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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Combining LSTM Network Model and Wavelet Transform for Predicting Self-interacting Proteins
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TL;DR: Zhang et al. as mentioned in this paper developed a platform named ADEIP (http://gb.whu.edu.cn/ADEIP or http://geneyun.net/adeIP), integrating the age-dependent gene expression and immune profiles across tissues.
References
More filters
Journal ArticleDOI
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Journal ArticleDOI
Cytoscape 2.8
TL;DR: Version 2.8 introduces two powerful new features—Custom Node Graphics and Attribute Equations—which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities.
Journal ArticleDOI
A cytokine-mediated link between innate immunity, inflammation, and cancer
Wan-Wan Lin,Michael Karin +1 more
TL;DR: An overview of the current understanding of the role of inflammation-induced cytokines in tumor initiation, promotion, and progression is provided.
Journal ArticleDOI
Innate immunity and intestinal microbiota in the development of Type 1 diabetes
Li Wen,Ruth E. Ley,Ruth E. Ley,Pavel Volchkov,Peter B. Stranges,Lia Avanesyan,Austin C. Stonebraker,Changyun Hu,F. Susan Wong,Gregory L. Szot,Jeffrey A. Bluestone,Jeffrey I. Gordon,Alexander V. Chervonsky +12 more
TL;DR: It is found that MyD88 deficiency changes the composition of the distal gut microbiota, and that exposure to the microbiota of specific pathogen-free MyD 88-negative NOD donors attenuates T1D in germ-free NOD recipients.
Journal ArticleDOI
The IntAct molecular interaction database in 2012
Samuel Kerrien,Bruno Aranda,Lionel Breuza,Alan Bridge,Fiona Broackes-Carter,Carol Chen,Margaret Duesbury,Marine Dumousseau,M Feuermann,Ursula Hinz,Christine Jandrasits,Rafael C. Jimenez,Jyoti Khadake,Usha Mahadevan,Patrick Masson,Ivo Pedruzzi,Eric Pfeiffenberger,Pablo Porras,Arathi Raghunath,Bernd Roechert,Sandra Orchard,Henning Hermjakob +21 more
TL;DR: Two levels of curation are now available within the IntAct database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported.
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