An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent. Keywords: Protein function prediction, Disease gene prioritizationpublishedVersio

Function of the alpha1B1 subunit of Na +, K + ATPase during zebrafish heart development

Die Zebrafischmutation heart and mind (had), welche die alpha1B1-Untereinheit der Na+,K+ ATPase betrifft, verzögert die Streckung des Herzschlauches und führt zu weiteren Entwicklungsanomalien, die an andere Zellpolaritätsmutanten wie nagie oko (nok) und heart and soul (has) erinnern. In dieser Arbeit habe ich die Funktion und Regulation von Had/Na+,K+ ATPase während der Herzmorphogenese des Zebrafisches und seine möglichen Interaktionen mit Has/Prkci und Nok/Mpp5 untersucht. In konnte nachweisen, dass genetische Interaktionen zwischen had und nok in der Aufrechterhaltung von Zonula-Occludens-1-(ZO-1)-positiven Adhäsionsbändern Adhäsionsbändern in myokardialen Zellen während der Herzentwicklung nachweisen. Meine Ergebnisse deuten darauf hin, dass die Interaktion zwischen Nok/Mpp5 und Had/Na+,K+ ATPase zur Aufrechterhaltung der myokardialen ZO-1-Adhäsionsbändern die Funktion der Na-Pumpe erfordert und dass die korrekte Ionengradienten zur Aufrechterhaltung der myokardialen Integrität beiträgt. Meine Ergebnisse zeigen eine Phosphorylierung des N-terminalen Endes von Had/ Na+,K+ ATPase durch PKCs. PKCs wurden bereits mit der Regulation der Na-Pumpen-Funktion durch Phosphorylierung von N-terminalen Resten in Verbindung gebracht. Meine Ergebnisse legen die Möglichkeit nahe, dass dieser Mechanismus im Zebrafisch konserviert ist. Die Analyse der subzelluläre Lokalisation einer Phosphorylierungs-defizienten Form von Had/Na+,K+ ATPase legt nahe, dass während Herzschlauch-elongation die Had/Na+,K+ ATPase-Aktivität an der Zellmembran durch die Phosphorylierung an einer amino-terminalen Amino-säure reguliert wird. Frühere Studien legen nahe, dass die Herzmorphogenese durch direkte Phosphorylierung von Has/Prkci-Zielen gesteuert wird. Die Identifikation von Has/Prkci-Phosphorylierungs-Zielen könnte dazu beitragen, Herzmorphogenese besser zu verstehen. Aus diesem Grund wurde ein chemisch-genetischer Ansatz entwickelt, um direkte Phosphorylierungs-Ziele von Has/Prkci zu identifizieren.The zebrafish heart and mind (had) mutation which disrupts the alpha1B1 subunit of Na+,K+ ATPase causes heart tube elongation defects and other developmental abnormalities that are reminiscent of several epithelial cell polarity mutants including nagie oko (nok) and heart and soul (has). In this work, I investigated the function and regulatory mechanisms of Had/Na+,K+ ATPase during zebrafish cardiac morphogenesis, as well as its´ possible interactions with Has/Prkci and Nok/Mpp5. In this study, I demonstrate genetic interactions between had and nok in maintaining Zonula occludens-1 (ZO-1) positive junction belts within myocardial cells during heart development. My results strongly suggest that the interaction between Nok/Mpp5 and Had/Na+,K+ ATPase in the maintenance of myocardial ZO-1 junction belts requires the Na pump function and that the correct ionic balance contributes to the maintenance of myocardial integrity. My results show phosphorylation of the N-terminal intracellular tail of Had/Na+,K+ ATPase by PKCs. PKCs have previously been implicated in the regulation of the Na pump function via phosphorylation of N-terminal residues. Therefore, my results raise the possibility that this mechanism is conserved in the zebrafish embryo. The analysis of the subcellular distribution of a phosphorylation-deficient form of Had/Na+,K+ ATPase suggests that, during heart tube elongation, Had/Na+,K+ ATPase activity is regulated at the membrane via phosphorylation at an amino-terminal site. Previous studies suggest that heart morphogenesis is driven via direct phosphorylation of Has/Prkci targets. Therefore, identification of Has/Prkci phosphorylation targets would contribute to better understand cardiac morphogenesis. For this purpose, a chemical genetic approach was designed to identify Has/Prcki direct phosphorylation targets

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

BackgroundA major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging.ResultsWe conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2.ConclusionsThe top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent

An expanded evaluation of protein function prediction methods shows an improvement in accuracy

Background: A major bottleneck in our understanding of the molecular underpinnings of life is the assignment of function to proteins. While molecular experiments provide the most reliable annotation of proteins, their relatively low throughput and restricted purview have led to an increasing role for computational function prediction. However, assessing methods for protein function prediction and tracking progress in the field remain challenging. Results: We conducted the second critical assessment of functional annotation (CAFA), a timed challenge to assess computational methods that automatically assign protein function. We evaluated 126 methods from 56 research groups for their ability to predict biological functions using Gene Ontology and gene-disease associations using Human Phenotype Ontology on a set of 3681 proteins from 18 species. CAFA2 featured expanded analysis compared with CAFA1, with regards to data set size, variety, and assessment metrics. To review progress in the field, the analysis compared the best methods from CAFA1 to those of CAFA2. Conclusions: The top-performing methods in CAFA2 outperformed those from CAFA1. This increased accuracy can be attributed to a combination of the growing number of experimental annotations and improved methods for function prediction. The assessment also revealed that the definition of top-performing algorithms is ontology specific, that different performance metrics can be used to probe the nature of accurate predictions, and the relative diversity of predictions in the biological process and human phenotype ontologies. While there was methodological improvement between CAFA1 and CAFA2, the interpretation of results and usefulness of individual methods remain context-dependent.Medicine, Faculty ofScience, Faculty ofOther UBCNon UBCPsychiatry, Department ofReviewedFacult

Additional file 1 of An expanded evaluation of protein function prediction methods shows an improvement in accuracy

A document containing a subset of CAFA2 analyses that are equivalent to those provided about the CAFA1 experiment in the CAFA1 supplement. (PDF 11100 kb