Predicting subcellular localization via protein motif co-occurrence.
Genome Res
; 14(10A): 1957-66, 2004 Oct.
Article
em En
| MEDLINE
| ID: mdl-15466294
ABSTRACT
The prediction of subcellular localization of proteins from their primary sequence is a challenging problem in bioinformatics. We have created a Bayesian network localization predictor called PSLT that is based on the combinatorial presence of InterPro motifs and specific membrane domains in human proteins. This probabilistic framework generates a likelihood of localization to all organelles and allows to predict multicompartmental proteins. When used to predict on nine compartments, PSLT achieves an accuracy of 78% as estimated by using a 10-fold cross-validation test and a coverage of 74%. When used to predict the localization of proteins from other closely related species, it achieves a prediction accuracy and a coverage >80%. We compared the localization predictions of PSLT to those determined through GFP-tagging and microscopy for a group of human proteins. We found two general classes of proteins that are mislocalized by the GFP-tagging strategy but are correctly localized by PSLT. This suggests that PSLT can be used in combination with experimental approaches for localization to identify proteins for which additional experimental validation is required. We used our predictor to annotate all 9793 human proteins from SWISS-PROT release 41.25, 16% of which are predicted by PSLT to be present in more than one compartment.
Texto completo:
1
Base de dados:
MEDLINE
Assunto principal:
Frações Subcelulares
/
Proteínas
Tipo de estudo:
Prognostic_studies
/
Risk_factors_studies
Limite:
Humans
Idioma:
En
Revista:
Genome Res
Assunto da revista:
BIOLOGIA MOLECULAR
/
GENETICA
Ano de publicação:
2004
Tipo de documento:
Article
País de afiliação:
Canadá