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The representation of protein complexes in the Protein Ontology (PRO)

Carol J Bult, Harold J Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A Blake, Cathy Wu
2011 BMC Bioinformatics  
Description: We describe here how the PRO Consortium is meeting the challenge of representing species-specific protein complexes, how protein complex representation in PRO supports annotation of protein  ...  Representing species-specific proteins and protein complexes in ontologies that are both humanand machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets.  ...  Acknowledgements The Protein Ontology is supported by National Institutes of Health (R01GM080646) and supplement grants (R01GM080646-03S1, R01GM080646-04S2  ... 
doi:10.1186/1471-2105-12-371 pmid:21929785 pmcid:PMC3189193 fatcat:zrv5okkqg5cnzdisysikm3wfzm

Knowledge Representation of Protein PTMs and Complexes in the Protein Ontology: Application to Multi-Faceted Disease Analysis

Karen Ross, Catalina O. Tudor, Gang Li, Ruoyao Ding, Irem Çelen, Julie Cowart, Cecilia N. Arighi, Darren A. Natale, Cathy H. Wu
2014 International Conference on Biomedical Ontology  
PRO framework for representation of PTM forms, complexes, and protein families, as well as their attributes and relationships.  ...  The Protein Ontology (PRO) is a valuable resource to study the relation between PTM and disease because it represents individual proteins and protein complex subunits at the proteoform (e.g., isoform,  ...  Used in conjunction with other bioinformatic resources, the Protein Ontology (http://pir.georgetown.edu/pro/pro.shtml; PRO [5] ) enables the structured representation and interpretation of this information  ... 
dblp:conf/icbo/RossTLDCCANW14 fatcat:ujiodx2jgjeivmqcvmvu2pkyfa

Representing Modification Sites in PRO

Jonathan P. Bona, Alan Ruttenberg, Jenny Rouleau
2014 International Conference on Biomedical Ontology  
This paper presents a model for explicit representations of amino acid sites in the protein ontology.  ...  We handle sites that are the locations of post-translational modifications, focusing on histone proteins as our initial test case.  ...  INTRODUCTION The Protein Ontology [1] (PRO) "... provides an ontological representation of protein-related entities by explicitly defining them and showing the relationships between them." 1 Representable  ... 
dblp:conf/icbo/BonaRR14 fatcat:jnrcy4gmabhrbd3siqz4crqpuu

Protein Ontology (PRO): enhancing and scaling up the representation of protein entities

Darren A. Natale, Cecilia N. Arighi, Judith A. Blake, Jonathan Bona, Chuming Chen, Sheng-Chih Chen, Karen R. Christie, Julie Cowart, Peter D'Eustachio, Alexander D. Diehl, Harold J. Drabkin, William D. Duncan (+10 others)
2016 Nucleic Acids Research  
The Protein Ontology (PRO; http://purl.obolibrary. org/obo/pr) formally defines and describes taxonspecific and taxon-neutral protein-related entities in three major areas: proteins related by evolution  ...  To enhance this ability, and to facilitate the comparison of such entities described in different resources, we developed a standardized representation of proteoforms using UniProtKB as a sequence reference  ...  ACKNOWLEDGEMENTS The authors thank the collaborating groups mentioned in this manuscript for their contribution to PRO and/or usage of PRO. Author contributions are as follows: Writing  ... 
doi:10.1093/nar/gkw1075 pmid:27899649 pmcid:PMC5210558 fatcat:xwzphiew4rcuzjmvb55fw4wf5i

Bronchoalveolar lavage (BAL) cells in idiopathic pulmonary fibrosis express a complex pro-inflammatory, pro-repair, angiogenic activation pattern, likely associated with macrophage iron accumulation

Jungnam Lee, Ivan Arisi, Ermanno Puxeddu, Lazarus K. Mramba, Massimo Amicosante, Carmen M. Swaisgood, Marco Pallante, Mark L. Brantly, C. Magnus Sköld, Cesare Saltini, Gernot Zissel
2018 PLoS ONE  
Bronchoalveolar lavage (BAL) cells in idiopathic pulmonary fibrosis express a complex proinflammatory, pro-repair, angiogenic activation pattern, likely associated with macrophage iron accumulation.  ...  O'Donnell for English language editing the manuscript and Federica Sangiuolo (University Tor Vergata, Roma, IT) for her help at the inception of this study.  ...  Gene Ontology and Pathway analysis of differentially expressed genes in IPF, was performed using the iPathways web resource (http://www.advaitabio.com/ipathwayguide) with the Gene Ontology (GO) Consortium  ... 
doi:10.1371/journal.pone.0194803 pmid:29649237 pmcid:PMC5896901 fatcat:3qebomqb7nbljjfm6oz3fhn4s4

