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Study of gene function based on spatial co-expression in a high-resolution mouse brain atlas

Zheng Liu, S Frank Yan, John R Walker, Theresa A Zwingman, Tao Jiang, Jing Li, Yingyao Zhou
2007 BMC Systems Biology  
The Allen Brain Atlas (ABA) project systematically profiles three-dimensional highresolution gene expression in postnatal mouse brains for thousands of genes.  ...  In this proof-of-concept study, we studied the hypothesis that genes sharing similar three-dimensional expression profiles in the mouse brain are likely to share similar biological functions.  ...  We applied the HRC algorithm to study several genes of biological interest in order to assess the feasibility of carrying out a functional genomics study based on spatial gene expression in the mouse brain  ... 
doi:10.1186/1752-0509-1-19 pmid:17437647 pmcid:PMC1863433 fatcat:yfu3lhaheffghkaszzju2afgve

Brain transcriptome atlases: a computational perspective

Ahmed Mahfouz, Sjoerd M. H. Huisman, Boudewijn P. F. Lelieveldt, Marcel J. T. Reinders
2016 Brain Structure and Function  
Brain transcriptome atlases provide valuable insights into gene expression patterns across different brain areas throughout the course of development.  ...  We provide a comprehensive overview of the various computational methods used to analyze brain transcriptome atlases.  ...  Acknowledgements This research has received partial funding from The Netherlands Technology Foundation (STW), as part of the STW Project 12721 (Genes in Space) under the Imaging Genetics (IMA-GENE) Perspective  ... 
doi:10.1007/s00429-016-1338-2 pmid:27909802 pmcid:PMC5406417 fatcat:zflsrogrsze53jro2ayrcdffs4

A high-resolution anatomical framework of the neonatal mouse brain for managing gene expression data

Erh-Fang Lee
2007 Frontiers in Neuroinformatics  
This study aims to provide a high-resolution atlas and use it as an anatomical framework to localize the gene expression data for mouse brain on postnatal day 0 (P0).  ...  The region-specific anatomical framework based on the neonatal atlas allows for the analysis of gene activity within a high-resolution anatomical space at an early developmental stage.  ...  Resources at the National Institutes of Health (NIH).  ... 
doi:10.3389/neuro.11.006.2007 pmid:18974801 pmcid:PMC2525996 fatcat:fgbaobfdpfbxpp6ammfh4sccim

Using MERSCOPE to Generate a Cell Atlas of the Mouse Brain that Includes Lowly Expressed Genes

George Emanuel, Jiang He
2021 Microscopy Today  
Recently, a high-resolution cell atlas generated by MERFISH (multiplex error-robust fluorescence in situ hybridization) technology has mapped this spectacular organ with unmatched resolution, depth, and  ...  Abstract:The structure and organization of cells within organs is essential to their function, but nowhere in the body is this more spectacular than the brain.  ...  Neurotransmitter receptors come in many shapes and sizes based on functionality and are expressed by neurons at varying levels.  ... 
doi:10.1017/s1551929521001346 fatcat:edodmp24rzfdrp5rwxejainsni

Application of Computational Biology for Decoding Brain Transcriptomes

Jie Li, Guang-Zhong Wang
2019 Genomics, Proteomics & Bioinformatics  
The rapid development of high-throughput sequencing technologies has generated massive valuable brain transcriptome atlases, providing great opportunities for systematically investigating gene expression  ...  characteristics across various brain regions throughout a series of developmental stages.  ...  We thank Lijun Lian for the critical reading of the manuscript.  ... 
doi:10.1016/j.gpb.2019.03.003 pmid:31655213 pmcid:PMC6943780 fatcat:kqcjfr6cyrff3mtsiltmef35mu

