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InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation
2012
Nucleic Acids Research
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More recently, InnateDB has also initiated the curation of allergy-and asthma-related interactions. ...
In this article, we provide details of recent updates and improvements to the database. ...
We would also like to thank all the previous members of the InnateDB development and curation teams (http://www.innatedb.com/ about). ...
doi:10.1093/nar/gks1147
pmid:23180781
pmcid:PMC3531080
fatcat:jmmbldnvuzgg7fm4vjbqnoknrm
InnateDB: facilitating systems-level analyses of the mammalian innate immune response
2008
Molecular Systems Biology
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InnateDB is a publicly available, manually curated, integrative biology database of the human and mouse molecules, experimentally verified interactions and pathways involved in innate immunity, along with ...
InnateDB (www.innatedb.ca) has been developed to facilitate systems-level analyses that will provide better insight into the complex networks of pathways and interactions that govern the innate immune ...
Acknowledgements We thank Kathleen Wee, Eddie Yuen, Patrick Taylor, Sheena Tam, Tom Yang and other members of the Pathogenomics of Innate Immunity project for their assistance in manual curation of InnateDB ...
doi:10.1038/msb.2008.55
pmid:18766178
pmcid:PMC2564732
fatcat:7kmlt4upyne2hp3akijsyr32xu
Chromosome-level de novo assembly of the pig-tailed macaque genome using linked-read sequencing and HiC proximity scaffolding
[article]
2019
bioRxiv
pre-print
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Old world monkey species share over 93% genome homology with humans and develop many disease phenotypes similar to those of humans, making them highly valuable animal models for the study of numerous human ...
To close this gap and enhance functional genomics approaches, we employed a combination of de novo linked-read assembly and scaffolding using proximity ligation assay (HiC) to assemble the pig-tailed macaque ...
Acknowledgements: This work used the Genome Sequencing Service Center by Stanford Center for Genomics and Personalized Medicine Sequencing Center, supported by the grant award NIH S10OD020141 and samples ...
doi:10.1101/635045
fatcat:y3qsku2blbd7bdvekua2gcyd64
Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks
2016
F1000Research
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Breuer K, Foroushani AK, Laird MR, et al.: InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. Nucleic Acids Res. 2013; 41(Database issue): D1228-1233. ...
Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest ...
pathway, and innate immune response
A B among the top 10 enriched terms (FDR < 0.05) for the contextual hubs but not the degree-based hubs (Supplementary Table 3 and Supplementary Table 4 ). ...
doi:10.12688/f1000research.9118.1
fatcat:w35fpty47rhmjibyltwu63cw6u
Contextual Hub Analysis Tool (CHAT): A Cytoscape app for identifying contextually relevant hubs in biological networks
2016
F1000Research
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A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2019; you can also visit the original URL.
The file type is application/pdf.
Breuer K, Foroushani AK, Laird MR, et al.: InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. Nucleic Acids Res. 2013; 41(Database issue): D1228-1233. ...
Highly connected nodes (hubs) in biological networks are topologically important to the structure of the network and have also been shown to be preferentially associated with a range of phenotypes of interest ...
pathway, and innate immune response among the top 10 enriched terms (FDR < 0.05) for the contextual hubs but not the degree-based hubs (Supplementary Table 3 and Supplementary Table 4 ). ...
doi:10.12688/f1000research.9118.2
pmid:27853512
pmcid:PMC5105880
fatcat:25nlevzckvcxhej744s6rhpgh4
Towards a unified open access dataset of molecular interactions
2020
Nature Communications
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In this update to the work of the IMEx Consortium, we discuss how this initiative has been working in practice, how it has ensured database sustainability, and how it is meeting emerging annotation challenges ...
through the introduction of new interactor types and data formats. ...
Acknowledgements The IntAct team at EMBL-EBI received funding from EMBL core funding, Open Targets (grant agreements OTAR-044 and OTAR02-048) and the Wellcome Trust ...
doi:10.1038/s41467-020-19942-z
pmid:33262342
pmcid:PMC7708836
fatcat:soyrqsypencbrkmqwxzjz6crp4
Upregulated VEGFA and DLL4 act as potential prognostic genes for clear cell renal cell carcinoma
2018
OncoTargets and Therapy
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Cytoscape software and InnateDB database, respectively. ...
This study was aimed to explore the prognostic genes for ccRCC, focusing on the roles of vascular endothelial growth factor A (VEGFA) and Delta-like ligand 4 (DLL4) in the disease.Materials and methods ...
InnateDB: systems biology of innate immunity and beyond – recent updates and continuing curation. Gautier L, Cope L, Bolstad BM, Irizarry RA. ...
doaj:e8b9542082954fc88ea6c7810d0fafba
fatcat:fyjr3t3oizb2dpusajzmcj7tue
Whole blood transcriptional responses of very preterm infants during late-onset sepsis
2020
PLoS ONE
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Host immune responses during late-onset sepsis (LOS) in very preterm infants are poorly characterised due to a complex and dynamic pathophysiology and challenges in working with small available blood volumes ...
At the transcriptional-level cytokine responses during LOS were characterised by over-representation of IFN-α/β, IFN-γ, IL-1 and IL-6 signalling pathways and up-regulation of genes for inflammatory responses ...
