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Signaling network of dendritic cells in response to pathogens: a community-input supported knowledgebase

Sonali Patil, Hanna Pincas, Jeremy Seto, German Nudelman, Irina Nudelman, Stuart C Sealfon
2010 BMC Systems Biology  
Dendritic cells are antigen-presenting cells that play an essential role in linking the innate and adaptive immune systems.  ...  Initially assembled using CellDesigner software, it provides an annotated graphical representation of interactions stored in Systems Biology Mark-up Language.  ...  Current databases of signaling networks of the innate immune response include free online resources such as the Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway database http://www.genome.jp/kegg  ... 
doi:10.1186/1752-0509-4-137 pmid:20929569 pmcid:PMC2958907 fatcat:gepm2pre2jcgbnbbcst23gubrm

Analyzing Functional Pathways and constructing gene-gene network for Narcolepsy based on candidate genes

Hui Ouyang, Zechen Zhou, Qiwen Zheng, Jun Zhang
2020 International Journal of Medical Sciences  
and protein-protein interaction (PPI) networks for narcolepsy.  ...  molecular function, 2) KEGG pathway enrichment analysis revealed selective enrichment of genes in cytokine-cytokine receptor interaction signaling pathways, and 3) five hub genes were identified (IFNAR1  ...  Yiqun Wu from Peking University, Healthscience Center for advice, Shiying Wang from Peking University, College of Life Sciences for help with statistical analyses, and Prof.  ... 
doi:10.7150/ijms.41812 pmid:32669953 pmcid:PMC7359385 fatcat:anxycvairrhffjiyx637og4kga

iMAC: An interactive atlas to explore phenotypic differences between in vivo, ex vivo and in vitro-derived myeloid cells in the Stemformatics platform [article]

Nadia Rajab, Paul Angel, Mariola Kurowska-Stolarska, Simon Milling, Chris Pacheco Rivera, Matt Rutar, Jarny Choi, Christine A Wells
2019 bioRxiv   pre-print
biology, and particularly whether these can model resident tissue macrophage specialisation.  ...  Macrophages isolated from different tissues have distinct niche roles that maintain tissue homeostasis, as well as providing surveillance for tissue injury or infection.  ...  ., 2012) and transcriptional responses to innate immune stimuli (Schroder et al., 2012) .  ... 
doi:10.1101/719237 fatcat:oakh4a3cajeo7oizl6d5n2q3ke

Immune Heterogeneity of Glioblastoma Subtypes: Extrapolation from the Cancer Genome Atlas

T. Doucette, G. Rao, A. Rao, L. Shen, K. Aldape, J. Wei, K. Dziurzynski, M. Gilbert, A. B. Heimberger
2013 Cancer immunology research  
Results: We found an enrichment of genes within the mesenchymal subtype that are reflective of antitumor proinflammatory responses, including both adaptive and innate immunity and immunosuppression.  ...  database.  ...  Acknowledgments We thank Audria Patrick and David M. Wildrick for editorial assistance. Grant Support Grant support was provided by the NIH RO1-CA1208113 (to A.B. Heimberger), 5P50 CA127001 (to T.  ... 
doi:10.1158/2326-6066.cir-13-0028 pmid:24409449 pmcid:PMC3881271 fatcat:jjuttr3ktjdovmhb4rikl77bhy

Gene correlation network analysis to identify regulatory factors in sciatic nerve injury

Liuxun Li, Xiaokang Du, Haiqian Ling, Yuhang Li, Xuemin Wu, Anmin Jin, Meiling Yang
2021 Journal of Orthopaedic Surgery and Research  
In addition, immune infiltration analysis was accomplished by CIBERSORT. Finally, Drug–Gene Interaction database (DGIdb) was employed for predicting the possible therapeutic agents.  ...  GSEA also supported that gene sets with the highest significance were mostly related to the cytokinecytokine receptor interaction.  ...  Acknowledgements We acknowledge GEO database for providing their platforms and contributors for uploading their meaningful datasets.  ... 
doi:10.1186/s13018-021-02756-0 pmid:34663380 pmcid:PMC8522103 fatcat:5bsojwfnevgfvps7mqzxyodrue

