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Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain
Allen Brain Atlas (ABA) provides a valuable resource of spatial/temporal gene expressions in mammalian brains. Despite rich information extracted from this database, current analyses suffer from several limitations. First, most studies are either gene-centric or region-centric, thus are inadequate t...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Nature Publishing Group
2016
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4726224/ https://www.ncbi.nlm.nih.gov/pubmed/26786896 http://dx.doi.org/10.1038/srep19274 |
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author | Chou, Shen-Ju Wang, Chindi Sintupisut, Nardnisa Niou, Zhen-Xian Lin, Chih-Hsu Li, Ker-Chau Yeang, Chen-Hsiang |
author_facet | Chou, Shen-Ju Wang, Chindi Sintupisut, Nardnisa Niou, Zhen-Xian Lin, Chih-Hsu Li, Ker-Chau Yeang, Chen-Hsiang |
author_sort | Chou, Shen-Ju |
collection | PubMed |
description | Allen Brain Atlas (ABA) provides a valuable resource of spatial/temporal gene expressions in mammalian brains. Despite rich information extracted from this database, current analyses suffer from several limitations. First, most studies are either gene-centric or region-centric, thus are inadequate to capture the superposition of multiple spatial-temporal patterns. Second, standard tools of expression analysis such as matrix factorization can capture those patterns but do not explicitly incorporate spatial dependency. To overcome those limitations, we proposed a computational method to detect recurrent patterns in the spatial-temporal gene expression data of developing mouse brains. We demonstrated that regional distinction in brain development could be revealed by localized gene expression patterns. The patterns expressed in the forebrain, medullary and pontomedullary, and basal ganglia are enriched with genes involved in forebrain development, locomotory behavior, and dopamine metabolism respectively. In addition, the timing of global gene expression patterns reflects the general trends of molecular events in mouse brain development. Furthermore, we validated functional implications of the inferred patterns by showing genes sharing similar spatial-temporal expression patterns with Lhx2 exhibited differential expression in the embryonic forebrains of Lhx2 mutant mice. These analysis outcomes confirm the utility of recurrent expression patterns in studying brain development. |
format | Online Article Text |
id | pubmed-4726224 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2016 |
publisher | Nature Publishing Group |
record_format | MEDLINE/PubMed |
spelling | pubmed-47262242016-01-27 Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain Chou, Shen-Ju Wang, Chindi Sintupisut, Nardnisa Niou, Zhen-Xian Lin, Chih-Hsu Li, Ker-Chau Yeang, Chen-Hsiang Sci Rep Article Allen Brain Atlas (ABA) provides a valuable resource of spatial/temporal gene expressions in mammalian brains. Despite rich information extracted from this database, current analyses suffer from several limitations. First, most studies are either gene-centric or region-centric, thus are inadequate to capture the superposition of multiple spatial-temporal patterns. Second, standard tools of expression analysis such as matrix factorization can capture those patterns but do not explicitly incorporate spatial dependency. To overcome those limitations, we proposed a computational method to detect recurrent patterns in the spatial-temporal gene expression data of developing mouse brains. We demonstrated that regional distinction in brain development could be revealed by localized gene expression patterns. The patterns expressed in the forebrain, medullary and pontomedullary, and basal ganglia are enriched with genes involved in forebrain development, locomotory behavior, and dopamine metabolism respectively. In addition, the timing of global gene expression patterns reflects the general trends of molecular events in mouse brain development. Furthermore, we validated functional implications of the inferred patterns by showing genes sharing similar spatial-temporal expression patterns with Lhx2 exhibited differential expression in the embryonic forebrains of Lhx2 mutant mice. These analysis outcomes confirm the utility of recurrent expression patterns in studying brain development. Nature Publishing Group 2016-01-20 /pmc/articles/PMC4726224/ /pubmed/26786896 http://dx.doi.org/10.1038/srep19274 Text en Copyright © 2016, Macmillan Publishers Limited http://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons license, users will need to obtain permission from the license holder to reproduce the material. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ |
spellingShingle | Article Chou, Shen-Ju Wang, Chindi Sintupisut, Nardnisa Niou, Zhen-Xian Lin, Chih-Hsu Li, Ker-Chau Yeang, Chen-Hsiang Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain |
title | Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain |
title_full | Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain |
title_fullStr | Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain |
title_full_unstemmed | Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain |
title_short | Analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain |
title_sort | analysis of spatial-temporal gene expression patterns reveals dynamics and regionalization in developing mouse brain |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4726224/ https://www.ncbi.nlm.nih.gov/pubmed/26786896 http://dx.doi.org/10.1038/srep19274 |
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