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Gene ORGANizer: linking genes to the organs they affect

One of the biggest challenges in studying how genes work is understanding their effect on the physiology and anatomy of the body. Existing tools try to address this using indirect features, such as expression levels and biochemical pathways. Here, we present Gene ORGANizer (geneorganizer.huji.ac.il)...

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Detalles Bibliográficos
Autores principales: Gokhman, David, Kelman, Guy, Amartely, Adir, Gershon, Guy, Tsur, Shira, Carmel, Liran
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Oxford University Press 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570240/
https://www.ncbi.nlm.nih.gov/pubmed/28444223
http://dx.doi.org/10.1093/nar/gkx302
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author Gokhman, David
Kelman, Guy
Amartely, Adir
Gershon, Guy
Tsur, Shira
Carmel, Liran
author_facet Gokhman, David
Kelman, Guy
Amartely, Adir
Gershon, Guy
Tsur, Shira
Carmel, Liran
author_sort Gokhman, David
collection PubMed
description One of the biggest challenges in studying how genes work is understanding their effect on the physiology and anatomy of the body. Existing tools try to address this using indirect features, such as expression levels and biochemical pathways. Here, we present Gene ORGANizer (geneorganizer.huji.ac.il), a phenotype-based tool that directly links human genes to the body parts they affect. It is built upon an exhaustive curated database that links >7000 genes to ∼150 anatomical parts using >150 000 gene-organ associations. The tool offers user-friendly platforms to analyze the anatomical effects of individual genes, and identify trends within groups of genes. We demonstrate how Gene ORGANizer can be used to make new discoveries, showing that chromosome X is enriched with genes affecting facial features, that positive selection targets genes with more constrained phenotypic effects, and more. We expect Gene ORGANizer to be useful in a variety of evolutionary, medical and molecular studies aimed at understanding the phenotypic effects of genes.
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spelling pubmed-55702402017-08-29 Gene ORGANizer: linking genes to the organs they affect Gokhman, David Kelman, Guy Amartely, Adir Gershon, Guy Tsur, Shira Carmel, Liran Nucleic Acids Res Web Server Issue One of the biggest challenges in studying how genes work is understanding their effect on the physiology and anatomy of the body. Existing tools try to address this using indirect features, such as expression levels and biochemical pathways. Here, we present Gene ORGANizer (geneorganizer.huji.ac.il), a phenotype-based tool that directly links human genes to the body parts they affect. It is built upon an exhaustive curated database that links >7000 genes to ∼150 anatomical parts using >150 000 gene-organ associations. The tool offers user-friendly platforms to analyze the anatomical effects of individual genes, and identify trends within groups of genes. We demonstrate how Gene ORGANizer can be used to make new discoveries, showing that chromosome X is enriched with genes affecting facial features, that positive selection targets genes with more constrained phenotypic effects, and more. We expect Gene ORGANizer to be useful in a variety of evolutionary, medical and molecular studies aimed at understanding the phenotypic effects of genes. Oxford University Press 2017-07-03 2017-04-21 /pmc/articles/PMC5570240/ /pubmed/28444223 http://dx.doi.org/10.1093/nar/gkx302 Text en © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research. http://creativecommons.org/licenses/by-nc/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
spellingShingle Web Server Issue
Gokhman, David
Kelman, Guy
Amartely, Adir
Gershon, Guy
Tsur, Shira
Carmel, Liran
Gene ORGANizer: linking genes to the organs they affect
title Gene ORGANizer: linking genes to the organs they affect
title_full Gene ORGANizer: linking genes to the organs they affect
title_fullStr Gene ORGANizer: linking genes to the organs they affect
title_full_unstemmed Gene ORGANizer: linking genes to the organs they affect
title_short Gene ORGANizer: linking genes to the organs they affect
title_sort gene organizer: linking genes to the organs they affect
topic Web Server Issue
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5570240/
https://www.ncbi.nlm.nih.gov/pubmed/28444223
http://dx.doi.org/10.1093/nar/gkx302
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