A Functional and Regulatory Map of Asthma

Noa Novershtern, Zohar Itzhaki, Ohad Manor, Nir Friedman, Naftali Kaminski
2008 American Journal of Respiratory Cell and Molecular Biology  
Using this collection we generated a high-level map of the functional themes that characterize animal models of asthma, dominated by innate and adaptive immune response.  ...  Analysis of IL-13-dependent response using protein interaction networks highlights a role for TGF-b1 as a key regulator of asthma.  ...  It is enriched for general components of the immune response: innate and adaptive responses, complement system; chemokines and cytokines, and their receptors ( Figure 4B and Table 3 ).  ... 
doi:10.1165/rcmb.2007-0151oc pmid:17921359 pmcid:PMC2258452 fatcat:5q34aozwa5gs3gznrnzdo5quzu

Cataloguing of Potential HIV Susceptibility Factors during the Menstrual Cycle of Pig-Tailed Macaques by Using a Systems Biology Approach

S. A. Vishwanathan, A. Burgener, S. E. Bosinger, G. K. Tharp, P. C. Guenthner, N. B. Patel, K. Birse, D. L. Hanson, G. R. Westmacott, T. R. Henning, J. Radzio, J. G. Garcia-Lerma (+4 others)
2015 Journal of Virology  
assays and multiplex chemokine and cytokine measurements) to characterize the effects of hormonal changes on the expression of innate factors and secreted proteins in the macaque vagina.  ...  Thus, our study showed that specific pathways and proteins or genes might work in tandem to regulate innate immunity, thus fostering further investigation and future design of approaches to help counter  ...  ACKNOWLEDGMENTS We thank James Mitchell, Shanon Ellis, and Frank Deyounks for animal technical assistance and our veterinarians and colleagues in the Animal Resources Branch (ARB) for help with macaque-related  ... 
doi:10.1128/jvi.00263-15 pmid:26109722 pmcid:PMC4542353 fatcat:njwfnuyo7rgfnhwd3wgss3mvou

Microdialysis Sampling from Wound Fluids Enables Quantitative Assessment of Cytokines, Proteins, and Metabolites Reveals Bone Defect-Specific Molecular Profiles

Yvonne Förster, Johannes R. Schmidt, Dirk K. Wissenbach, Susanne E. M. Pfeiffer, Sven Baumann, Lorenz C. Hofbauer, Martin von Bergen, Stefan Kalkhof, Stefan Rammelt, Thomas R. Howdieshell
2016 PLoS ONE  
Here, we describe an approach for sampling and quantification of cytokines and metabolites by using microdialysis, combined with solid phase extractions of proteins from wound fluids.  ...  Moreover, by analyzing downstream adaptions of the cells on protein level and focusing on early immune response, several proteins involved in the immune cell migration and activity could be identified  ...  Acknowledgments The authors thank Ute Hempel, Carolin Preissler, Wenling Gao and Jacqueline Kobelt for their excellent technical assistance. Author Contributions  ... 
doi:10.1371/journal.pone.0159580 pmid:27441377 pmcid:PMC4956113 fatcat:mrbc5vfslnejrbtsbtth6koqa4

Identification of Vital Hub Genes and Potential Molecular Pathways of Dermatomyositis by Bioinformatics Analysis

Xueren Ouyang, Yuning Zeng, Xiaotao Jiang, Hua Xu, Yile Ning, Ming Yi
2021 BioMed Research International  
immune-related biological processes and pathways.  ...  Omnibus (GEO) database.  ...  As an important part of the immune system, Janus Kinase (JAK) family genes are involved in and mediate innate and adaptive immune processes in the human body.  ... 
doi:10.1155/2021/9991726 pmid:34580642 pmcid:PMC8464434 fatcat:yjhgxvrxcvfvhohsfqbeyjnbmy

Integrated bioinformatic analysis of differentially expressed genes and signaling pathways in plaque psoriasis

Yu‑Jing Zhang, Yu‑Zhe Sun, Xing‑Hua Gao, Rui‑Qun Qi
2019 Molecular Medicine Reports  
Psoriasis is an immune-mediated cutaneous disorder with a high incidence and prevalence. Patients with psoriasis may experience irritation, pain and psychological problems.  ...  The gene ontology (Go) and Kyoto encyclopedia of Genes and Genomes (KeGG) pathway enrichment were analyzed using the daVid online analysis tool.  ...  Funding The present study was supported by the national natural Science Foundation of china (grant no. 81673070) and the national Key Basic research Program of china (grant no. 2013cB531604).  ... 
doi:10.3892/mmr.2019.10241 fatcat:mixmj46d7fdk3dfwezf33s75lu

