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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Evidence of a dysregulated Vitamin D pathway in SARS-CoV-2 infected patient's lung cells
Bijesh George,Bijesh George,Ravikumar Amjesh,Aswathy Mary Paul,Aswathy Mary Paul,Madhavan Radhakrishna Pillai,Rakesh Kumar,Rakesh Kumar,Rakesh Kumar +8 more
TL;DR: In this paper, the role of the vitamin D pathway and vitamin D-modulated genes in lung cells of patients infected with SARS-CoV-2 remains unknown, however, the authors provided computational evidence to implicate a dysregulated vitaminD pathway in the pathobiology of SARS CoV2 infection.
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Yu Qiao Chen,Jiacheng Dai,Longmei Tang,T. Mikhailova,Qiudong Liang,Miao Li,Jiaqi Zhou,Cynthia Shannon Weickert,Chao Chen,Chunyu Liu +9 more
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Construction of a Prognostic Immune-Related LncRNA Risk Model for Gastric Cancer
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NetControl4BioMed: A web-based platform for controllability analysis of protein-protein interaction networks.
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TL;DR: NetControl4BioMed as mentioned in this paper is a web-based application that allows users to generate or upload directed protein-protein interaction networks and to perform target structural network controllability analyses on them.
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