Co-expression Profiling of Autism Genes in the Mouse Brain

Idan Menashe, Pascal Grange, Eric C. Larsen, Sharmila Banerjee-Basu, Partha P. Mitra, Michael Hawrylycz
2013 PLoS Computational Biology  
In conclusion, our study provides a detailed profiling of co-expression patterns of autism genes in the mouse brain, and suggests specific brain regions and new candidate genes that could be involved in  ...  To date, a number of genes have been associated with ASD. However, the temporal and spatial co-expression of these genes in the brain remain unclear.  ...  A major strength of our study is the utilization of the Allen Mouse Brain Atlas [30] [31] [32] [33] which comprises a high-resolution genome-wide exploration of gene expression in the adult mouse brain  ... 
doi:10.1371/journal.pcbi.1003128 pmid:23935468 pmcid:PMC3723491 fatcat:y4hw2ef4mrdf5jab35a4qddkpu

Computational neuroanatomy and co-expression of genes in the adult mouse brain, analysis tools for the Allen Brain Atlas

Pascal Grange, Michael Hawrylycz, Partha P. Mitra
2013 Quantitative Biology  
We expose new methods based on the underlying high-dimensional geometry of voxel space and gene space, and on simulations of the distribution of co-expression networks of a given size.  ...  We apply them to the Allen Atlas of the adult mouse brain, and to the coexpression network of a set of genes related to nicotine addiction retrieved from the NicSNP database.  ...  This research is supported by the NIH-NIDA Grant (1R21DA027644-01, Computational analysis of co-expression networks in the mouse and human brain).  ... 
doi:10.1007/s40484-013-0011-5 fatcat:h6vyvyf2pjhjrdz6y2wttmfjq4

Allen Brain Atlas: an integrated spatio-temporal portal for exploring the central nervous system

Susan M. Sunkin, Lydia Ng, Chris Lau, Tim Dolbeare, Terri L. Gilbert, Carol L. Thompson, Michael Hawrylycz, Chinh Dang
2012 Nucleic Acids Research  
for 3D navigation of anatomy and gene expression, and an interactive reference atlas viewer.  ...  The Allen Brain Atlas (http://www.brain-map.org) provides a unique online public resource integrating extensive gene expression data, connectivity data and neuroanatomical information with powerful search  ...  They also thank the Allen Institute's Web Development and Visualization team consisting of Felix Lee, David Feng and Guangyu Gu for user interface  ... 
doi:10.1093/nar/gks1042 pmid:23193282 pmcid:PMC3531093 fatcat:pzedl5ubjfaaxa6vh5qrwoabgu

Computational neuroanatomy and co-expression of genes in the adult mouse brain, analysis tools for the Allen Brain Atlas [article]

Pascal Grange, Michael Hawrylycz, Partha P. Mitra
2013 arXiv   pre-print
We expose new methods based on the underlying high-dimensional geometry of voxel space and gene space, and on simulations of the distribution of co-expression networks of a given size.  ...  We apply them to the Allen Atlas of the adult mouse brain, and to the co-expression network of a set of genes related to nicotine addiction retrieved from the NicSNP database.  ...  This research is supported by the NIH-NIDA Grant 1R21DA027644-01, Computational analysis of co-expression networks in the mouse and human brain.  ... 
arXiv:1301.1730v1 fatcat:erm3a2c2krgc7f2h4vmugbmonq

Statistical analysis of co-expression properties of sets of genes in the mouse brain [article]

Pascal Grange, Partha P. Mitra
2011 arXiv   pre-print
It is based on graph-theoretic properties of co-expression coefficients between pairs of genes. We apply this method to mouse genes from the Allen Gene Expression Atlas.  ...  We propose a quantitative method to estimate the statistical properties of sets of genes for which expression data are available and co-registered to a reference atlas of the brain.  ...  of co-expression, in order to interpret them in terms of connections [9, 10] . 2 Model and gene-expression data 2.1 Data: the Allen Gene Expression Atlas (AGEA) The Allen Gene Expression Atlas is a high-resolution  ... 
arXiv:1111.6200v2 fatcat:pwo4zk4fhzcczlcjwq3vb6ujca

