Prediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining
KAUST DepartmentBio-Ontology Research Group (BORG)
Computational Bioscience Research Center (CBRC)
Computer Science Program
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
Permanent link to this recordhttp://hdl.handle.net/10754/617797
MetadataShow full item record
AbstractThe widening gap between known proteins and their functions has encouraged the development of methods to automatically infer annotations. Automatic functional annotation of proteins is expected to meet the conflicting requirements of maximizing annotation coverage, while minimizing erroneous functional assignments. This trade-off imposes a great challenge in designing intelligent systems to tackle the problem of automatic protein annotation. In this work, we present a system that utilizes rule mining techniques to predict metabolic pathways in prokaryotes. The resulting knowledge represents predictive models that assign pathway involvement to UniProtKB entries. We carried out an evaluation study of our system performance using cross-validation technique. We found that it achieved very promising results in pathway identification with an F1-measure of 0.982 and an AUC of 0.987. Our prediction models were then successfully applied to 6.2 million UniProtKB/TrEMBL reference proteome entries of prokaryotes. As a result, 663,724 entries were covered, where 436,510 of them lacked any previous pathway annotations.
CitationPrediction of Metabolic Pathway Involvement in Prokaryotic UniProtKB Data by Association Rule Mining 2016, 11 (7):e0158896 PLOS ONE
SponsorsIB, RH and VS were supported by funding provided by the King Abdullah University of Science and Technology.
PublisherPublic Library of Science (PLoS)
- Rule Mining Techniques to Predict Prokaryotic Metabolic Pathways.
- Authors: Saidi R, Boudellioua I, Martin MJ, Solovyev V
- Issue date: 2017
- Mining GO annotations for improving annotation consistency.
- Authors: Faria D, Schlicker A, Pesquita C, Bastos H, Ferreira AE, Albrecht M, Falcão AO
- Issue date: 2012
- UniProt: the universal protein knowledgebase in 2021.
- Authors: UniProt Consortium.
- Issue date: 2021 Jan 8
- Annotation enrichment analysis: an alternative method for evaluating the functional properties of gene sets.
- Authors: Glass K, Girvan M
- Issue date: 2014 Feb 26
- Integrating protein-protein interactions and text mining for protein function prediction.
- Authors: Jaeger S, Gaudan S, Leser U, Rebholz-Schuhmann D
- Issue date: 2008 Jul 22