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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Neutrophil recruitment and function in endometriosis patients and a syngeneic murine model
Lindsey K. Symons,Jessica E. Miller,Kathrin Tyryshkin,Stephany P. Monsanto,Ryan Marks,Harshavardhan Lingegowda,Kaitlin Vanderbeck,Timothy Childs,Steven L. Young,Bruce A. Lessey,Madhuri Koti,Chandrakant Tayade +11 more
TL;DR: It is demonstrated that neutrophils reside within patient endometriotic lesions and that patient lesions possess a microenvironment that may influence neutrophil recruitment and function, and this work provides the first evidence that systemic circulating Neutrophils from endometiosis patients display distinct transcriptomic differences compared neutrophiles from healthy control subjects.
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Alveolar macrophages from tuberculosis patients display an altered inflammatory gene expression profile
Lelia Lavalett,Héctor A. Rodriguez,Hector Ortega,Wolfgang Sadee,Larry S. Schlesinger,Luis F. Barrera +5 more
TL;DR: The observed changes in mRNA expression profiles may partially account for the inability of AMsTB to effectively control Mtb infection, suggesting that a balanced control of pro- and anti-inflammatory immune responses is crucial for infection control.
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Comparative Characterization of Osteoclasts Derived From Murine Bone Marrow Macrophages and RAW 264.7 Cells Using Quantitative Proteomics.
TL;DR: This work quantified the global protein changes in osteoclasts derived from BMMs and RAW 264.7 cells at 1, 3, and 5 days of differentiation and found that biological processes known to be dependent on M‐CSF were significantly different, including cell cycle control, cytoskeletal organization, and apoptosis.
Journal ArticleDOI
Linking transcriptional changes over time in stimulated dendritic cells to identify gene networks activated during the innate immune response.
TL;DR: A high-probability network of genes activated during the innate immune response is identified using a novel approach to analyze time-course gene expression profiles of activated immune cells in combination with a large gene regulatory and protein-protein interaction network.
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MicroRNA Profiling of Sendai Virus Infected A549 Cells Identifies miR-203 as an Interferon-inducible Regulator of IFIT1/ISG56
TL;DR: Small-RNA profiling was used to analyze the miRNA content of human A549 cells at steady state and following infection with the Cantell strain of Sendai virus, a potent inducer of IFN and cellular antiviral responses, indicating that miR-203 is an IFN-inducible miRNA that can negatively regulate a number of cellular mRNAs by destabilizing its mRNA transcript.
References
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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
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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
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