AmyCo: the amyloidoses collection

Nastou, Katerina C.; Nasi, Georgia I.; Tsiolaki, Paraskevi L.; Litou, Zoi I.; Iconomidou, Vassiliki A.

doi:10.1080/13506129.2019.1603143

Cited by 13 publications

(5 citation statements)

References 57 publications

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“…Despite the mystery surrounding clusterin’s implication in AD, it is a known fact that it co-localizes with A β fibrillar deposits (12). This is also true for other amyloidoses, in which clusterin is an amyloid associated protein (17).…”

Section: Introductionmentioning

confidence: 87%

Clusterin in Alzheimer’s disease: an amyloidogenic inhibitor of amyloid formation

Spatharas

Nasi

Tsiolaki

et al. 2021

Preprint

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Clusterin is a heterodimeric glycoprotein (alpha- and beta-chain), which has been described as an extracellular molecular chaperone. In humans, clusterin is an amyloid associated protein, co-localizing with fibrillar deposits in several amyloidoses, including Alzheimer's disease. To clarify its potential implication in amyloid formation, we located aggregation-prone regions within the sequence of clusterin a-chain, via computational methods. We had peptide-analogues of each region chemically synthesized and experimentally demonstrated that all of them can form amyloid-like fibrils. We also provide evidence that the same peptide-analogues can inhibit amyloid-beta fibril formation. These findings elucidate parts of the molecular mechanism in which clusterin inhibits amyloid formation. At the same time, they hint that molecular chaperones with amyloidogenic properties might have a role in the regulation of amyloid formation, essentially acting as functional amyloids.

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Section: Introductionmentioning

confidence: 87%

Clusterin in Alzheimer’s disease: an amyloidogenic inhibitor of amyloid formation

Spatharas

Nasi

Tsiolaki

et al. 2021

Preprint

Self Cite

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“…The Amyloidoses Collection (AmyCo) database specifically collects information on amyloidoses and other diseases related to amyloid deposition ( 29 ). It contains manually curated data from 249 articles on 75 diseases classified into two broad groups: amyloidoses and clinical conditions associated with amyloidosis, including precursors and proteins co-deposited with amyloid deposits.…”

Section: Methodsmentioning

confidence: 99%

Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration

et al. 2022

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The scientific knowledge about which genes are involved in which diseases grows rapidly, which makes it difficult to keep up with new publications and genetics datasets. The DISEASES database aims to provide a comprehensive overview by systematically integrating and assigning confidence scores to evidence for disease–gene associations from curated databases, genome-wide association studies (GWAS) and automatic text mining of the biomedical literature. Here, we present a major update to this resource, which greatly increases the number of associations from all these sources. This is especially true for the text-mined associations, which have increased by at least 9-fold at all confidence cutoffs. We show that this dramatic increase is primarily due to adding full-text articles to the text corpus, secondarily due to improvements to both the disease and gene dictionaries used for named entity recognition, and only to a very small extent due to the growth in number of PubMed abstracts. DISEASES now also makes use of a new GWAS database, Target Illumination by GWAS Analytics, which considerably increased the number of GWAS-derived disease–gene associations. DISEASES itself is also integrated into several other databases and resources, including GeneCards/MalaCards, Pharos/Target Central Resource Database and the Cytoscape stringApp. All data in DISEASES are updated on a weekly basis and is available via a web interface at https://diseases.jensenlab.org, from where it can also be downloaded under open licenses. Database URL: https://diseases.jensenlab.org

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“…These aggregates, known as "amyloid fibrils", have been associated with a diverse group of diseases known as "amyloidoses"; examples include the Alzheimer's and Parkinson's diseases, Type 2 diabetes, Creutzfeldt-Jakob Syndrome and many others. AmyCo (the Amyloidoses Collection) [245] is a freely available collection of amyloidoses and other clinical disorders related to amyloid deposition. AmyCo classifies 75 diseases into 2 distinct categories, amyloidoses and other clinical conditions associated with amyloidoses.…”

Section: Disease-related Interactionsmentioning

confidence: 99%

Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review

et al. 2021

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Technological advances in high-throughput techniques have resulted in tremendous growth of complex biological datasets providing evidence regarding various biomolecular interactions. To cope with this data flood, computational approaches, web services, and databases have been implemented to deal with issues such as data integration, visualization, exploration, organization, scalability, and complexity. Nevertheless, as the number of such sets increases, it is becoming more and more difficult for an end user to know what the scope and focus of each repository is and how redundant the information between them is. Several repositories have a more general scope, while others focus on specialized aspects, such as specific organisms or biological systems. Unfortunately, many of these databases are self-contained or poorly documented and maintained. For a clearer view, in this article we provide a comprehensive categorization, comparison and evaluation of such repositories for different bioentity interaction types. We discuss most of the publicly available services based on their content, sources of information, data representation methods, user-friendliness, scope and interconnectivity, and we comment on their strengths and weaknesses. We aim for this review to reach a broad readership varying from biomedical beginners to experts and serve as a reference article in the field of Network Biology.

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AmyCo: the amyloidoses collection

Abstract: Welcome to AmyCo, a freely available, literature-curated collection of amyloidoses and other pathological conditions associated with the deposition of amyloid fibrils. Manual Contents 1.

Cited by 13 publications

References 57 publications

Clusterin in Alzheimer’s disease: an amyloidogenic inhibitor of amyloid formation

Clusterin in Alzheimer’s disease: an amyloidogenic inhibitor of amyloid formation

Diseases 2.0: a weekly updated database of disease–gene associations from text mining and data integration

Biomolecule and Bioentity Interaction Databases in Systems Biology: A Comprehensive Review

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