Microglia: Agents of the CNS Pro-Inflammatory Response

José A. Rodríguez-Gómez, Edel Kavanagh, Pinelopi Engskog-Vlachos, Mikael K.R. Engskog, Antonio J. Herrera, Ana M. Espinosa-Oliva, Bertrand Joseph, Nabil Hajji, José L. Venero, Miguel A. Burguillos
2020 Cells  
Finally, we also discuss current thoughts on the impact of pro-inflammatory microglia in neurodegenerative diseases.  ...  This review aimed to discuss our current knowledge of pro-inflammatory microglia from different angles, including recent research highlights such as the role of exosomes in spreading neuroinflammation  ...  Schematic representation of epigenetic control of the inflammatory response in microglia.  ... 
doi:10.3390/cells9071717 pmid:32709045 fatcat:cwi4itpcrzgjje3k6nh73uwte4

Pro-tumorigenic Effects of miR-31 Loss in Mesothelioma

Sergey V. Ivanov, Chandra M. V. Goparaju, Peter Lopez, Jiri Zavadil, Ginat Toren-Haritan, Shai Rosenwald, Moshe Hoshen, Ayelet Chajut, Dalia Cohen, Harvey I. Pass
2010 Journal of Biological Chemistry  
Re-introduction of miR-31 suppressed the cell cycle and inhibited expression of multiple factors involved in cooperative maintenance of DNA replication and cell cycle progression, including pro-survival  ...  We and others previously linked loss of the 9p21.3 chromosome in MM with short time to tumor recurrence.  ...  Acknowledgments-We thank the New York University Cancer Institute Genomics Facility for expert assistance with gene expression profiling.  ... 
doi:10.1074/jbc.m110.100354 pmid:20463022 pmcid:PMC2906272 fatcat:hm2jzrrvejhqxns7w4qsyxhklq

Alterations in the chondrocyte surfaceome in response to pro-inflammatory cytokines

Bernadette Jeremiasse, Csaba Matta, Christopher R. Fellows, David J. Boocock, Julia R. Smith, Susan Liddell, Floris Lafeber, Willem E. van Spil, Ali Mobasheri
2020 BMC Molecular and Cell Biology  
Our results provide, for the first time, a repository for proteomic data on differentially expressed low-abundance membrane proteins on the surface of chondrocytes in response to pro-inflammatory stimuli  ...  A high number of proteins exhibited different expression patterns following chondrocyte stimulation with pro-inflammatory cytokines.  ...  Cytokine treatment results in the over-representation of different pathways and protein interactions When the proteins uniquely identified in either control or cytokine-treated samples were submitted to  ... 
doi:10.1186/s12860-020-00288-9 pmid:32586320 fatcat:gwcfatsafvboveyyqis33vbtlm

Oral Neutrophil Transcriptome Changes Result in a Pro-Survival Phenotype in Periodontal Diseases

Flavia S. Lakschevitz, Guy M. Aboodi, Michael Glogauer, Charles C. Caldwell
2013 PLoS ONE  
Periodontal diseases are inflammatory processes that occur following the influx of neutrophils into the periodontal tissues in response to the subgingival bacterial biofilm.  ...  In the present study we compare the gene expression profile changes in neutrophils as they migrate from the circulation into the oral tissues in patients with chronic periodontits and matched healthy subjects  ...  Acknowledgments The authors give special thanks to Chunxiang Sun and Yongqiang Wang (Matrix Dynamics Group, University of Toronto) for their help with laboratory work; Pingzhao Hu (Statistical Analysis  ... 
doi:10.1371/journal.pone.0068983 pmid:23874838 pmcid:PMC3708893 fatcat:3c6t3vsxxfa2rexqhxhg25sfsy

Phosphoproteomics reveals network rewiring to a pro-adhesion state in annexin-1-deficient mammary epithelial cells

Asfa Alli-Shaik, Sheena Wee, Lina H. K. Lim, Jayantha Gunaratne
2017 Breast Cancer Research  
A majority of these phosphorylation changes occurred on proteins associated with cytoskeletal reorganization spanning the focal adhesion, stress fibers, and also the microtubule network proposing new roles  ...  Integrative analysis revealed regulation of the WNT and Hippo signaling pathways in ANXA1-deficient mammary epithelial cells, wherein there is downregulation of transcriptional effects of TEA domain family  ...  Funding This work is supported by the Agency for Science, Technology and Research (A*STAR), Singapore.  ... 
doi:10.1186/s13058-017-0924-4 pmid:29233185 pmcid:PMC5727667 fatcat:byuhloabgjedjgjkmt5jqtwpsq

Transcriptional activator TAp63 is upregulated in muscular atrophy during ALS and induces the pro-atrophic ubiquitin ligase Trim63

