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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Dissertation
Characterisation of Lentiviral Vpr Function and Mechanism
TL;DR: Insight is provided into the role of Vpr in antagonising innate immune sensing using overexpression assays that have been used widely in the literature describing Vpr and indicate that observations using these assays, apparently demonstrating specific degradation of host cellular proteins, should be interpreted cautiously.
Posted ContentDOI
Network medicine links SARS-CoV-2/COVID-19 infection to brain microvascular injury and neuroinflammation in dementia-like cognitive impairment
Yadi Zhou,Jielin Xu,Yuan Hou,James B. Leverenz,James B. Leverenz,Asha R. Kallianpur,Asha R. Kallianpur,Reena Mehra,Yunlong Liu,Haiyuan Yu,Andrew A. Pieper,Lara Jehi,Lara Jehi,Feixiong Cheng,Feixiong Cheng,Feixiong Cheng +15 more
TL;DR: In this article, a network-based, multimodal genomics comparison of COVID-19 and neurologic complications was conducted, and the authors found significant connections between COVID19 and neuroinflammation and brain microvascular injury pathways and processes which are implicated in Alzheimers disease.
Journal ArticleDOI
Mutant p53 Mediates Sensitivity to Cancer Treatment Agents in Oesophageal Adenocarcinoma Associated with MicroRNA and SLC7A11 Expression
Ann-Kathrin Eichelmann,George C. Mayne,George C. Mayne,Karen Chiam,Steven L. Due,Isabell Bastian,Frederike Butz,Tingting Wang,Pamela J. Sykes,Nicholas J. Clemons,David Shi Hao Liu,Michael Michael,Michael Michael,Christos S. Karapetis,Christos S. Karapetis,Richard Hummel,David I. Watson,David I. Watson,Damian J. Hussey,Damian J. Hussey +19 more
TL;DR: In this paper, the role of mutant (mut-) p53 and SLC7A11 in a CRISPR-mediated JH-EsoAd1 TP53 knockout model was investigated.
Design and data analysis of kinome microarrays
TL;DR: It is shown that PHOSFER and DAPPLE are suitable for identifying phosphorylation sites in a wide variety of organisms, including cow, honeybee, and soybean, and this technology can potentially be applied to any organism having a sequenced genome.
Journal ArticleDOI
Integrative genomics of the mammalian alveolar macrophage response to intracellular mycobacteria.
Thomas J. Hall,Michael P. Mullen,Gillian P. McHugo,Kate E. Killick,S.C. Ring,Donagh P. Berry,Carolina N. Correia,John A. Browne,Stephen V. Gordon,David E. MacHugh +9 more
TL;DR: The results show that network-based integration of relevant transcriptomics data can extract additional information from large genome-wide associations and that this approach could also be used to integrate relevant functional genomics outputs with results from genomic association studies for human tuberculosis caused by the related Mycobacterium tuberculosis.
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