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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Anxiolytic Drug FGIN-1-27 Ameliorates Autoimmunity by Metabolic Reprogramming of Pathogenic Th17 Cells.
Anju Singh,Myagmarjav Dashnyam,Bryan Chim,Thelma M. Escobar,Andrés E. Dulcey,Xin Hu,Kelli M. Wilson,Prasanthi P. Koganti,Camille A. Spinner,Xin Xu,Ajit Jadhav,Noel Southall,Juan J. Marugan,Vimal Selvaraj,Vanja Lazarevic,Stefan A. Muljo,Marc Ferrer +16 more
TL;DR: The findings suggest that the small molecule FGIN-1-27 can be re-purposed to relieve autoimmunity by metabolic reprogramming of pathogenic Th17 cells.
Journal ArticleDOI
Adding biological meaning to human protein-protein interactions identified by yeast two-hybrid screenings: A guide through bioinformatics tools
TL;DR: A pipeline to deal with Y2H results using bioinformatics tools freely available for academics is suggested and it is strongly believed that both approaches are not exclusive and that PPINs can use as a complementary methodology and rich-source of information to the initial study proposal.
Journal ArticleDOI
Gene expression profiling studies in regenerating nerves in a mouse model for CMT1X: uninjured Cx32-knockout peripheral nerves display expression profile of injured wild type nerves.
TL;DR: A role for Cx32 is supported in non- myelinating and regenerating populations of Schwann cells in normal axonal maintenance in re-myelination, and regeneration of peripheral nerve following injury, to establish the necessary conditions for successful regeneration and remyelination following nerve injury.
Journal ArticleDOI
Role of Fasciola hepatica Small RNAs in the Interaction With the Mammalian Host
Santiago Fontenla,Mauricio Langleib,Eduardo de la Torre-Escudero,Maria F. Dominguez,Mark W. Robinson,José F. Tort +5 more
TL;DR: Several functions related to the host immune response or modulation were enriched among the targets of the most highly expressed parasite miRNAs, stressing that they might be key players during the establishment and maintenance of infection.
Journal ArticleDOI
Mapping of Protein-Protein Interactions: Web-Based Resources for Revealing Interactomes.
TL;DR: Community available computational programs for predicting PPIs and web-based resources for storing experimentally annotated interactions are reviewed and reliable computational PPI predictions can speed up new target discoveries through prioritization of therapeutically relevant protein-protein complexes for experimental studies.
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