ArticleNucleic acids research2007
A systematic strategy for large-scale analysis of genotype phenotype correlations: identification of candidate genes involved in African trypanosomiasis.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers.
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Who cites it
20 citing papers in PubMed, 60 citations in OpenAlex.
- Article
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- The Taverna workflow suite: designing and executing workflows of Web Services on the desktop, web or in the cloud.Nucleic acids research · 2013Article
- Genetic analysis of the Trichuris muris-induced model of colitis reveals QTL overlap and a novel gene cluster for establishing colonic inflammation.BMC genomics · 2013Article
- QTL/microarray approach using pathway information.Algorithms for molecular biology : AMB · 2012Article
- Genetic and expression analysis of cattle identifies candidate genes in pathways responding to Trypanosoma congolense infection.Proceedings of the National Academy of Sciences of the United States of America · 2011Article
- A comprehensive genetic analysis of candidate genes regulating response to Trypanosoma congolense infection in mice.PLoS neglected tropical diseases · 2010Article
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- myExperiment: a repository and social network for the sharing of bioinformatics workflows.Nucleic acids research · 2010Article
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- Host genetic variation affects resistance to infection with a highly pathogenic H5N1 influenza A virus in mice.Journal of virology · 2009Article
- Structuring and extracting knowledge for the support of hypothesis generation in molecular biology.BMC bioinformatics · 2009Article
- XMPP for cloud computing in bioinformatics supporting discovery and invocation of asynchronous web services.BMC bioinformatics · 2009Article
- Mining biological pathways using WikiPathways web services.PloS one · 2009Article
- Using microarrays to identify positional candidate genes for QTL: the case study of ACTH response in pigs.BMC proceedings · 2009Article
- Methodology capture: discriminating between the "best" and the rest of community practice.BMC bioinformatics · 2008Article
- Performing statistical analyses on quantitative data in Taverna workflows: an example using R and maxdBrowse to identify differentially-expressed genes from microarray data.BMC bioinformatics · 2008Article
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Authors and funding
8 authors at 2 institutions in 1 country.
Funding
Abstract
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/.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.