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      Social network architecture of human immune cells unveiled by quantitative proteomics

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          Abstract

          Immune cells give rise to the most interconnected system in the body. Meissner and colleagues perform comprehensive proteomics and secretomics to describe in detail the ‘social network’ of human immune cells and throw light on previously unknown cell connectivities.

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          Gene Ontology: tool for the unification of biology

          Michael Ashburner, Catherine A. Ball, Judith Blake … (2002)
          Genomic sequencing has made it clear that a large fraction of the genes specifying the core biological functions are shared by all eukaryotes. Knowledge of the biological role of such shared proteins in one organism can often be transferred to other organisms. The goal of the Gene Ontology Consortium is to produce a dynamic, controlled vocabulary that can be applied to all eukaryotes even as knowledge of gene and protein roles in cells is accumulating and changing. To this end, three independent ontologies accessible on the World-Wide Web (http://www.geneontology.org) are being constructed: biological process, molecular function and cellular component.
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            The Proteomics Identifications (PRIDE) database and associated tools: status in 2013

            Juan Antonio Vizcaíno, Richard Côté, Attila Csordas … (2012)
            The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride) database at the European Bioinformatics Institute is one of the most prominent data repositories of mass spectrometry (MS)-based proteomics data. Here, we summarize recent developments in the PRIDE database and related tools. First, we provide up-to-date statistics in data content, splitting the figures by groups of organisms and species, including peptide and protein identifications, and post-translational modifications. We then describe the tools that are part of the PRIDE submission pipeline, especially the recently developed PRIDE Converter 2 (new submission tool) and PRIDE Inspector (visualization and analysis tool). We also give an update about the integration of PRIDE with other MS proteomics resources in the context of the ProteomeXchange consortium. Finally, we briefly review the quality control efforts that are ongoing at present and outline our future plans.
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              CCR7 and its ligands: balancing immunity and tolerance.

              Reinhold Förster, Ana Clara Davalos-Misslitz, Antal Rot (2008)
              A key feature of the immune system is its ability to induce protective immunity against pathogens while maintaining tolerance towards self and innocuous environmental antigens. Recent evidence suggests that by guiding cells to and within lymphoid organs, CC-chemokine receptor 7 (CCR7) essentially contributes to both immunity and tolerance. This receptor is involved in organizing thymic architecture and function, lymph-node homing of naive and regulatory T cells via high endothelial venules, as well as steady state and inflammation-induced lymph-node-bound migration of dendritic cells via afferent lymphatics. Here, we focus on the cellular and molecular mechanisms that enable CCR7 and its two ligands, CCL19 and CCL21, to balance immunity and tolerance.
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                Author and article information

                Journal
                Title: Nature Immunology
                Abbreviated Title: Nat Immunol
                Publisher: Springer Nature
                ISSN (Print): 1529-2908
                ISSN (Electronic): 1529-2916
                Publication date Created: March 6 2017
                Publication date (Print): March 6 2017
                Volume:
                Issue:
                Article
                DOI: 10.1038/ni.3693
                PubMed ID: 28263321
                SO-VID: 12d33571-f37c-4613-9293-42a467b52663
                Copyright © © 2017
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