InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation
Karin Breuer,Amir Foroushani,Matthew R. Laird,Carol Chen,Anastasia Sribnaia,Raymond Lo,Geoffrey L. Winsor,Robert E. W. Hancock,Fiona S. L. Brinkman,David J. Lynn +9 more
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TLDR
The recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism, and a range of improvements to the integrated bioinformatics solutions are reported.Abstract:
InnateDB (http://www.innatedb.com) is an integrated analysis platform that has been specifically designed to facilitate systems-level analyses of mammalian innate immunity networks, pathways and genes. In this article, we provide details of recent updates and improvements to the database. InnateDB now contains >196 000 human, mouse and bovine experimentally validated molecular interactions and 3000 pathway annotations of relevance to all mammalian cellular systems (i.e. not just immune relevant pathways and interactions). In addition, the InnateDB team has, to date, manually curated in excess of 18 000 molecular interactions of relevance to innate immunity, providing unprecedented insight into innate immunity networks, pathways and their component molecules. More recently, InnateDB has also initiated the curation of allergy- and asthma-related interactions. Furthermore, we report a range of improvements to our integrated bioinformatics solutions including web service access to InnateDB interaction data using Proteomics Standards Initiative Common Query Interface, enhanced Gene Ontology analysis for innate immunity, and the availability of new network visualizations tools. Finally, the recent integration of bovine data makes InnateDB the first integrated network analysis platform for this agriculturally important model organism.read more
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Evolution of the highly networked deubiquitinating enzymes USP4, USP15, and USP11
Caitlyn Vlasschaert,Caitlyn Vlasschaert,Xuhua Xia,Josée Coulombe,Douglas A. Gray,Douglas A. Gray +5 more
TL;DR: The analyses indicate that USP4 and USP15 arose from whole genome duplication prior to the emergence of jawed vertebrates, and it is confirmed that viability is contingent on a functional copy of USP5 or USP6, while USP11 was generated later in vertebrate evolution by small-scale duplication of the USP 4-encoding region.
Journal ArticleDOI
Reconstruction and Application of Protein-Protein Interaction Network.
TL;DR: This work systematically reviewed the development of PIN in the past fifteen years, with respect to its reconstruction and application of function annotation, subsystem investigation, evolution analysis, hub protein analysis, and regulation mechanism analysis.
Journal ArticleDOI
Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis)
Daniela Iamartino,Ezequiel L. Nicolazzi,Curtis P. Van Tassell,James M. Reecy,Eric R. Fritz-Waters,James E. Koltes,Stefano Biffani,Tad S. Sonstegard,Steven G. Schroeder,Paolo Ajmone-Marsan,Riccardo Negrini,R. Pasquariello,Paola Ramelli,A. Coletta,José Fernando Garcia,Ahmad Ali,Luigi Ramunno,Gianfranco Cosenza,Denise Aparecida Andrade de Oliveira,Marcela Gonçalves Drummond,Eduardo Bastianetto,Alessandro Davassi,Ali Pirani,Fiona Brew,John L. Williams +24 more
TL;DR: The 90K buffalo SNP chip described here is suitable for the analysis of the genomes of river buffalo breeds, and could be used for genetic diversity studies and potentially as a starting point for genome-assisted selection programmes.
Journal ArticleDOI
Merging and scoring molecular interactions utilising existing community standards: tools, use-cases and a case study
Jose M. Villaveces,Rafael C. Jimenez,Pablo Porras,Noemi del-Toro,Margaret Duesbury,Marine Dumousseau,Sandra Orchard,H. Choi,Peipei Ping,Nobel C. Zong,Manor Askenazi,Bianca Habermann,Henning Hermjakob +12 more
TL;DR: This manuscript introduces both a merging algorithm and a scoring system for molecular interactions based on the proteomics standard initiative–molecular interaction standards and provides community access to the tool suite.
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Lysosome-Dependent Activation of Human Dendritic Cells by the Vaccine Adjuvant QS-21.
Iain Welsby,Sophie Detienne,Francisca N'Kuli,Séverine Thomas,Sandrine Wouters,Viviane Bechtold,Dominique De Wit,Romain Gineste,Thomas Reinheckel,Abdelatif Elouahabi,Pierre J. Courtoy,Arnaud M. Didierlaurent,Stanislas Goriely +12 more
TL;DR: It is reported that QS-21 directly activated human monocyte-derived dendritic cells (moDCs) and promoted a pro-inflammatory transcriptional program in vivo and provides new insights into the pathways involved in the direct activation of antigen-presenting cells by a clinically relevant Qs-21 formulation.
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