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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Candidate genes associated with the heritable humoral response to Mycobacterium avium ssp. paratuberculosis in dairy cows have factors in common with gastrointestinal diseases in humans.
TL;DR: The existence of genetic variation for MAP susceptibility in a large data set of dairy cows signifies the potential of breeding programs for reducing MAP susceptibility and the identification of susceptible QTL facilitates greater biological understanding of bovine paratuberculosis and potential therapeutic targets for future investigation.
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Systems integration of innate and adaptive immunity.
Daniel E. Zak,Alan Aderem +1 more
TL;DR: Systems vaccinology is an iterative approach in which mechanistic hypotheses-derived from analysis of clinical studies-are evaluated in model systems, and then used to guide the development of new vaccine strategies.
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Changes in the Composition of the Gut Microbiota and the Blood Transcriptome in Preterm Infants at Less than 29 Weeks Gestation Diagnosed with Bronchopulmonary Dysplasia.
Feargal J. Ryan,Damian P. Drew,Chloe Douglas,Lex E. X. Leong,Max Moldovan,Miriam A. Lynn,Naomi H. Fink,Anastasia Sribnaia,Irmeli A. Penttila,Andrew J McPhee,Carmel T Collins,Maria Makrides,Robert A. Gibson,Geraint B. Rogers,David J. Lynn +14 more
TL;DR: There are significant differences in the gut microbiota of infants born at <29 weeks gestation and subsequently diagnosed with BPD, which are particularly pronounced when infants are stratified by birth mode, and an association between the composition of the microbiota and immune gene expression in blood in early life is identified.
Journal ArticleDOI
CellNetVis: a web tool for visualization of biological networks using force-directed layout constrained by cellular components
Henry Heberle,Marcelo Falsarella Carazzolle,Guilherme P. Telles,Gabriela Vaz Meirelles,Rosane Minghim +4 more
TL;DR: CellNetVis is proposed, a web tool to easily display biological networks in a cell diagram employing a constrained force-directed layout algorithm, and demonstrated to be applicable for dynamic investigation of complex networks over a consistent representation of a cell on the Web, with capabilities not matched elsewhere.
Journal ArticleDOI
Linking indirect effects of cytomegalovirus in transplantation to modulation of monocyte innate immune function.
Pritha Sen,Adrian R. Wilkie,Fei Ji,Yiming Yang,Yiming Yang,Ian J. Taylor,Miguel Velazquez-Palafox,Emilia A. H. Vanni,Jean M. Pesola,Rosio Fernandez,Han Chen,Liza M. Morsett,Erik R. Abels,Mary E. Piper,Rebekah J. Lane,Suzanne E. Hickman,Terry K. Means,Eric S. Rosenberg,Ruslan I. Sadreyev,Bo Li,Bo Li,Donald M. Coen,Jay A. Fishman,Joseph El Khoury +23 more
TL;DR: It is demonstrated that CMV modulates both immunosuppressive and immunostimulatory monocyte phenotypes, explaining in part, its paradoxical “indirect effects” in transplantation.
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