A multimodal, multidimensional atlas of the C57BL/6J mouse brain

Allan MacKenzie-Graham, Erh-Fang Lee, Ivo D. Dinov, Mihail Bota, David W. Shattuck, Seth Ruffins, Heng Yuan, Fotios Konstantinidis, Alain Pitiot, Yi Ding, Guogang Hu, Russell E. Jacobs (+1 others)
2004 Journal of Anatomy  
We have developed a digital atlas of the adult C57BL/6J mouse brain as a comprehensive framework for storing and accessing the myriad types of information about the mouse brain.  ...  Atlases are an invaluable aid in understanding the impact of such manipulations by providing a standard for comparison.  ...  We also wish to thank the members of the Laboratory of Neuro Imaging.  ... 
doi:10.1111/j.1469-7580.2004.00264.x pmid:15032916 pmcid:PMC1571243 fatcat:sjzdvome2zelte3bc56e3vxwse

Clustering of spatial gene expression patterns in the mouse brain and comparison with classical neuroanatomy

Jason W. Bohland, Hemant Bokil, Sayan D. Pathak, Chang-Kyu Lee, Lydia Ng, Christopher Lau, Chihchau Kuan, Michael Hawrylycz, Partha P. Mitra
2010 Methods  
Spatial gene expression profiles provide a novel means of exploring the structural organization of the brain.  ...  Computational analysis of these patterns is made possible by genome-scale mapping of the C57BL/6J mouse brain in the Allen Brain Atlas.  ...  Description of method Allen Brain Atlas The Allen Brain Atlas (http://mouse.brain-map.org) provides cellular resolution expression profiles for $20,000 genes in the male, 56-day old C57BL/6J mouse brain  ... 
doi:10.1016/j.ymeth.2009.09.001 pmid:19733241 fatcat:dvpsspr4lbfepda7xbbgsaylee

Global analysis of gene expression and projection target correlations in the mouse brain

Ahmed Fakhry, Tao Zeng, Hanchuan Peng, Shuiwang Ji
2015 Brain Informatics  
Here we extended those studies to perform a global, integrative analysis of gene expression and projection target correlations in the mouse brain.  ...  Recent studies have shown that projection targets in the mouse neocortex are correlated with their gene expression patterns.  ...  Open Access This article is distributed under the terms of the Creative Commons Attribution License which permits any use, distribution, and reproduction in any medium, provided the original author(s)  ... 
doi:10.1007/s40708-015-0014-2 pmid:27747484 pmcid:PMC4883149 fatcat:mgjhxeofrvftfflmb7raer4nni

Exploration and visualization of gene expression with neuroanatomy in the adult mouse brain

Christopher Lau, Lydia Ng, Carol Thompson, Sayan Pathak, Leonard Kuan, Allan Jones, Mike Hawrylycz
2008 BMC Bioinformatics  
Results: Brain Explorer enables users to visualize gene expression data from the C57Bl/6J mouse brain in 3D at a resolution of 100 μm 3 , allowing co-display of several experiments as well as 179 reference  ...  This paper describes the implementation and utility of Brain Explorer, a 3D visualization tool for studying in situ hybridization-based (ISH) expression patterns in the Allen Brain Atlas, a genome-wide  ...  The authors also thank John Morris for assistance in formulating the direction of this manuscript.  ... 
doi:10.1186/1471-2105-9-153 pmid:18366675 pmcid:PMC2375125 fatcat:de4ysph2ijfhveeb7qdxg4ma4m

Candidate gene prioritization based on spatially mapped gene expression: an application to XLMR

Rosario M. Piro, Ivan Molineris, Ugo Ala, Paolo Provero, Ferdinando Di Cunto
2010 Computer applications in the biosciences : CABIOS  
Results: Here, we report a large-scale analysis of spatial, i.e. 3D, gene-expression data from an entire organ (the mouse brain) for the purpose of evaluating and ranking positional candidate genes, showing  ...  that the spatial gene-expression patterns can be successfully exploited for the prediction of gene-phenotype associations not only for mouse phenotypes, but also for human central nervous system-related  ...  Conflict of Interest: none declared.  ... 
doi:10.1093/bioinformatics/btq396 pmid:20823330 pmcid:PMC2935433 fatcat:cyck67yslfctnd764b54ali4g4
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