In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases

Peter McGarvey, Baris E. Suzek, Shruti Rao, Subha Madhavan, James N. Baraniuk, Samir Lababidi, Andrea Sutherland, Richard Forshee
2007 Proceedings of the International Conference on Bioinformatics, Computational Biology and Biomedical Informatics - BCB'13  
Classification of genes into twelve immune system related categories identified more "Th17 T-cell subtype" genes in RA than the other AIDs, and more "Chemokine plus Receptors" genes associated with RA  ...  In order to identify biologically plausible pathways to adverse autoimmune events of vaccine-related AID, we used a systems biology approach to create a matrix of innate and adaptive immune mechanisms  ...  Acknowledgements We thank Simina Boca for advice on the statistical analysis.  ... 
doi:10.1145/2506583.2506657 dblp:conf/bcb/McGarveySRMBLSF13 fatcat:pxh7st7omrbuvjca7nuhshjkx4

In silico analysis of autoimmune diseases and genetic relationships to vaccination against infectious diseases

Peter B McGarvey, Baris E Suzek, James N Baraniuk, Shruti Rao, Brian Conkright, Samir Lababidi, Andrea Sutherland, Richard Forshee, Subha Madhavan
2014 BMC Immunology  
Classification of genes into twelve immune system related categories identified more "Th17 T-cell subtype" genes in RA than the other AIDs, and more "Chemokine plus Receptors" genes associated with RA  ...  In order to identify biologically plausible pathways to adverse autoimmune events of vaccine-related AID, we used a systems biology approach to create a matrix of innate and adaptive immune mechanisms  ...  Acknowledgements We thank Simina Boca for advice on the statistical analysis.  ... 
doi:10.1186/s12865-014-0061-0 pmid:25486901 pmcid:PMC4266212 fatcat:h3ntiuoj7vcczcvzkx4mhvmglm

Contrasting Gene Expression Profiles of Monocytes and Lymphocytes From Peste-Des-Petits-Ruminants Virus Infected Goats

Sajad Ahmad Wani, Amit Ranjan Sahu, Raja Ishaq Nabi Khan, Aruna Pandey, Shikha Saxena, Neelima Hosamani, Waseem Akram Malla, Dheeraj Chaudhary, Sonam Kanchan, Vaishali Sah, Kaushal Kishor Rajak, D. Muthuchelvan (+8 others)
2019 Frontiers in Immunology  
In this study, transcriptome analysis of PPRV infected PBMC subsets-T helper cells, T cytotoxic cells, monocytes, and B lymphocytes was done to delineate their role in host response.  ...  ISGs-ISG15, Mx1, Mx2, RSAD2, IFIT3, and IFIT5 that play a role in antiviral response and the genes for viral sensors-MDA5, LGP2, and RIG1, were found to be upregulated in lymphocytes and downregulated  ...  MIF regulation of innate immunity.  ... 
doi:10.3389/fimmu.2019.01463 pmid:31333643 pmcid:PMC6624447 fatcat:hrufczb7ond2llnbcl7k6qdje4

Influenza A virus infects pulmonary microvascular endothelial cells leading to microvascular leakage and release of pro-inflammatory cytokines

Tiantian Han, Yanni Lai, Yong Jiang, Xiaohong Liu, Danhua Li
2021 PeerJ  
of pro-inflammatory cytokines, but does not efficiently replicate in endothelial cells.  ...  ), "Influenza A", and also played a key role in anti-inflammation and regulation of immunity.  ...  Endothelial cells are potential targets for suppressing excessive innate inflammation. (3) The CC enrichment results were mainly related to the extracellular region and vesicle lumen.  ... 
doi:10.7717/peerj.11892 pmid:34414033 pmcid:PMC8344683 fatcat:ivxmwrnbkraprdf3cbkx274q2q

Elucidating the molecular pathways and immune system transcriptome during ischemia-reperfusion injury in renal transplantation

Jinhua Zhang, Xiangling Wei, Zuofu Tang, Bin Miao, Yingxun Luo, Xiao Hu, You Luo, Yu Zhou, Ning Na
2020 International Immunopharmacology  
The xCell analysis identified immune cells that are significantly changed after reperfusion, including hematopoietic stem cells, M2 macrophages, monocytes, Treg cells, conventional dendritic cells, and  ...  These data reveal the important role of the NOD-like receptor signaling pathway during IRI, and the close relationship between this pathway and infiltration of specific immune cell types.  ...  Innate immunity mainly contributes to the early injury response via non-antigen-specific interactions with neutrophils, monocytes/macrophages, conventional dendritic cells (cDCs), NK cells, and natural  ... 
doi:10.1016/j.intimp.2020.106246 pmid:32044658 fatcat:55jmkk3dfvh6pcahwejmvrimuy
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