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InnateDB: systems biology of innate immunity and beyond—recent updates and continuing curation

Karin Breuer, Amir K. Foroushani, Matthew R. Laird, Carol Chen, Anastasia Sribnaia, Raymond Lo, Geoffrey L. Winsor, Robert E. W. Hancock, Fiona S. L. Brinkman, David J. Lynn
2012 Nucleic Acids Research  
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

David J Lynn, Geoffrey L Winsor, Calvin Chan, Nicolas Richard, Matthew R Laird, Aaron Barsky, Jennifer L Gardy, Fiona M Roche, Timothy H W Chan, Naisha Shah, Raymond Lo, Misbah Naseer (+11 others)
2008 Molecular Systems Biology  
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]

Morteza Roodgar, Afshin Babveyh, Lan Huong, Wenyu Zhou, Rahul Sinha, Hayan Lee, John B Hanks, Mohan Avula, Lihua Jiang, Hoyong Lee, Giltae Song, Hassan Chaib (+7 others)
2019 bioRxiv   pre-print
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

Tanja Muetze, Ivan H. Goenawan, Heather L. Wiencko, Manuel Bernal-Llinares, Kenneth Bryan, David J. Lynn
2016 F1000Research  
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

Tanja Muetze, Ivan H. Goenawan, Heather L. Wiencko, Manuel Bernal-Llinares, Kenneth Bryan, David J. Lynn
2016 F1000Research  
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

Pablo Porras, Elisabet Barrera, Alan Bridge, Noemi Del-Toro, Gianni Cesareni, Margaret Duesbury, Henning Hermjakob, Marta Iannuccelli, Igor Jurisica, Max Kotlyar, Luana Licata, Ruth C Lovering (+15 others)
2020 Nature Communications  
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

Wang X, Zhang J, Wang Y, Tu M, Wang Y, Shi G
2018 OncoTargets and Therapy  
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 beyondrecent 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

Sherrianne Ng, Tobias Strunk, Amy H. Lee, Erin E. Gill, Reza Falsafi, Tabitha Woodman, Julie Hibbert, Robert E. W. Hancock, Andrew Currie, Francisco J. Esteban
2020 PLoS ONE  
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

Puneet Talwar, Renu Gupta, Suman Kushwaha, Rachna Agarwal, Luciano Saso, Shrikant Kukreti, Ritushree Kukreti
2018 Current Neuropharmacology  
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

Donghyun Shin, Sung Yong Chang, Paul Bogere, KyeongHye Won, Jae-Young Choi, Yeon-Jae Choi, Hak Kyo Lee, Jin Hur, Byung-Yong Park, Younghoon Kim, Jaeyoung Heo, Chrysoula Tassou
2019 PLoS ONE  
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]

Maria A. Duque-Correa, Fernanda Schreiber, Faye H. Rodgers, David Goulding, Sally Forrest, Ruby White, Amy Buck, Richard K. Grencis, Matthew Berriman
2020 bioRxiv   pre-print
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

Pablo Augusto de Souza Fonseca, Samir Id-Lahoucine, Antonio Reverter, Juan F Medrano, Marina S Fortes, Joaquim Casellas, Filippo Miglior, Luiz Brito, Maria Raquel S Carvalho, Flávio S Schenkel, Loan T Nguyen, Laercio R Porto-Neto (+2 others)
2018 PLoS ONE  
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

Robin Haw, Henning Hermjakob, Peter D'Eustachio, Lincoln Stein
2011 Proteomics  
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]

Anya C Jones, Denise Anderson, Niamh M Troy, Dominic Mallon, Rochelle Hartmann, Michael Serralha, Barbara J Holt, Anthony Bosco, Patrick G Holt
2018 bioRxiv   pre-print
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]

Bernd Sokolowski, Sandra Orchar
2011 Selected Works in Bioinformatics  
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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