Yannick von Grabowiecki, Paula Abreu, Orphee Blanchard, Lavinia Palamiuc, Samir Benosman, Sophie Mériaux, Véronique Devignot, Isabelle Gross, Georg Mellitzer, José L Gonzalez de Aguilar, Christian Gaiddon
2016 eLife  
In particular, we observed increased p63 protein levels in the fibers of atrophic muscles via denervation-dependent and -independent mechanisms.  ...  We then characterized the induction of several p53 family members (p53, p63, p73) and a correlation between the levels of p53 family target genes and the severity of muscle atrophy in ALS patients and  ...  of patients and under the ethical rules established by the Italian ethical counsel.  ... 
doi:10.7554/elife.10528 pmid:26919175 pmcid:PMC4786414 fatcat:x35jrd5r2fdhlfxb7sq5yai6xy

Expression and functional activity of pro-oxidants and antioxidants in murine heart exposed to acute hypobaric hypoxia

Jayashree Karar, Karamjit S. Dolt, Manoj K. Mishra, Ehtesham Arif, Saleem Javed, M.A. Qadar Pasha
2007 FEBS Letters  
Interestingly, the protein level of Cyba, a subunit of NADPH oxidase, was markedly decreased in AHH exposed heart, suggesting the involvement of some stress response pathways.  ...  The AHH exposure also caused a significant reduction (50%) in the level of GSH (P < 0.05). The present study provides a retrospective insight on the cellular antioxidant defense mechanisms under AHH.  ...  Divekar, Defence Institute of Physiology and Allied Sciences for their co-operation in the simulation experiments. We also thank Mr. Raj, Institute of Genomics and Integrative Biology and Ms.  ... 
doi:10.1016/j.febslet.2007.08.044 pmid:17825300 fatcat:jzarvpc2jvgjdcywxv5rghhgze

A balance between NF-Y and p53 governs the pro- and anti-apoptotic transcriptional response

Paolo Benatti, Valentina Basile, Daniele Merico, Luca Isaia Fantoni, Enrico Tagliafico, Carol Imbriano
2008 Nucleic Acids Research  
A role of p53 and Bcl-2 family members is important. NF-YB inactivation is sufficient to functionally activate p53, in the absence of DNA damage.  ...  In this study, we examined the functional and molecular effects of NF-YB knockdown. Cell cycle progression is affected with a G2/M-specific depletion.  ...  The translocation of p53 to the mitochondria and the formation of complexes with the anti-apoptotic Bcl-2 family proteins induce the release of sequestered pro-apoptotic proteins and subsequent permeabilization  ... 
doi:10.1093/nar/gkm1046 pmid:18187512 pmcid:PMC2275158 fatcat:mwnzaggltfegdmu372sj3mtv3u

Computational drug repositioning for peripheral arterial disease: prediction of anti-inflammatory and pro-angiogenic therapeutics

Liang-Hui Chu, Brian H. Annex, Aleksander S. Popel
2015 Frontiers in Pharmacology  
By compiling the drug information in two drug databases DrugBank and PharmGKB, we predict FDA-approved drugs whose targets are the proteins annotated as anti-angiogenic and pro-inflammatory, respectively  ...  Specifically, the proteins in the PADPIN were classified as belonging to the angiome, immunome, and arteriome, characterizing the processes of angiogenesis, immune response/inflammation, and arteriogenesis  ...  Acknowledgments LC, AP, and BA proposed the idea; LC implemented the simulation; LC, BA, and AP edited the paper.  ... 
doi:10.3389/fphar.2015.00179 pmid:26379552 pmcid:PMC4548203 fatcat:ytgomb4c4ffedabepqvkekvvmu

Novel identified aluminum hydroxide-induced pathways prove monocyte activation and pro-inflammatory preparedness

Sietske Kooijman, Jolanda Brummelman, Cécile A.C.M. van Els, Fabio Marino, Albert J.R. Heck, Geert P.M. Mommen, Bernard Metz, Gideon F.A. Kersten, Jeroen L.A. Pennings, Hugo D. Meiring
2018 Journal of Proteomics  
Significance: Aluminum salts are the most used adjuvants in human vaccines but a comprehensive understanding of the working mechanism of alum adjuvants at the molecular level is still elusive.  ...  This study highlights the mechanisms of the most commonly used adjuvant in human vaccines by combing proteomics, transcriptomics and cytokine analysis revealing new potential mechanisms of action for Al  ...  We acknowledge Hilde Vrieling for performing the autofluorescent verification experiments for the flow cytometry data and for the THP-1 set up experiments.  ... 
doi:10.1016/j.jprot.2017.12.021 pmid:29317357 fatcat:h6zae2pcofd6dc4bzksxesiafa
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