Annotating activation/inhibition relationships to protein-protein interactions using Gene Ontology relations

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Background: Signaling pathways can be reconstructed by identifying 'effect types' (i.e. activation/inhibition) of protein-protein interactions (PPIs). Effect types are composed of 'directions' (i.e. upstream/downstream) and 'signs' (i.e. positive/negative), thereby requiring directions as well as signs of PPIs to predict signaling events from PPI networks. Here, we propose a computational method for systemically annotating effect types to PPIs using relations between functional information of proteins. Results: We used regulates, positively regulates, and negatively regulates relations in Gene Ontology (GO) to predict directions and signs of PPIs. These relations indicate both directions and signs between GO terms so that we can project directions and signs between relevant GO terms to PPIs. Independent test results showed that our method is effective for predicting both directions and signs of PPIs. Moreover, our method outperformed a previous GO-based method that did not consider the relations between GO terms. We annotated effect types to human PPIs and validated several highly confident effect types against literature. The annotated human PPIs are available in Additional file 2 to aid signaling pathway reconstruction and network biology research. Conclusions: We annotated effect types to PPIs by using regulates, positively regulates, and negatively regulates relations in GO. We demonstrated that those relations are effective for predicting not only signs, but also directions of PPIs. The usefulness of those relations suggests their potential applications to other types of interactions such as protein-DNA interactions.
Publisher
BIOMED CENTRAL LTD
Issue Date
2018-04
Language
English
Article Type
Article; Proceedings Paper
Keywords

PATHWAYS; DATABASE; DISEASE; CANCER; UPDATE

Citation

BMC SYSTEMS BIOLOGY, v.12

ISSN
1752-0509
DOI
10.1186/s12918-018-0535-4
URI
http://hdl.handle.net/10203/242280
Appears in Collection
BiS-Journal Papers(저널논문)
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