Application of comparative biology in GO functional annotation: the mouse model - PubMed (original) (raw)

Application of comparative biology in GO functional annotation: the mouse model

Harold J Drabkin et al. Mamm Genome. 2015 Oct.

Abstract

The Gene Ontology (GO) is an important component of modern biological knowledge representation with great utility for computational analysis of genomic and genetic data. The Gene Ontology Consortium (GOC) consists of a large team of contributors including curation teams from most model organism database groups as well as curation teams focused on representation of data relevant to specific human diseases. Key to the generation of consistent and comprehensive annotations is the development and use of shared standards and measures of curation quality. The GOC engages all contributors to work to a defined standard of curation that is presented here in the context of annotation of genes in the laboratory mouse. Comprehensive understanding of the origin, epistemology, and coverage of GO annotations is essential for most effective use of GO resources. Here the application of comparative approaches to capturing functional data in the mouse system is described.

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Figures

Fig. 1

Fig. 1

Importing mouse annotations from rat or human genes based on orthology to mouse genes. Each specific load is assigned a specific MGD reference. Since the evidence code is assertion by orthology as determined by MGD, the provider of the annotations is MGD. Annotations are obtained from the designated authorities for GO annotation for human (GOA) or rat (RGD) genes

Fig. 2

Fig. 2

Exporting mouse annotations to non-mouse genes based on orthology. The orthologous non-mouse gene becomes the gene that is annotated by an experimental method described in the publication. The bottom two panels depict the non-mouse annotation at either the GOC site (Amigo browser) or GOA (QuickGO)

Fig. 3

Fig. 3

The PAINT tool overlays experimental GO annotations onto externally constructed Panther phylogenetic trees and allows curators to remove any inappropriate or misplaced sequences before propagating annotations. When needed, new annotations can be made which will be included in PAINT once they have been added to the GO Consortium annotation database. The curator can then determine which annotations represent ancestral functions which should be propagated to an ancestral sequence node. PAINT automatically propagates GO terms from the ancestor node to all descendant sequences that are not already annotated to that term experimentally, except where the curator blocks propagation due to divergence in function. The annotations are exported from PAINT and incorporated into the GO Consortium annotation database

Fig. 4

Fig. 4

Complex query for mouse genes located on chromosome 3 that are annotated to protein tyrosine kinase activity and are associated with diabetes

Fig. 5

Fig. 5

Complex GXD query for mouse genes annotated to protein tyrosine kinase activity and are expressed in Tyler Stages 17–19 metanephric mesenchyme

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