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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Transcriptome-Based Network Analysis Reveals a Spectrum Model of Human Macrophage Activation
Jia Xue,Susanne Schmidt,Jil Sander,Astrid M. Draffehn,Wolfgang Krebs,Inga Quester,Dominic De Nardo,Trupti D. Gohel,Martina Emde,Lisa Schmidleithner,Hariharasudan Ganesan,Andrea Niño-Castro,Michael R. Mallmann,Larisa I. Labzin,Heidi Theis,Michael Kraut,Marc Beyer,Eicke Latz,Eicke Latz,Tom C. Freeman,Thomas Ulas,Joachim L. Schultze +21 more
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Sandra Orchard,Mais G. Ammari,Bruno Aranda,Lionel Breuza,Leonardo Briganti,Fiona Broackes-Carter,Nancy H. Campbell,Gayatri Chavali,Carol Chen,Noemi del-Toro,Margaret Duesbury,Marine Dumousseau,Eugenia Galeota,Ursula Hinz,Marta Iannuccelli,Sruthi Jagannathan,Rafael C. Jimenez,Jyoti Khadake,Astrid Lagreid,Luana Licata,Ruth C. Lovering,Birgit H M Meldal,Anna N. Melidoni,Mila Milagros,Daniele Peluso,Livia Perfetto,Pablo Porras,Arathi Raghunath,Sylvie Ricard-Blum,Bernd Roechert,Andre Stutz,Michael Tognolli,Kim Van Roey,Gianni Cesareni,Henning Hermjakob +34 more
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NetworkAnalyst for statistical, visual and network-based meta-analysis of gene expression data
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References
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Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions
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TL;DR: Comprehensive functional analysis showed that the housekeeping set is substantially larger than previously thought, and is enriched with vital processes such as oxidative phosphorylation, ubiquitin-dependent proteolysis, translation and energy metabolism.
Journal ArticleDOI
Cerebral: a Cytoscape plugin for layout of and interaction with biological networks using subcellular localization annotation.
TL;DR: Cerebral automatically generates a view of the network in the style of traditional pathway diagrams, providing an intuitive interface for the exploration of a biological pathway or system.
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