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Study of gene function based on spatial co-expression in a high-resolution mouse brain atlas
2007
BMC Systems Biology
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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
2016
Brain Structure and Function
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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
2007
Frontiers in Neuroinformatics
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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
2021
Microscopy Today
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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
2019
Genomics, Proteomics & Bioinformatics
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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
2013
PLoS Computational Biology
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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
2013
Quantitative Biology
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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
2012
Nucleic Acids Research
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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]
2013
arXiv
pre-print
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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]
2011
arXiv
pre-print
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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
2004
Journal of Anatomy
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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
2010
Methods
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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
2015
Brain Informatics
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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
2008
BMC Bioinformatics
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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
2010
Computer applications in the biosciences : CABIOS
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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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