Prioritising candidate genes causing QTL using hierarchical orthologous groups
| Autor: | Christophe Dessimoz, Alex Warwick Vesztrocy, Henning Redestig |
|---|---|
| Jazyk: | angličtina |
| Rok vydání: | 2018 |
| Předmět: |
0106 biological sciences
0301 basic medicine Statistics and Probability Candidate gene Arabidopsis/genetics Genomics Molecular Sequence Annotation Oryza/genetics Quantitative Trait Loci Software Arabidopsis Eccb 2018: European Conference on Computational Biology Proceedings Computational biology Biology Quantitative trait locus 01 natural sciences Biochemistry 03 medical and health sciences Molecular Biology Gene food and beverages Oryza Phenotypic trait Computer Science Applications Computational Mathematics 030104 developmental biology Genes Computational Theory and Mathematics Trait Identification (biology) UniProt 010606 plant biology & botany |
| Zdroj: | Bioinformatics, vol. 34, no. 17, pp. i612-i619 Bioinformatics |
| Popis: | Motivation: A key goal in plant biotechnology applications is the identification of genes associated to particular phenotypic traits (for example: yield, fruit size, root length). Quantitative Trait Loci (QTL) studies identify genomic regions associated with a trait of interest. However, to infer potential causal genes in these regions, each of which can contain hundreds of genes, these data are usually intersected with prior functional knowledge of the genes. This process is however laborious, particularly if the experiment is performed in a non-model species, and the statistical significance of the inferred candidates is typically unknown. Results: This paper introduces QTLSearch, a method and software tool to search for candidate causal genes in QTL studies by combining Gene Ontology annotations across many species, leveraging hierarchical orthologous groups. The usefulness of this approach is demonstrated by re-analysing two metabolic QTL studies: one in Arabidopsis thaliana, the other in Oryza sativa subsp. indica. Even after controlling for statistical significance, QTLSearch inferred potential causal genes for more QTL than BLAST-based functional propagation against UniProtKB/Swiss-Prot, and for more QTL than in the original studies. Availability and implementation: QTLSearch is distributed under the LGPLv3 license. It is available to install from the Python Package Index (as qtlsearch), with the source available from https://bitbucket.org/alex-warwickvesztrocy/qtlsearch. Supplementary information: Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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