GlyCosmos Portal

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Welcome to GlyCosmos

The GlyCosmos Portal is a Web portal aiming to integrate the glycosciences with the life sciences. It consists of Standards, Repositories and Data Resources, providing information about genes, proteins, lipids, pathways and diseases.

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Search by text Search by organisms Search by graphic Search by mass GNOme Structure Browser Search by composition

Glycan Converters Programmatic Access

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GlyCosmos PubAnnotations

Genes 393515 Entries

Integrated list of glycan-related genes extracted KEGG GENES Database, UniProt, GlycoGene Database (GGDB), Plant GARDEN and FlyGlycoDB. Glycan-related genes including glycosyltransferase, hydrolase activity (acting on glycosyl bonds), carbohydrate metabolic process, etc .

Glycoproteins 126547 Entries

Integrated list of glycoproteins extracted from UniProt and annotated with glycosylation data from GlyGen, GlyConnect, GlycoProtDB and The O-GlcNAc Database. For each entry, information such as glycosylation site, glycans, diseases, 3D structures, and pathway information are available.

Lectins 5271 Entries

Integrated list of Lectins, including proteins with carbohydrate binding function obtained from UniProt and lectin data from Lectin Frontier DataBase (LfDB), UniLectin and CarboGrove. Glycosylation site information, along with glycan-binding patterns are also integrated where available.

Glycolipids 6046 Entries

Glycolipid entries from the LIPID MAPS Structure Database (LMSD).

Glycans 244842 Entries

The list of validated glycans extracted from GlyTouCan, updated weekly.

Pathways 8115 Entries

Integrated of pathway data, containing glycoproteins and glycans obtained from Reactome and the Metabolism of carbohydrates in Escherichia coli O-antigens obtained from ECODAB. Search by pathway name, species, and protein name.

Diseases 7942 Entries

List of diseases involving glycan related genes. The information of each database of Glyco-Disease Genes Database (GDGDB), DisGeNET, and Alliance of Genome Resources is integrated into one list.

Organisms 30690 Entries

List of all species in GlyCosmos Resources.

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SugarDrawer

SugarDrawer is a simple user interface providing the basic functionality for drawing and searching glycan structures with known topology. Those who wish to draw more complex glycans can use the Web version of GlycanBuilder.

GlycanBuilder

Web-based user interface for GlycanBuilder, with all the functionality provided by the standalone version. Databases including GlyTouCan, GlyCosmos glycans and GlycoNAVI can also be searched.

Glycan Converters

Glycan structure conversion tools between WURCS, GlycoCT, IUPAC, etc. Image generation and validation functionality are also available.

GlycoMaple

GlycoMaple is a visualization tool for glycosylation pathways in human and mouse. Glycogene expression data can be uploaded or selected from RNA-Seq data from the Human Protein Atlas in the mouse version. Similar data can be selected from Mouse Haemopedia for cell lines in mouse. The expression values will be reflected across various glycan-related pathways at once, and comparisons can be made between samples.

GlycomeAtlas

GlycomeAtlas is a specialised database that provides comprehensive information on glycan structures and their distribution in different human, mouse and zebrafish t

LM-GlycomeAtlas

LM-GlycomeAtlas is a web tool visualizing the data from Lectin Array analyses by the Kuno Laboratory at AIST.

GALAXY

GALAXY (Glycoanalysis by the Three Axes of MS and Chromatography) is a database of elution data on glycan structures of glycoproteins analysed by high-performance liquid chromatography (HPLC). The database includes data on 650 neutral, sialylated, glucuronylated, and/or sulfated N-linked oligosaccharides, which are expressed by a diagram in the shape of a tree with a tri-mannosyl core as the trunk and spreading branches .

MCAW

Glycan structure alignment tool for multiple glycan structures to analyze their commonalities as glycan profiles.

GlycoSim

Glycan biosynthesis simulation tool.

