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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MetaPathways : a modular pipeline for the analysis of environmental sequence information
TL;DR: A modular analytical pipeline is developed, MetaPathways, allowing for the large-scale and systematic processing and integration of many forms of environmental sequence information, and attempts to bring functional analysis back to the metabolic map through the creation of environmental pathway/genome databases (ePGDBs).
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PBMCs transcriptome profiles identified breed-specific transcriptome signatures for PRRSV vaccination in German Landrace and Pietrain pigs
Md. Aminul Islam,Md. Aminul Islam,Christiane Neuhoff,Sharmin Aqter Rony,Sharmin Aqter Rony,Christine Große-Brinkhaus,Muhammad Jasim Uddin,Muhammad Jasim Uddin,Michael Hölker,Dawit Tesfaye,Ernst Tholen,Karl Schellander,Maren Julia Pröll-Cornelissen +12 more
TL;DR: Investigating the breed difference in innate immune response to PRRSV vaccination between German Landrace (DL) and Pietrain (Pi) pigs provided insights of breed-specific host transcriptome responses to PR RSV vaccination which might contribute in better understanding of PPRS resistance in pigs.
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Development and Clinical Validation of a 90-Gene Expression Assay for Identifying Tumor Tissue Origin
Qing Ye,Qifeng Wang,Peng Qi,Chen Jinying,Yifeng Sun,Shichai Jin,Wanli Ren,Chengshu Chen,Mei Liu,Midie Xu,Gang Ji,Jun Yang,Ling Nie,Qinghua Xu,Deshuang Huang,Xiang Du,Xiaoyan Zhou +16 more
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SARS-CoV-2 transcriptome analysis and molecular cataloguing of immunodominant epitopes for multi-epitope based vaccine design.
Sandeep K. Kushwaha,Veerbhan Kesarwani,Samraggi Choudhury,Sonu Gandhi,Shailesh Narain Sharma +4 more
TL;DR: Targeted expression profiling and differential gene expression analysis of major histocompatibility complexes and innate immune system genes were performed through SARS-CoV-2 infected RNA-seq data of human cell line, and virus transcriptome was generated for T-and B-cell epitope prediction.
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Transcriptome Modifications in Porcine Adipocytes via Toll-Like Receptors Activation
Manami Igata,Md. Aminul Islam,Md. Aminul Islam,Asuka Tada,Michihiro Takagi,A. K. M. Humayun Kober,A. K. M. Humayun Kober,Leonardo Albarracin,Leonardo Albarracin,Leonardo Albarracin,Hisashi Aso,Wakako Ikeda-Ohtsubo,Kenji Miyazawa,Kazutoyo Yoda,Fang He,Hideki Takahashi,Julio Villena,Julio Villena,Haruki Kitazawa +18 more
TL;DR: This work characterized the global transcriptome modifications in porcine intramuscular mature adipocytes (pMA), differentiated from PPI, following stimulation with Pam3csk4, Poly(I:C) or LPS which are ligands for TLR2, TLR3, and TLR4, respectively, and identified key regulatory genes that could be used as biomarkers for the evaluation of treatments having immunomodularoty and/or metabolic functional beneficial effects in por
References
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