Localizing genes to cerebellar layers by classifying ISH images.

Gene expression controls how the brain develops and functions. Understanding control processes in the brain is particularly hard since they involve numerous types of neurons and glia, and very little is known about which genes are expressed in which cells and brain layers. Here we describe an approa...

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Autores principales:	Lior Kirsch, Noa Liscovitch, Gal Chechik
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Biology (General) QH301-705.5
Acceso en línea:	https://doaj.org/article/430ffb1a5cd84763853b4348ca99954d
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spelling	oai:doaj.org-article:430ffb1a5cd84763853b4348ca99954d2021-11-18T05:52:38ZLocalizing genes to cerebellar layers by classifying ISH images.1553-734X1553-735810.1371/journal.pcbi.1002790https://doaj.org/article/430ffb1a5cd84763853b4348ca99954d2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23284274/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Gene expression controls how the brain develops and functions. Understanding control processes in the brain is particularly hard since they involve numerous types of neurons and glia, and very little is known about which genes are expressed in which cells and brain layers. Here we describe an approach to detect genes whose expression is primarily localized to a specific brain layer and apply it to the mouse cerebellum. We learn typical spatial patterns of expression from a few markers that are known to be localized to specific layers, and use these patterns to predict localization for new genes. We analyze images of in-situ hybridization (ISH) experiments, which we represent using histograms of local binary patterns (LBP) and train image classifiers and gene classifiers for four layers of the cerebellum: the Purkinje, granular, molecular and white matter layer. On held-out data, the layer classifiers achieve accuracy above 94% (AUC) by representing each image at multiple scales and by combining multiple image scores into a single gene-level decision. When applied to the full mouse genome, the classifiers predict specific layer localization for hundreds of new genes in the Purkinje and granular layers. Many genes localized to the Purkinje layer are likely to be expressed in astrocytes, and many others are involved in lipid metabolism, possibly due to the unusual size of Purkinje cells.Lior KirschNoa LiscovitchGal ChechikPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 8, Iss 12, p e1002790 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Lior Kirsch Noa Liscovitch Gal Chechik Localizing genes to cerebellar layers by classifying ISH images.
description	Gene expression controls how the brain develops and functions. Understanding control processes in the brain is particularly hard since they involve numerous types of neurons and glia, and very little is known about which genes are expressed in which cells and brain layers. Here we describe an approach to detect genes whose expression is primarily localized to a specific brain layer and apply it to the mouse cerebellum. We learn typical spatial patterns of expression from a few markers that are known to be localized to specific layers, and use these patterns to predict localization for new genes. We analyze images of in-situ hybridization (ISH) experiments, which we represent using histograms of local binary patterns (LBP) and train image classifiers and gene classifiers for four layers of the cerebellum: the Purkinje, granular, molecular and white matter layer. On held-out data, the layer classifiers achieve accuracy above 94% (AUC) by representing each image at multiple scales and by combining multiple image scores into a single gene-level decision. When applied to the full mouse genome, the classifiers predict specific layer localization for hundreds of new genes in the Purkinje and granular layers. Many genes localized to the Purkinje layer are likely to be expressed in astrocytes, and many others are involved in lipid metabolism, possibly due to the unusual size of Purkinje cells.
format	article
author	Lior Kirsch Noa Liscovitch Gal Chechik
author_facet	Lior Kirsch Noa Liscovitch Gal Chechik
author_sort	Lior Kirsch
title	Localizing genes to cerebellar layers by classifying ISH images.
title_short	Localizing genes to cerebellar layers by classifying ISH images.
title_full	Localizing genes to cerebellar layers by classifying ISH images.
title_fullStr	Localizing genes to cerebellar layers by classifying ISH images.
title_full_unstemmed	Localizing genes to cerebellar layers by classifying ISH images.
title_sort	localizing genes to cerebellar layers by classifying ish images.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/430ffb1a5cd84763853b4348ca99954d
work_keys_str_mv	AT liorkirsch localizinggenestocerebellarlayersbyclassifyingishimages AT noaliscovitch localizinggenestocerebellarlayersbyclassifyingishimages AT galchechik localizinggenestocerebellarlayersbyclassifyingishimages
_version_	1718424722061918208

Localizing genes to cerebellar layers by classifying ISH images.

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