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      An extension of Drugst.One for expert curation and refinement of disease modules

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            Abstract

            Understanding diseases is difficult due to a lack of insight into the underlying biological mechanisms, resulting in imprecise treatments based solely on symptoms. Disease modules offer distinct perspectives on complex diseases and establish a basis for mechanistic drug repurposing. However, disease module inference does not pay attention to pathway annotations. Since drug repurposing aims to hint at biological pathways, this information is crucial and should be considered when exploring the underlying mechanisms within protein-protein interaction networks.

            Drugst.One, a versatile web tool for disease module visualization and drug repurposing, does not offer pathway enrichment and visualization. To enable deeper analyses of these modules, we extended existing functionality in Drugst.One with functionality for investigating enriched pathways. Our extension for Drugst.Onesupports genesets from KEGG, Reactome, and WikiPathways. Further, we offer network clustering methods to detect communities.

            This advancement contrasts previous methods by providing a user-friendly approach for comprehensive pathway analysis and module refinement within the Drugst.One framework suited for expert curation. Contributing to the broader context of computational drug repurposing and disease module interpretation, this extension offers a streamlined approach for assessing pathway involvement and functional refinement within disease modules.

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            Author and article information

            Conference
            RExPO24 Conference
            REPO4EU
            2 May 2024
            Affiliations
            [1 ] Technical University of Munich, Munich, Germany ( https://ror.org/02kkvpp62)
            [2 ] University of Hamburg, Hamburg, Germany ( https://ror.org/00g30e956)
            [3 ] Maastricht University, Maastricht, The Netherlands ( https://ror.org/02jz4aj89)
            [4 ] Zagazig University, Zagazig, Egypt ( https://ror.org/053g6we49)
            Author notes
            Author information
            https://orcid.org/0009-0007-3502-3033
            https://orcid.org/0000-0002-5706-2718
            https://orcid.org/0000-0002-3882-0093
            https://orcid.org/0000-0002-3992-0125
            https://orcid.org/0000-0003-4408-0068
            https://orcid.org/0000-0002-4201-7973
            https://orcid.org/0000-0003-0419-5549
            https://orcid.org/0000-0002-0282-0462
            https://orcid.org/0000-0002-0941-4168
            Article
            10.58647/REXPO.24000044.v1
            1c2f8832-d373-43f1-bdfb-2f9b85e758aa

            This work has been published open access under Creative Commons Attribution License CC BY 4.0 , which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Conditions, terms of use and publishing policy can be found at www.scienceopen.com .

            RExPO24
            3
            Munich, Germany
            3-5 July 2024
            History
            : 2 May 2024
            Product

            REPO4EU

            Funding
            Funded by: funder-id , European Union;
            Award ID: 101057619
            Categories

            Data sharing not applicable to this article as no datasets were generated or analysed during the current study.
            Bioinformatics & Computational biology
            Disease module refinement,actionable signaling modules,pathway enrichment visualization,Drugst.One,protein-protein interaction networks,expert curation,drug repurposing,semi-manual approach

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