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
STAT3 and NF-κB are Simultaneously Suppressed in Dendritic Cells in Lung Cancer
Rui Li,Fang Fang,Ming Jiang,Chenguang Wang,Jiajia Ma,Wenyao Kang,Qiuyan Zhang,Yuhui Miao,Dong Wang,Yugang Guo,Linnan Zhang,Yang Guo,Hui Zhao,De Yang,Zhigang Tian,Weihua Xiao +15 more
TL;DR: In the present study, an in vitro study model for tumour-induced dendritic cell (DC) dysfunction was established by culturing DCs with pooled sera from multiple non-small cell lung cancer (NSCLC) patients and demonstrated that tumours-induced human monocyte-derived DCs exhibited systematic functional deficiencies.
Journal ArticleDOI
Personalized Transcriptomics Reveals Heterogeneous Immunophenotypes in Children with Viral Bronchiolitis
Anya C. Jones,Anya C. Jones,Denise Anderson,Sally Galbraith,Emmanuelle Fantino,Diana Gutierrez Cardenas,James F. Read,James F. Read,Michael Serralha,Barbara J. Holt,Deborah H. Strickland,Peter D. Sly,Anthony Bosco,Patrick G. Holt,Patrick G. Holt +14 more
TL;DR: N-of-1-pathways analysis confirmed differential upregulation of innate immunity in infants and natural killer cell networks in children, and additionally demonstrated covert AVB response subphenotypes that were independent of chronologic age.
Journal ArticleDOI
The evolution and functional diversification of the deubiquitinating enzyme superfamily.
Caitlyn Vlasschaert,Caitlyn Vlasschaert,David P. Cook,David P. Cook,Xuhua Xia,Douglas A. Gray,Douglas A. Gray +6 more
TL;DR: The evolutionary history of the entire class of deubiquitinating enzymes is determined, including the sequence and means of duplication for all paralogous pairs, and examples of DUB gene subfunctionalization, neofunctionalization, and nonfunctionalization are revealed.
Journal ArticleDOI
Ketogenic diet attenuates hepatopathy in mouse model of respiratory chain complex III deficiency caused by a Bcs1l mutation
Janne Purhonen,Jayasimman Rajendran,Matthias Mörgelin,Kristiina Uusi-Rauva,Shintaro Katayama,Kaarel Krjutškov,Elisabet Einarsdottir,Elisabet Einarsdottir,Vidya Velagapudi,Juha Kere,Matti Jauhiainen,Vineta Fellman,Vineta Fellman,Jukka Kallijärvi +13 more
TL;DR: A striking beneficial hepatic response to KD is revealed in mice with mitochondrial hepatopathy and warrant further investigations of dietary modification in the management of these conditions in patients.
Journal ArticleDOI
Transcriptome Analysis of The Inflammatory Responses of Bovine Mammary Epithelial Cells: Exploring Immunomodulatory Target Genes for Bovine Mastitis
Aminul Islam,Michihiro Takagi,Kohtaro Fukuyama,Ryoya Komatsu,Leonardo Albarracin,Tomonori Nochi,Yoshihito Suda,Wakako Ikeda-Ohtsubo,Victor P.M.G. Rutten,Victor P.M.G. Rutten,Willem van Eden,Julio Villena,Hisashi Aso,Haruki Kitazawa +13 more
TL;DR: The identification of transcriptional markers of mastitis specific for individual inflammatory factors such as LPS, Pam3CSK4 or CyPA, which can be evaluated in vitro in BME cells, may enable the development of novel diagnostics and/or immunomodulatory treatments, providing new tools for the effective management ofmastitis in dairy cows.
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