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
Reads0
Chats0
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
Citations
More filters
Journal ArticleDOI
OmicsNet: a web-based tool for creation and visual analysis of biological networks in 3D space.
Guangyan Zhou,Jianguo Xia +1 more
TL;DR: A novel web-based tool that allows users to easily create different types of molecular interaction networks and visually explore them in a three-dimensional (3D) space and a rich set of functions have been implemented to allow users to perform coloring, shading, topology analysis, and enrichment analysis.
Journal ArticleDOI
Discerning molecular interactions: A comprehensive review on biomolecular interaction databases and network analysis tools.
TL;DR: The distinctive attribute mentioned in this review is not only to provide an overview of tools and web servers for gene and protein-protein interaction (PPI) network analysis but also to extract useful and meaningful information from the interaction networks.
Journal ArticleDOI
Protein–protein interactions and genetic diseases: The interactome ☆
TL;DR: How the architecture of molecular protein networks has informed disease biology, and how these data are now being computationally integrated with the newest genomic technologies are discussed to improve the understanding of molecular processes perturbed by genetics in human diseases.
Journal ArticleDOI
In silico polypharmacology of natural products.
TL;DR: The promise of cancer immunotherapies and combination therapies that target tumor ecosystems (e.g. clones or 'selfish' sub-clones) via exploiting the immunological and inflammatory 'side' effects of natural products in the cancer post-genomics era is highlighted.
Journal ArticleDOI
ATG16L1 orchestrates interleukin-22 signaling in the intestinal epithelium via cGAS-STING.
Konrad Aden,Florian Tran,Go Ito,Go Ito,Raheleh Sheibani-Tezerji,Simone Lipinski,Johannes Kuiper,Markus Tschurtschenthaler,Markus Tschurtschenthaler,Svetlana Saveljeva,Joya Bhattacharyya,Robert Häsler,Kareen Bartsch,Anne Luzius,Marlene Jentzsch,Maren Falk-Paulsen,Stephanie T. Stengel,Lina Welz,Robin Schwarzer,Björn Rabe,Winfried Barchet,Stefan Krautwald,Gunther Hartmann,Manolis Pasparakis,Richard S. Blumberg,Stefan Schreiber,Arthur Kaser,Philip Rosenstiel +27 more
TL;DR: An unexpected role of ATG16L1 is demonstrated in coordinating the outcome of IL-22 signaling in the intestinal epithelium, which potentiates endogenous ileal inflammation and causes widespread necroptotic epithelial cell death in Atg16l1&Dgr;IEC mice.
References
More filters
Journal ArticleDOI
Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
Paul Shannon,Andrew Markiel,Owen Ozier,Nitin S. Baliga,Jonathan T. Wang,Daniel Ramage,Nada Amin,Benno Schwikowski,Trey Ideker +8 more
TL;DR: Several case studies of Cytoscape plug-ins are surveyed, including a search for interaction pathways correlating with changes in gene expression, a study of protein complexes involved in cellular recovery to DNA damage, inference of a combined physical/functional interaction network for Halobacterium, and an interface to detailed stochastic/kinetic gene regulatory models.
Journal ArticleDOI
Cytoscape 2.8
TL;DR: Version 2.8 introduces two powerful new features—Custom Node Graphics and Attribute Equations—which can be used jointly to greatly enhance Cytoscape's data integration and visualization capabilities.
Journal ArticleDOI
A cytokine-mediated link between innate immunity, inflammation, and cancer
Wan-Wan Lin,Michael Karin +1 more
TL;DR: An overview of the current understanding of the role of inflammation-induced cytokines in tumor initiation, promotion, and progression is provided.
Journal ArticleDOI
Innate immunity and intestinal microbiota in the development of Type 1 diabetes
Li Wen,Ruth E. Ley,Ruth E. Ley,Pavel Volchkov,Peter B. Stranges,Lia Avanesyan,Austin C. Stonebraker,Changyun Hu,F. Susan Wong,Gregory L. Szot,Jeffrey A. Bluestone,Jeffrey I. Gordon,Alexander V. Chervonsky +12 more
TL;DR: It is found that MyD88 deficiency changes the composition of the distal gut microbiota, and that exposure to the microbiota of specific pathogen-free MyD 88-negative NOD donors attenuates T1D in germ-free NOD recipients.
Journal ArticleDOI
The IntAct molecular interaction database in 2012
Samuel Kerrien,Bruno Aranda,Lionel Breuza,Alan Bridge,Fiona Broackes-Carter,Carol Chen,Margaret Duesbury,Marine Dumousseau,M Feuermann,Ursula Hinz,Christine Jandrasits,Rafael C. Jimenez,Jyoti Khadake,Usha Mahadevan,Patrick Masson,Ivo Pedruzzi,Eric Pfeiffenberger,Pablo Porras,Arathi Raghunath,Bernd Roechert,Sandra Orchard,Henning Hermjakob +21 more
TL;DR: Two levels of curation are now available within the IntAct database, with both IMEx-level annotation and less detailed MIMIx-compatible entries currently supported.
Related Papers (5)
The Reactome Pathway Knowledgebase.
Antonio Fabregat,Konstantinos Sidiropoulos,Phani V. Garapati,Marc Gillespie,Marc Gillespie,Kerstin Hausmann,Robin Haw,Bijay Jassal,S Jupe,Florian Korninger,Sheldon J. McKay,Lisa Matthews,Bruce May,Marija Milacic,Karen Rothfels,Veronica Shamovsky,Marissa Webber,Joel Weiser,Mark Williams,Guanming Wu,Lincoln Stein,Lincoln Stein,Lincoln Stein,Henning Hermjakob,Henning Hermjakob,Peter D'Eustachio +25 more
Gene Ontology: tool for the unification of biology
M Ashburner,Catherine A. Ball,Judith A. Blake,David Botstein,Heather Butler,J. M. Cherry,Allan Peter Davis,Kara Dolinski,Selina S. Dwight,J.T. Eppig,Midori A. Harris,David P. Hill,Laurie Issel-Tarver,Andrew Kasarskis,Suzanna E. Lewis,John C. Matese,Joel E. Richardson,M. Ringwald,Gerald M. Rubin,Gavin Sherlock +19 more
Human Protein Reference Database—2009 update
T. S. Keshava Prasad,Renu Goel,Kumaran Kandasamy,Kumaran Kandasamy,Shivakumar Keerthikumar,Sameer Kumar,Suresh Mathivanan,Deepthi Telikicherla,Rajesh Raju,Beema Shafreen,Abhilash K. Venugopal,Lavanya Balakrishnan,Arivusudar Marimuthu,Sutopa Banerjee,Devi S. Somanathan,Aimy Sebastian,Sandhya G. Rani,Somak Ray,C. J. Harrys Kishore,Sashi Kanth,Mukhtar Ahmed,Manoj Kumar Kashyap,Manoj Kumar Kashyap,Riaz Mohmood,Y. L. Ramachandra,Venkatarangaiah Krishna,B. Abdul Rahiman,Subburaman Mohan,Prathibha Ranganathan,Subhashri Ramabadran,Raghothama Chaerkady,Akhilesh Pandey +31 more