Dataset Information

SugarBindDB, a resource of glycan-mediated host-pathogen interactions.

ABSTRACT: The SugarBind Database (SugarBindDB) covers knowledge of glycan binding of human pathogen lectins and adhesins. It is a curated database; each glycan-protein binding pair is associated with at least one published reference. The core data element of SugarBindDB is a set of three inseparable components: the pathogenic agent, a lectin/adhesin and a glycan ligand. Each entity (agent, lectin or ligand) is described by a range of properties that are summarized in an entity-dedicated page. Several search, navigation and visualisation tools are implemented to investigate the functional role of glycans in pathogen binding. The database is cross-linked to protein and glycan-relaled resources such as UniProtKB and UniCarbKB. It is tightly bound to the latter via a substructure search tool that maps each ligand to full structures where it occurs. Thus, a glycan-lectin binding pair of SugarBindDB can lead to the identification of a glycan-mediated protein-protein interaction, that is, a lectin-glycoprotein interaction, via substructure search and the knowledge of site-specific glycosylation stored in UniCarbKB. SugarBindDB is accessible at: http://sugarbind.expasy.org.

SUBMITTER: Mariethoz J

PROVIDER: S-EPMC4702881 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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SugarBindDB, a resource of glycan-mediated host-pathogen interactions.

Mariethoz Julien J Khatib Khaled K Alocci Davide D Campbell Matthew P MP Karlsson Niclas G NG Packer Nicolle H NH Mullen Elaine H EH Lisacek Frederique F

Nucleic acids research 20151117 D1

The SugarBind Database (SugarBindDB) covers knowledge of glycan binding of human pathogen lectins and adhesins. It is a curated database; each glycan-protein binding pair is associated with at least one published reference. The core data element of SugarBindDB is a set of three inseparable components: the pathogenic agent, a lectin/adhesin and a glycan ligand. Each entity (agent, lectin or ligand) is described by a range of properties that are summarized in an entity-dedicated page. Several sear ...[more]

PMID: 26578555

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Project description:The goal of this project is to understand the etiology and pathology of host-pathogen interaction using high-throughput cellular phenotyping. By combining the expertise in pathogen biology, informatics and stem cell biology across the institute, this project will use targeted genetic modification in mouse embryonic stem cells to identify functions of host genes in innate immunity. We will also explore the biology of mouse embryonic stem cells and their differentiation into immune competent cells. To this end we will generate homozygous and inducible knockout lines in mouse embryonic stem cells, which will be differentiated into immune competent cells, such as macrophages or dendritic cells. These will be subjected to a panel of immune challenge and stimulation assays to characterise the functions of the disrupted genes. To identify new functions for mammalian genes in innate immunity we will:\Generate a panel of homozygous inducible gene knockout mouse ES cell lines working from a list of ca. 80 candidate genes (MGP phenotyping and GWAS hits). \Scale up differentiation protocols for immune challenge and stimulation assays.\Benchmark in vitro differentiated ES cell models against primary immune cells from selected MGP mouse lines and eventually against human iPS cells.\Screen a panel of 30 genetically modified cell lines in immunological challenge and stimulation assays, defining phenotypes at the cellular level by high content imaging, biochemically by assaying cytokine production, and at the molecular level by transcriptome analysis.\Define novel gene functions in innate immunity through network analysis of gene expression data from all challenged cell lines.\In the longer term scale up the production and phenotyping of genetically modified cell lines (mouse or human as appropriate).This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/

Dataset Information

SugarBindDB, a resource of glycan-mediated host-pathogen interactions.

Publications

SugarBindDB, a resource of glycan-mediated host-pathogen interactions.

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