EndoNet: an information resource about endocrine networks

Потапов, А. П.; Liebich, Ines; Dönitz, Jürgen; Schwarzer, Knut; Sasse, Nicole; Schoeps, Torsten; Crass, Torsten; Wingender, Edgar

doi:10.1093/nar/gkj121

Cited by 11 publications

(6 citation statements)

References 20 publications

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“…In comparison with the previous release published in 2006 ( 16 ), the number of entries for hormones, receptors and cells/tissues/organs and in particular the number of connections between these entities has significantly increased as shown in Table 1 . In the publicly accessible version, there are no orphan entries for hormones and receptors: that is, all of them are linked to the corresponding receptor or ligand entities, respectively, thereby increasing the size and the edge density of the whole network.…”

Section: Contentsmentioning

confidence: 78%

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EndoNet: an information resource about regulatory networks of cell-to-cell communication

Dönitz

Goemann

Lizé

et al. 2007

Nucleic Acids Research

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EndoNet is an information resource about intercellular regulatory communication. It provides information about hormones, hormone receptors, the sources (i.e. cells, tissues and organs) where the hormones are synthesized and secreted, and where the respective receptors are expressed. The database focuses on the regulatory relations between them. An elementary communication is displayed as a causal link from a cell that secretes a particular hormone to those cells which express the corresponding hormone receptor and respond to the hormone. Whenever expression, synthesis and/or secretion of another hormone are part of this response, it renders the corresponding cell an internal node of the resulting network. This intercellular communication network coordinates the function of different organs. Therefore, the database covers the hierarchy of cellular organization of tissues and organs as it has been modeled in the Cytomer ontology, which has now been directly embedded into EndoNet. The user can query the database; the results can be used to visualize the intercellular information flow. A newly implemented hormone classification enables to browse the database and may be used as alternative entry point. EndoNet is accessible at: http://endonet.bioinf.med.uni-goettingen.de/

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Section: Contentsmentioning

confidence: 78%

“…The need to combine the available information on cell-to-cell interaction was realized recently when the EndoNet database was developed ( 16 ). Many of such intercellular regulatory pathways display the property of a cascade in which the initial signal is multiplied over several steps.…”

Section: Introductionmentioning

confidence: 99%

EndoNet: an information resource about regulatory networks of cell-to-cell communication

Dönitz

Goemann

Lizé

et al. 2007

Nucleic Acids Research

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“…The results from text-mining were cross-checked with the contents of the EndoNet database [43] and the confirmed entities were used as seed proteins in the BIANA tool for reconstruction of the dementia-related hormonal network (DHN) at level 2 [44]. The initial protein-protein interaction network was constructed around the seed set.…”

Section: Methodsmentioning

confidence: 99%

A network model of genomic hormone interactions underlying dementia and its translational validation through serendipitous off-target effect

Younesi

Hofmann‐Apitius

2013

Journal of Translational Medicine

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BackgroundWhile the majority of studies have focused on the association between sex hormones and dementia, emerging evidence supports the role of other hormone signals in increasing dementia risk. However, due to the lack of an integrated view on mechanistic interactions of hormone signaling pathways associated with dementia, molecular mechanisms through which hormones contribute to the increased risk of dementia has remained unclear and capacity of translating hormone signals to potential therapeutic and diagnostic applications in relation to dementia has been undervalued.MethodsUsing an integrative knowledge- and data-driven approach, a global hormone interaction network in the context of dementia was constructed, which was further filtered down to a model of convergent hormone signaling pathways. This model was evaluated for its biological and clinical relevance through pathway recovery test, evidence-based analysis, and biomarker-guided analysis. Translational validation of the model was performed using the proposed novel mechanism discovery approach based on ‘serendipitous off-target effects’.ResultsOur results reveal the existence of a well-connected hormone interaction network underlying dementia. Seven hormone signaling pathways converge at the core of the hormone interaction network, which are shown to be mechanistically linked to the risk of dementia. Amongst these pathways, estrogen signaling pathway takes the major part in the model and insulin signaling pathway is analyzed for its association to learning and memory functions. Validation of the model through serendipitous off-target effects suggests that hormone signaling pathways substantially contribute to the pathogenesis of dementia.ConclusionsThe integrated network model of hormone interactions underlying dementia may serve as an initial translational platform for identifying potential therapeutic targets and candidate biomarkers for dementia-spectrum disorders such as Alzheimer’s disease.

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“…Various type of databases; for example SwePep [ 9 ] for endogenous peptides and PepBank [ 10 ] for peptides collected from literature using text mining tools, came into existence recently. There are a few databases which maintain information about ligands and their receptors like PRRDB [ 11 ], GLIDA [ 12 ], and EndoNet [ 13 ]. PRRDB, an immunological database, provides information regarding Pattern Recognition Receptors and their ligands.…”

Section: Introductionmentioning

confidence: 99%

Hmrbase: a database of hormones and their receptors

et al. 2009

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BackgroundHormones are signaling molecules that play vital roles in various life processes, like growth and differentiation, physiology, and reproduction. These molecules are mostly secreted by endocrine glands, and transported to target organs through the bloodstream. Deficient, or excessive, levels of hormones are associated with several diseases such as cancer, osteoporosis, diabetes etc. Thus, it is important to collect and compile information about hormones and their receptors.DescriptionThis manuscript describes a database called Hmrbase which has been developed for managing information about hormones and their receptors. It is a highly curated database for which information has been collected from the literature and the public databases. The current version of Hmrbase contains comprehensive information about ~2000 hormones, e.g., about their function, source organism, receptors, mature sequences, structures etc. Hmrbase also contains information about ~3000 hormone receptors, in terms of amino acid sequences, subcellular localizations, ligands, and post-translational modifications etc. One of the major features of this database is that it provides data about ~4100 hormone-receptor pairs. A number of online tools have been integrated into the database, to provide the facilities like keyword search, structure-based search, mapping of a given peptide(s) on the hormone/receptor sequence, sequence similarity search. This database also provides a number of external links to other resources/databases in order to help in the retrieving of further related information.ConclusionOwing to the high impact of endocrine research in the biomedical sciences, the Hmrbase could become a leading data portal for researchers. The salient features of Hmrbase are hormone-receptor pair-related information, mapping of peptide stretches on the protein sequences of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission, DrugPedia linkage etc. Hmrbase is available online for public from .

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EndoNet: an information resource about endocrine networks

Cited by 11 publications

References 20 publications

EndoNet: an information resource about regulatory networks of cell-to-cell communication

EndoNet: an information resource about regulatory networks of cell-to-cell communication

A network model of genomic hormone interactions underlying dementia and its translational validation through serendipitous off-target effect

Hmrbase: a database of hormones and their receptors

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