Acknowledgments The authors thank the research nurses and doctors at King Edward Memorial Hospital, Perth, Australia, for recruiting and collecting patient samples. ...
doi:10.1371/journal.pone.0233841
pmid:32479514
fatcat:k7gw75kxjnaczaeflsokmdyxjm
Viral induced oxidative and inflammatory response in Alzheimer's disease pathogenesis with identification of potential drug candidates: A systematic review using systems biology approach
2018
Current Neuropharmacology
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Here, we aim to identify the potential viral pathogens leading to aberrant inflammatory and oxidative stress response in AD along with potential drug candidates using systems biology approach. ...
We retrieved protein interactions of amyloid precursor protein (APP) and tau protein (MAPT) from NCBI and genes for oxidative stress from NetAge, for inflammation from NetAge and InnateDB databases. ...
Sanjay Kumar, Council of Scientific and Industrial Research -Institute of Genomics and Integrative Biology (CSIR-IGIB) for their motivation and unconditional support. ...
doi:10.2174/1570159x16666180419124508
pmid:29676229
fatcat:sj3k26753bdt3j7bmlz3cqlvpe
Beneficial roles of probiotics on the modulation of gut microbiota and immune response in pigs
2019
PLoS ONE
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Further gene ontology and immune DB analysis determined 8 genes associated with innate defense response and cytokine production. ...
However, gaps still remain in the exact roles played by probiotics in modulation of gut microbiota and immune response. ...
InnateDB: systems biology of innate immunity and beyond-recent updates and continuing curation. Nucleic acids research. 2012; 41(D1):D1228-D33. 42. Cromwell GL. ...
doi:10.1371/journal.pone.0220843
pmid:31461453
pmcid:PMC6713323
fatcat:yplkhqcmvbc45bpc7qjhbmkgc4
Development of caecaloids to study host-pathogen interactions: new insights into immunoregulatory functions of Trichuris muris extracellular vesicles in the caecum
[article]
2020
bioRxiv
pre-print
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Thus, exploiting this system we investigated the responses of caecal IECs to extracellular vesicles (EVs) secreted/excreted by the intracellular helminth Trichuris muris. ...
The remarkable similarity in the IECs composition and spatial conformation of caecaloids and their tissue of origin enables their use as an in vitro model to study host interactions with important caecal ...
InnateDB: systems biology of innate 543 immunity and beyond--recent updates and continuing curation. ...
doi:10.1101/2020.05.11.087684
fatcat:4mrplyuktvd2xetzchmihmaghy
Combining multi-OMICs information to identify key-regulator genes for pleiotropic effect on fertility and production traits in beef cattle
2018
PLoS ONE
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The lack of understanding on the biological processes responsible for the regulation of these traits results in the decrease of selection efficiency and the selection of undesirable hitchhiking effects ...
These genes will be further investigated to better understand the biological processes involved in the expression of complex traits and assist in the identification of functional variants associated with ...
InnateDB: systems biology of innate immunity and beyond-recent updates and continuing curation. Nucleic acids research. 2012; 41(D1):D1228-D33. 31. Bretones G, Delgado MD, Leó n J. ...
doi:10.1371/journal.pone.0205295
pmid:30335783
pmcid:PMC6193631
fatcat:dkj3sxvobfgqtfhik26lt5cz4i
Reactome pathway analysis to enrich biological discovery in proteomics data sets
2011
Proteomics
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The Pathway Browser is a Systems Biology Graphical Notation (SBGN)-like visualization system that supports manual navigation of pathways by zooming, scrolling and event highlighting, and that exploits ...
Reactome (http://www.reactome.org) is an open source, expert-authored, peer-reviewed, manually curated database of reactions, pathways and biological processes. ...
Acknowledgments Development of the Reactome website, data model and data analysis tools described in this tutorial are a result of concerted work of the Reactome curators and developers. ...
doi:10.1002/pmic.201100066
pmid:21751369
pmcid:PMC4617659
fatcat:vbijvdmnuvbdrc4xicxpnq2zoy
Rewiring of Th-memory-associated gene co-expression networks underlie immunotherapy-induced changes in symptom expression in mite-sensitised atopics
[article]
2018
bioRxiv
pre-print
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Continuing SCIT to 24mths stabilised symptoms at 47% of baseline, accompanied by upregulation of the Type1-IFN-associated network module and its merging into the Th2/FOXP3/IL2/Inflammation module. ...
Objective: To explore the potential for unbiased systems-level gene co-expression network analysis to advance understanding of immunotherapy mechanisms. ...
InnateDB: systems biology of innate immunity and beyond--recent updates and continuing curation. Yu H, Kim PM, Sprecher E, Trifonov V, Gerstein M. ...
doi:10.1101/473561
fatcat:ezs4rb2a2fak7ltwqoede7fgdy
Exploiting Protein Interaction Networks to Unravel Complex Biological Questions
[chapter]
2011
Selected Works in Bioinformatics
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Acknowledgements We thank Margaret Harvey for a critical reading of the manuscript and Sophia Sokolowski for help with the figures. ...
This project was supported by grant R01-DC004295 to B.S. from the National Institute on Deafness and Other Communication Disorders. ...
InnateDB (www.innatedb.ca/)-a database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans and mice to microbial infection ...
doi:10.5772/20915
fatcat:6ae4gwhhwjhutexfoa34g67npy
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