Transcriptome Architecture of Adult Mouse Brain Revealed by Sparse Coding of Genome-Wide In Situ Hybridization Images

Li Yujie; Chen Hanbo; Jiang Xi; Li Xiang; Lv Jinglei; Li Meng; Peng Hanchuan; Tsien Joe Z.; Liu Tianming

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Transcriptome Architecture of Adult Mouse Brain Revealed by Sparse Coding of Genome-Wide In Situ Hybridization Images

机译：通过稀疏编码的基因组型原位杂交图像的稀疏编码显示成年小鼠脑的转录组体系结构

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摘要

Highly differentiated brain structures with distinctly different phenotypes are closely correlated with the unique combination of gene expression patterns. Using a genome-wide in situ hybridization image dataset released by Allen Mouse Brain Atlas, we present a data-driven method of dictionary learning and sparse coding. Our results show that sparse coding can elucidate patterns of transcriptome organization of mouse brain. A collection of components obtained from sparse coding display robust region-specific molecular signatures corresponding to the canonical neuroanatomical subdivisions including fiber tracts and ventricular systems. Other components revealed finer anatomical delineation of domains previously considered homogeneous. We also build an open-access informatics portal that contains the detail of each component along with its ontology and expressed genes. This portal allows intuitive visualization, interpretation and explorations of the transcriptome architecture of a mouse brain.

机译：具有明显不同表型的高度分化的脑结构与基因表达模式的独特组合密切相关。使用Allen Mouse Brain Atlas释放的基因组杂交图像数据集，我们介绍了一种数据驱动的字典学习方法和稀疏编码。我们的结果表明，稀疏编码可以阐明小鼠脑的转录组织的模式。从稀疏编码显示的组分集合，该组分对应于包括纤维束和心室系统的规范神经杀菌细胞的稳健区域特异性分子签名。其他组分揭示了先前被认为是均匀的域的更精细的解剖学描绘。我们还构建了一个开放式信息仪门户，包含每个组件的细节以及其本体和表达的基因。该门户允许直观可视化，解释和探索小鼠脑的转录组体系结构。

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《Neuroinformatics》 |2017年第3期|共11页
作者
Li Yujie; Chen Hanbo; Jiang Xi; Li Xiang; Lv Jinglei; Li Meng; Peng Hanchuan; Tsien Joe Z.; Liu Tianming;
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作者单位

Univ Georgia Dept Comp Sci Cort Architecture Imaging &

Discovery Lab Athens GA 30602 USA;

Univ Georgia Dept Comp Sci Cort Architecture Imaging &

Discovery Lab Athens GA 30602 USA;

Univ Georgia Dept Comp Sci Cort Architecture Imaging &

Discovery Lab Athens GA 30602 USA;

Univ Georgia Dept Comp Sci Cort Architecture Imaging &

Discovery Lab Athens GA 30602 USA;

Univ Georgia Dept Comp Sci Cort Architecture Imaging &

Discovery Lab Athens GA 30602 USA;

Augusta Univ Med Coll Georgia Brain &

Behav Discovery Inst Augusta GA 30912 USA;

Allen Inst Brain Sci Seattle WA 98109 USA;

Augusta Univ Med Coll Georgia Brain &

Behav Discovery Inst Augusta GA 30912 USA;

Univ Georgia Dept Comp Sci Cort Architecture Imaging &

Discovery Lab Athens GA 30602 USA;

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原文格式 PDF
正文语种 eng
中图分类人工神经网络与计算;
关键词
Sparse coding; Data-driven gene clustering; Transcriptome; Mouse brain anatomy;

机译：稀疏编码;数据驱动基因聚类;转录组;小鼠脑解剖学;

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专利

1. Transcriptome Architecture of Adult Mouse Brain Revealed by Sparse Coding of Genome-Wide In Situ Hybridization Images [J] . Li Yujie, Chen Hanbo, Jiang Xi, Neuroinformatics . 2017,第3期

机译：通过稀疏编码的基因组型原位杂交图像的稀疏编码显示成年小鼠脑的转录组体系结构
2. Transcriptome analyses of adult mouse brain reveal enrichment of lncRNAs in specific brain regions and neuronal populations [J] . Beena M. Kadakkuzha, Xin-An Liu, Jennifer McCrate, Frontiers in Cellular Neuroscience . 2015,第1期

机译：成年小鼠大脑的转录组分析显示特定大脑区域和神经元群体中lncRNA的富集
3. MRI and in situ hybridization reveal early disturbances in brain size and gene expression in the megencephalic (mceph/mceph) mouse. [J] . Diez M, Schweinhardt P, Petersson S, The European Journal of Neuroscience . 2003,第12期

机译：MRI和原位杂交揭示了中脑型（mceph / mceph）小鼠大脑大小和基因表达的早期紊乱。
4. Gene expression detection and expression visualization in in-situ hybridized cross-sectional images of the mouse brain [C] . Sayan Pathak, Ed Lein, Simon Smith, Society of Photo-Optical Instrumentation Engineers (SPIE);SPIE Proceedings . 2005

机译：小鼠大脑原位杂交横截面图像中的基因表达检测和表达可视化
5. Comparative genome mapping: Mouse and rat homologies revealed by fluorescent in situ hybridization (FISH). [D] . Scalzi-Martin, Jane Marie. 1996

机译：比较基因组图谱：通过荧光原位杂交（FISH）揭示的小鼠和大鼠同源性。
6. Transcriptome architecture of adult mouse brain revealed by sparse coding of genome-wide in situ hybridization images [O] . Yujie Li, Hanbo Chen, Xi Jiang, -1

机译：通过全基因组原位杂交图像的稀疏编码揭示成年小鼠大脑的转录组结构
7. A genome-wide in situ hybridization map of RNA-binding proteins reveals anatomically restricted expression in the developing mouse brain [O] . McKee Adrienne E, Minet Emmanuel, Stern Charlene, 2005

机译：RNA结合蛋白的全基因组原位杂交图揭示了发育中的小鼠大脑中解剖学受限制的表达

Transcriptome Architecture of Adult Mouse Brain Revealed by Sparse Coding of Genome-Wide In Situ Hybridization Images

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