Susan M.;Swanson, Beryl E.;Vawter, Marquis P.;Williams, Derric;Wohnoutka, Paul;Zielke, H. Ronald;Geschwind, Daniel H.;Hof, Patrick R.;Smith, Stephen M.;Koch, Christof;Grant, Seth G. N.;Jones, Allan R.
通讯作者：
Jones, Allan R.