A systematic strategy for large-scale analysis of genotype-phenotype correlations: identification of candidate genes involved in African trypanosomiasis
It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing these large datasets and also represent a framework for the re-use and the explicit decl...
| Main Authors: | , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
Oxford University Press
2007
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/1869 |
| _version_ | 1855543565550092288 |
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| author | Fisher, P. Hedeler, C. Wolstencroft, K. Hulme, H. Noyes, H. Kemp, Stephen J. Stevens, R. Brass, A. |
| author_browse | Brass, A. Fisher, P. Hedeler, C. Hulme, H. Kemp, Stephen J. Noyes, H. Stevens, R. Wolstencroft, K. |
| author_facet | Fisher, P. Hedeler, C. Wolstencroft, K. Hulme, H. Noyes, H. Kemp, Stephen J. Stevens, R. Brass, A. |
| author_sort | Fisher, P. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing these large datasets and also represent a framework for the re-use and the explicit declaration of experimental methods. In this article, we highlight the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes. We show how automated approaches provide a systematic means to investigate genotype–phenotype correlations. This methodology was applied to a use case of resistance to African trypanosomiasis in the mouse. Pathways represented in the results identified Daxx as one of the candidate genes within the Tir1 QTL region. Subsequent re-sequencing in Daxx identified a deletion of an amino acid, identified in susceptible mouse strains, in the Daxx–p53 protein-binding region. This supports recent experimental evidence that apoptosis could be playing a role in the trypanosomiasis resistance phenotype. Workflows developed in this investigation, including a guide to loading and executing them with example data, are available at http://workflows.mygrid.org.uk/repository/myGrid/PaulFisher/. |
| format | Journal Article |
| id | CGSpace1869 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2007 |
| publishDateRange | 2007 |
| publishDateSort | 2007 |
| publisher | Oxford University Press |
| publisherStr | Oxford University Press |
| record_format | dspace |
| spelling | CGSpace18692023-12-08T19:36:04Z A systematic strategy for large-scale analysis of genotype-phenotype correlations: identification of candidate genes involved in African trypanosomiasis Fisher, P. Hedeler, C. Wolstencroft, K. Hulme, H. Noyes, H. Kemp, Stephen J. Stevens, R. Brass, A. trypanosomiasis genetics It is increasingly common to combine Microarray and Quantitative Trait Loci data to aid the search for candidate genes responsible for phenotypic variation. Workflows provide a means of systematically processing these large datasets and also represent a framework for the re-use and the explicit declaration of experimental methods. In this article, we highlight the issues facing the manual analysis of microarray and QTL data for the discovery of candidate genes underlying complex phenotypes. We show how automated approaches provide a systematic means to investigate genotype–phenotype correlations. This methodology was applied to a use case of resistance to African trypanosomiasis in the mouse. Pathways represented in the results identified Daxx as one of the candidate genes within the Tir1 QTL region. Subsequent re-sequencing in Daxx identified a deletion of an amino acid, identified in susceptible mouse strains, in the Daxx–p53 protein-binding region. This supports recent experimental evidence that apoptosis could be playing a role in the trypanosomiasis resistance phenotype. Workflows developed in this investigation, including a guide to loading and executing them with example data, are available at http://workflows.mygrid.org.uk/repository/myGrid/PaulFisher/. 2007-08 2010-06-13T16:08:24Z 2010-06-13T16:08:24Z Journal Article https://hdl.handle.net/10568/1869 en Open Access Oxford University Press Fisher, P.; Hedeler, C.; Wolstencroft, K.; Hulme, H.; Noyes, H.; Kemp, S.; Stevens, R.; Brass, A. 2007. A systematic strategy for large-scale analysis of genotype-phenotype correlations: identification of candidate genes involved in African trypanosomiasis. Nucleic Acids Research 35(16):5625-5633. |
| spellingShingle | trypanosomiasis genetics Fisher, P. Hedeler, C. Wolstencroft, K. Hulme, H. Noyes, H. Kemp, Stephen J. Stevens, R. Brass, A. A systematic strategy for large-scale analysis of genotype-phenotype correlations: identification of candidate genes involved in African trypanosomiasis |
| title | A systematic strategy for large-scale analysis of genotype-phenotype correlations: identification of candidate genes involved in African trypanosomiasis |
| title_full | A systematic strategy for large-scale analysis of genotype-phenotype correlations: identification of candidate genes involved in African trypanosomiasis |
| title_fullStr | A systematic strategy for large-scale analysis of genotype-phenotype correlations: identification of candidate genes involved in African trypanosomiasis |
| title_full_unstemmed | A systematic strategy for large-scale analysis of genotype-phenotype correlations: identification of candidate genes involved in African trypanosomiasis |
| title_short | A systematic strategy for large-scale analysis of genotype-phenotype correlations: identification of candidate genes involved in African trypanosomiasis |
| title_sort | systematic strategy for large scale analysis of genotype phenotype correlations identification of candidate genes involved in african trypanosomiasis |
| topic | trypanosomiasis genetics |
| url | https://hdl.handle.net/10568/1869 |
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