An annotated and curated relational database of glycan structures reported in the literature. GlycoSuiteDB contains information on the glycan type, core type, linkages and anomeric configurations, mass, composition and the analytical methods used by the researchers to determine the glycan structure.
Profiling N-linked glycopeptides is a particularly promising method because the population of N-linked glycosites represents the proteomes of plasma, the cell surface, and secreted proteins at very low redundancy and provides a compelling link between the tissue and plasma proteomes. UniPep is a database of human N-linked glycosites.
A database of glycoproteins with O-linked glycosylation sites. The criteria for inclusion are at least one experimentally verified O- or C-glycosylation site. The terminal sugar linked to serine or threonine is cited when known. O-GlycBase is non-redundant in the sense that it contains no identical sequences, unless there is conflicting glycosylation data.
Gathers information about bacterial and archaeal glycoproteins. ProGlycProt is a repository of published information and provides enough experimental information in the relationship between a glycoprotein, its oligosaccharyl/glycosyl transferases (OSTs/GTs), protein glycosylation-linked gene(s) and their genomic context. This database supplies an estimation of the extent of occurrence of protein glycosylation in prokaryotes.
A repository of 72 E. coli K antigens that provides information about sugar compositions, their anomeric and enantiomeric forms and linkages between the sugar monomers. The database also has the collection of 3D structural models of the K antigen repeating units that are derived from the above information. As the classification of E. coli into group 1, 2, 3 and 4 is developed based on K antigens, the database also contains information about the group based serotyping of E. coli K antigens. As the capsules are molecules of 100–10000 kD multimers, the database also provides the facility to generate polymeric structures of K antigen repeat units.
An innovative tool for analyzing glycan profiling data, without regard to the manner in which it has been obtained. GlycomeAtlas allows users to visualize and perform queries of glycome data. GlycomeAtlas is pre-loaded with glycome data as provided by the Consortium for Functional Glycomics (CFG). Moreover, users can load their own local glycome data into this tool to visualize and perform queries on their own data.
A mass spectrometry-based glycoproteomic characterization of zebrafish embryos was performed to identify the N-linked glycoproteins and N-linked glycosylation sites. To increase the number of glycopeptides, proteins from zebrafish were digested with two different proteases--chymotrypsin and trypsin--into peptides of different length. The N-glycosylated peptides of zebrafish were then captured by the solid-phase extraction of N-linked glycopeptides (SPEG) method and the peptides were identified with an LTQ OrbiTrap Velos mass spectrometer.
Protein glycosylation affects cellular functions of the central nervous system (CNS). GlycoFly is a database for Drosophila N-linked glycopeptides. It has been established as a resource for study of neurological disorders.
A glycoprotein database providing information of Asn (N)-glycosylated proteins and their glycosylated site(s), which were constructed by employing a bottom-up strategy using actual glycopeptide sequences identified by LC/MS-based glycoproteomic technologies. Current contents are glycoproteins identified from model organisms C.elegans and mouse (C57BL/6, male). The database is searchable using gene ID, gene name, and its description (protein name) as query.
Provides a list of all available experimental information on agl (archaeal glycosylation) genes and proteins. Aglgenes offers a web interface that does not requires any particular training. It includes a single search field that allows user to search through all published experimental data on genes and proteins involved in archaeal N-glycosylation. This database allows users to submit updates on existing entries or new information on archaeal N-glycosylation pathway components.
A meta-database involving 15 original databases in AIST and 5 cooperative databases in alliance with JCGG: Japan Consortium for Glycobiology and Glycotechnology. JCGGDB centers on a glycan structure database and accumulates information such as glycan preferences of lectins, glycosylation sites in proteins, and genes related to glycan syntheses from glycoscience and related fields.
Assists data interpretation to bring glycan analysis within the reach of any well-established laboratory. GlycoBase provides an open-access relational database of glycan structures and primary research data, accessed via a web-based interface. It was designed to support HILIC 2-aminobenzamide (2AB) approaches with an open-source philosophy intended to enhance software development, data management, and to progress the application of glycoinformatics in glycomics and glycoproteomics.
A database of O-GlcNAcylated proteins and sites based on experimental data curated from literature as well as from collaborating labs. The resource will facilitate research on O-GlcNAcylation and its proteomic identification.
Identifies glycosylation relevance in gut barrier in response to commensal and pathogenic bacteria for modulating the gut immune tolerance. The GlycoGAIT is a web database whose interface enables the users to quickly compare or interpret changes in expression patterns of glycome genomics below different gut associated inflammatory conditions. This tool delivers informations for glycogene expression analysis under inflammatory disease conditions. It brings also the gene set of glycogenes along with lectins along with publically available gene expression data obtained from human gastric biopsy samples with dysregulated immune function that aids in the systematic analysis of the gene expression changes in disease conditions at the transcriptome level.
Dr. Yashwanth Subbannayya obtained his M.Sc. degree in Medical Biochemistry from Manipal University. He qualified the competitive CSIR-UGC National Eligibility Test and joined the Institute of Bioinformatics, Bangalore as a UGC Junior Research Fellow. As part of his Ph.D. work, he studied the molecular mechanisms of gastric cancer in clinical specimens using quantitative proteomic technologies. This study, the results of which were published in Cancer Biology and Therapy, yielded a novel therapeutic target for gastric cancer- CAMKK2. Further, he also studied the serum proteome of gastric cancer patients and developed assays for potential markers using the revolutionary multiple reaction monitoring approach. The results of this study were published in Journal of Proteomics. In addition to his research work, he also trained extensively in sample preparation for mass spectrometry, fractionation techniques and gained expertise in quantitative proteomic techniques and data analysis. In addition, he also trained extensively in various validation platforms including immunohistochemsitry, multiple reaction monitoring and Western blot. He has also worked as a curator for several biological databases including NetPath, Human Protein Reference Database (HPRD) and Breast cancer database. His work in various research projects have yielded him 23 publications either as lead author or co-author in peer reviewed journals. He is a reviewer for the journal Proteomics.
Dr. Yashwanth Subbannayya joined the YU-IOB Center for Systems Biology and Molecular Medicine in June, 2015. During the initial period, his job consisted of assisting other personnel of the university in the establishment of YU-IOB Center for Systems Biology and Molecular Medicine. He was also involved in training of Ph.D. students in biological aspects. After the establishment of the center, he trained in cell culture techniques and metabolomics analysis. At YU-IOB CSBMM, he is studying the molecular mechanisms in various cancers including oral cancer. In addition, he is studying the molecular mechanisms as well as the metabolic constituents of traditional medicine formulations using mass spectrometry technologies. In June 2016, he convened the national symposium “Genomics in clinical practice: Future of precision medicine” held at Yenepoya University on June 1 and 2, 2016. The resource persons included 16 individuals from various academic organizations as well as industry. The symposium was attended by 218 participants from 24 institutions around India. He is a member of the Scientific Review Board of Yenepoya Research Centre where he facilitates timely scientific review of research projects.
Serge Perez Director of Research CNRS
French National Centre for Scientific Research