GRable

GRable is a software to estimate site-specific glycan compositions of glycopeptides, using an MS1-based glycoproteomic method named “Glyco-RIDGE” [Narimatsu et al. JPR2018].

Programmatic Access

News

New update to GlyCosmos has been released with new data for lectins, glycan species and updated glycan search functionality! See https://t.co/ZdhxWXkHbI for details.
— GlyCosmos (@GlyCosmos) December 18, 2023

Bridging Glycoinformatics and cheminformatics: integration efforts between GlyCosmos and PubChem | Glycobiology | Oxford Academic https://t.co/RIsTfoTZo2
— GlyCosmos (@GlyCosmos) May 3, 2023

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Other Related Resources

Alliance of Genome Resources

is a collaborative initiative focused on the genetics and genomics of key model organisms. It integrates data from various Model Organism Databases (MODs) into a unified system, combining the best features of each while maintaining community integrity. Current MODs include budding yeast, Caenorhabditis elegans, Drosophila, zebrafish, frog, mouse, rat, and the Gene Ontology Consortium.The Alliance of Genome Resources database features comprehensive datasets on disease associations and expression annotations across various model organisms.
Alliance of Genome Resources Consortium, 2024

CarboGrove

is a resource for analysed glycan array data. Using its ability to process and interpret data from all types of glycan arrays, the database contains results from 35 types of glycan arrays, 13 glycan families, 5 experimental methods, and 19 laboratories or companies.

CAZy

is a specialist database dedicated to the display and analysis of genomic, structural and biochemical information on Carbohydrate-Active Enzymes (CAZymes) and describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.

DisGeNET

integrates information on human gene-disease associations (GDAs) and variant-disease associations (VDAs) from various repositories including Mendelian, complex, and environmental diseases. The integration is performed using gene and disease vocabulary mapping and by using the DisGeNET association type ontology.
Piñero J, et al, 2020

GlycoBase

is a relational database which contains the HPLC elution positions for over 350 2-AB labelled N-glycan structures together with predicted products of exoglycosidase digestions.
Campbell MP, et al, 2008

GlycoEpitope

is a specialized database focused on glycan epitopes, which are the specific parts of glycan molecules recognized by antibodies. It provides detailed information on the structural features of glycan epitopes, their associated glycan structures, and their roles in immunological recognition. This database is a valuable resource for researchers studying glycan-antibody interactions, vaccine design, and the development of glycan-based diagnostics and therapeutics.

Glycoinformatics Consortium (GLIC)

provides and maintains a centralized source of software and databases for glycoscientists.

Glycomics@ExPASy

is the glycomics section of the SIB Bioinformatics Resource Portal which provides access to scientific databases and software tools in different areas of life sciences.

GlyConnect

is a specialized database dedicated to glycosylation and glycan-related information. It provides comprehensive data on glycan structures, glycosylation sites on proteins, and the enzymes involved in glycan biosynthesis and modification. GlyConnect integrates data from various sources to facilitate the study of glycan-protein interactions, glycan function in biological processes, and the role of glycosylation in health and disease. This resource is particularly useful for researchers exploring glycoscience, glycoproteomics, and the impact of glycosylation on protein function and cellular processes.

GlycoSim

is a Web tool to simulate glycosylation pathways.

GlycoStore

is a curated chromatographic, electrophoretic and mass-spectrometry composition database of N-, O-, glycosphingolipid (GSL) glycans and free oligosaccharides associated with a range of glycoproteins, glycolipids and biotherapeutics.
Campbell MP, et al, 2022

GlyGen

is a comprehensive database that focuses on glycomics, offering detailed information on glycan structures, glycoproteins, and glycosylation-related data. It provides an integrated view of glycan composition, glycosylation sites on proteins, and glycan-binding proteins, along with related functional annotations. GlyGen supports the study of glycan biology by facilitating the analysis of glycosylation patterns, glycan-protein interactions, and their implications in various biological contexts and diseases.

