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Linking gene expression to phenotypes via pathway information
Establishing robust links among gene expression, pathways and phenotypes is critical for understanding diseases and developing treatments. In recent years there have been many efforts to develop the computational means to traverse from genes to gene expression, model pathways and classify phenotypes...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2015
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4404592/ https://www.ncbi.nlm.nih.gov/pubmed/25901272 http://dx.doi.org/10.1186/s13326-015-0013-5 |
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author | Papatheodorou, Irene Oellrich, Anika Smedley, Damian |
author_facet | Papatheodorou, Irene Oellrich, Anika Smedley, Damian |
author_sort | Papatheodorou, Irene |
collection | PubMed |
description | Establishing robust links among gene expression, pathways and phenotypes is critical for understanding diseases and developing treatments. In recent years there have been many efforts to develop the computational means to traverse from genes to gene expression, model pathways and classify phenotypes. Numerous ontologies and other controlled vocabularies have been developed, as well as computational methods to combine and mine these data sets and establish connections. Here we discuss these efforts and identify areas of future work that could lead to a better integration of genes, pathways and phenotypes to provide insights into the mechanisms under which gene mutations affect expression and pathways and how these effects are manifested onto the phenotype. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13326-015-0013-5) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-4404592 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-44045922015-04-22 Linking gene expression to phenotypes via pathway information Papatheodorou, Irene Oellrich, Anika Smedley, Damian J Biomed Semantics Review Establishing robust links among gene expression, pathways and phenotypes is critical for understanding diseases and developing treatments. In recent years there have been many efforts to develop the computational means to traverse from genes to gene expression, model pathways and classify phenotypes. Numerous ontologies and other controlled vocabularies have been developed, as well as computational methods to combine and mine these data sets and establish connections. Here we discuss these efforts and identify areas of future work that could lead to a better integration of genes, pathways and phenotypes to provide insights into the mechanisms under which gene mutations affect expression and pathways and how these effects are manifested onto the phenotype. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13326-015-0013-5) contains supplementary material, which is available to authorized users. BioMed Central 2015-04-11 /pmc/articles/PMC4404592/ /pubmed/25901272 http://dx.doi.org/10.1186/s13326-015-0013-5 Text en © Papatheodorou et al.; licensee BioMed Central. 2015 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Review Papatheodorou, Irene Oellrich, Anika Smedley, Damian Linking gene expression to phenotypes via pathway information |
title | Linking gene expression to phenotypes via pathway information |
title_full | Linking gene expression to phenotypes via pathway information |
title_fullStr | Linking gene expression to phenotypes via pathway information |
title_full_unstemmed | Linking gene expression to phenotypes via pathway information |
title_short | Linking gene expression to phenotypes via pathway information |
title_sort | linking gene expression to phenotypes via pathway information |
topic | Review |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4404592/ https://www.ncbi.nlm.nih.gov/pubmed/25901272 http://dx.doi.org/10.1186/s13326-015-0013-5 |
work_keys_str_mv | AT papatheodorouirene linkinggeneexpressiontophenotypesviapathwayinformation AT oellrichanika linkinggeneexpressiontophenotypesviapathwayinformation AT smedleydamian linkinggeneexpressiontophenotypesviapathwayinformation |