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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Integrative Network Analysis of Predicted miRNA-Targets Regulating Expression of Immune Response Genes in Bovine Coronavirus Infection
Olanrewaju B. Morenikeji,Madeleine Wallace,Ellis Strutton,Kahleel Bernard,Elaine Yip,Bolaji N. Thomas +5 more
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In silico Analyses of Immune System Protein Interactome Network, Single-Cell RNA Sequencing of Human Tissues, and Artificial Neural Networks Reveal Potential Therapeutic Targets for Drug Repurposing Against COVID-19
Andrés López-Cortés,Patricia Guevara-Ramírez,Nikolaos C Kyriakidis,Carlos Barba-Ostria,Ángela León Cáceres,Ángela León Cáceres,Santiago Guerrero,Esteban Ortiz-Prado,Cristian R. Munteanu,Eduardo Tejera,Doménica Cevallos-Robalino,Ana María Gómez-Jaramillo,Katherine Simbaña-Rivera,Adriana Granizo-Martínez,Gabriela Pérez-M,Silvana Moreno,Jennyfer M. García-Cárdenas,Ana Karina Zambrano,Yunierkis Pérez-Castillo,Alejandro Cabrera-Andrade,Alejandro Cabrera-Andrade,Lourdes Puig San Andrés,Carolina Proaño-Castro,Jhommara Bautista,Andreina Quevedo,Nelson Varela,Luis A. Quiñones,César Paz-y-Miño +27 more
TL;DR: Muntisa et al. as discussed by the authors performed in silico analyses of immune system protein interactome network, single-cell RNA sequencing of human tissues, and artificial neural networks to reveal potential therapeutic targets for drug repurposing against COVID-19.
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Prediction and analysis of human-herpes simplex virus type 1 protein-protein interactions by integrating multiple methods
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Human gene expression profiling identifies key therapeutic targets in tuberculosis infection: A systematic network meta-analysis.
Aftab Alam,Nikhat Imam,Nikhat Imam,Mohd Faizan Siddiqui,Md. Kaisar Ali,Mohd Murshad Ahmed,Romana Ishrat +6 more
TL;DR: The transcriptome profiling and network approach can enhance the understanding of the molecular pathogenesis of tuberculosis infection and have implications for the plan and execution of mRNA expression tools to support early diagnostics and treatment of Mycobacterium tuberculosis (M.tb).
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Epithelial X-Box Binding Protein 1 Coordinates Tumor Protein p53-Driven DNA Damage Responses and Suppression of Intestinal Carcinogenesis
Lina Welz,Philip Rosenstiel,Nassim Kakavand,Dewei Zhu,Xiang Hang,Georg Laue,Go Ito,Go Ito,Miguel Silva,Christina Plattner,Neha Mishra,Felicitas Tengen,Christoph Ogris,Moritz Jesinghaus,Felix Wottawa,Philipp Arnold,Leena Kaikkonen,Stefanie Stengel,Florian Tran,Saumya Das,Arthur Kaser,Zlatko Trajanoski,Richard S. Blumberg,Christoph Roecken,Dieter Saur,Markus Tschurtschenthaler,Stefan Schreiber,Philip Rosenstiel,Konrad Aden +28 more
TL;DR: In this article, the role of XBP1 in orchestrating p53-driven DNA damage response was tested in vitro in mouse models of chronic intestinal epithelial cell (IEC) DNA damage via orthotopic tumor organoid transplantation.
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