Human Phenotype Ontology

provides a standardized vocabulary of phenotypic abnormalities encountered in human disease.
Gargano MA, et al, 2024

jPOST

is a proteomic database to integrate proteome datasets generated from multiple projects and institutions.

KEGG

is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.

LIPID MAPS Gene/Proteome Database (LMPD)

is comprised of lipid-related genes and proteins; LMPD contains data from Homo sapiens, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae, Caenorhabditis elegans, Escherichia coli, Macaca mulata, Drosophila melanogaster, Arabidopsis thaliana and Danio rerio.
Cotter D, et al, 2006

LIPID MAPS Structure Database (LMSD)

is a relational database encompassing structures and annotations of biologically relevant lipids and making it the largest public lipid-only database in the world.
Sud M, et al, 2007

MatrixDB

is a specialized database that provides information on extracellular matrix (ECM) proteins, their interactions, and related glycosaminoglycans. It catalogs the complex networks of ECM components and their roles in cell signaling, tissue structure, and disease processes.
Clerc O, et al, 2019

MIRAGE

(Minimum Information Required for A Glycomics Experiment) guidelines for publishing glycomics-related research articles.

PDBj

is part of the Japanese National Project on Protein Structural and Functional Analyses.

Plant GARDEN

has a vast collection of plant genomes that users can access and analyze. The database includes genomes of various plant species, belonging to diverse taxa, including angiosperms, gymnosperms, and algae.

PSICQUIC

is a tool designed for querying and retrieving data from various protein-protein interaction (PPI) databases. It provides a unified search interface that allows researchers to access and integrate interaction data from multiple sources, including databases like IntAct, MINT, DIP, and others.

PubChem

is an open chemistry database at the National Institutes of Health (NIH).

Reactome

is a comprehensive, open-source database that provides detailed information on biological pathways and processes. It includes curated pathways of human biology, encompassing molecular interactions, reactions, and cellular processes. Reactome is used by researchers to explore gene functions, understand disease mechanisms, and integrate large-scale data sets for systems biology studies.
Milacic M, et al, 2024

SugarBind

is a specialized database that catalogs the interactions between pathogenic microorganisms and host glycans. It focuses on identifying the specific glycan structures that pathogens bind to during infection processes. This resource aids researchers in understanding host-pathogen interactions, which can lead to the development of targeted therapies and diagnostic tools.
Mariethoz J, et al, 2015

The Human Protein Atlas

is a Swedish-based program initiated in 2003 with the aim to map all the human proteins in cells, tissues, and organs using an integration of various omics technologies, including antibody-based imaging, mass spectrometry-based proteomics, transcriptomics, and systems biology.

The O-GlcNAc Database

provides detailed information on O-GlcNAc-modified proteins, their modification sites, and the associated biological functions and processes. It integrates data on the enzymes responsible for O-GlcNAcylation, such as O-GlcNAc transferase and O-GlcNAcase, and their roles in cellular signaling and regulation.
Wulff-Fuentes E, et al, 2021

UniCarb-DB

is a repository of glycomics mass spectrometry data.

UniLectin

is a database dedicated to lectins, which are carbohydrate-binding proteins involved in a variety of biological processes, including cell-cell recognition, immune response, and pathogen-host interactions. UniLectin provides comprehensive information on lectin sequences, structures, carbohydrate specificities, and biological functions. It also includes data on lectin-ligand interactions and their roles in different physiological and pathological contexts.
Schnider B, et al, 2024

UniProt

is a comprehensive protein sequence and functional information database. It provides detailed, curated data on protein sequences, functions, structures, and interactions. UniProt is a crucial resource for researchers in proteomics and genomics, offering insights into protein function, biological processes, and disease associations.
UniProt Consortium, 2023

GlyTouCan

GlyComb

GlycoPOST

UniCarb-DR

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