Tissue-specific subnetworks and characteristics of publicly available human protein interaction databases.
Bioinformatics
; 27(17): 2414-21, 2011 Sep 01.
Article
en En
| MEDLINE
| ID: mdl-21798963
ABSTRACT
MOTIVATION Protein-protein interaction (PPI) databases are widely used tools to study cellular pathways and networks; however, there are several databases available that still do not account for cell type-specific differences. Here, we evaluated the characteristics of six interaction databases, incorporated tissue-specific gene expression information and finally, investigated if the most popular proteins of scientific literature are involved in good quality interactions. RESULTS:
We found that the evaluated databases are comparable in terms of node connectivity (i.e. proteins with few interaction partners also have few interaction partners in other databases), but may differ in the identity of interaction partners. We also observed that the incorporation of tissue-specific expression information significantly altered the interaction landscape and finally, we demonstrated that many of the most intensively studied proteins are engaged in interactions associated with low confidence scores. In summary, interaction databases are valuable research tools but may lead to different predictions on interactions or pathways. The accuracy of predictions can be improved by incorporating datasets on organ- and cell type-specific gene expression, and by obtaining additional interaction evidence for the most 'popular' proteins. CONTACT kitano@sbi.jp SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
Texto completo:
1
Bases de datos:
MEDLINE
Asunto principal:
Mapeo de Interacción de Proteínas
/
Bases de Datos de Proteínas
Tipo de estudio:
Prognostic_studies
Límite:
Humans
Idioma:
En
Revista:
Bioinformatics
Asunto de la revista:
INFORMATICA MEDICA
Año:
2011
Tipo del documento:
Article
País de afiliación:
Japón