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  1. Article: KeyPathwayMineR:

    Mechteridis, Konstantinos / Lauber, Michael / Baumbach, Jan / List, Markus

    Frontiers in genetics

    2022  Volume 12, Page(s) 812853

    Abstract: ... De ... ...

    Abstract De novo
    Language English
    Publishing date 2022-01-31
    Publishing country Switzerland
    Document type Journal Article ; Review
    ZDB-ID 2606823-0
    ISSN 1664-8021
    ISSN 1664-8021
    DOI 10.3389/fgene.2021.812853
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  2. Article ; Online: KeyPathwayMineR

    Konstantinos Mechteridis / Michael Lauber / Jan Baumbach / Markus List

    Frontiers in Genetics, Vol

    De Novo Pathway Enrichment in the R Ecosystem

    2022  Volume 12

    Abstract: De novo pathway enrichment is a systems biology approach in which OMICS data are projected onto a molecular interaction network to identify subnetworks representing condition-specific functional modules and molecular pathways. Compared to classical ... ...

    Abstract De novo pathway enrichment is a systems biology approach in which OMICS data are projected onto a molecular interaction network to identify subnetworks representing condition-specific functional modules and molecular pathways. Compared to classical pathway enrichment analysis methods, de novo pathway enrichment is not limited to predefined lists of pathways from (curated) databases and thus particularly suited for discovering novel disease mechanisms. While several tools have been proposed for pathway enrichment, the integration of de novo pathway enrichment in end-to-end OMICS analysis workflows in the R programming language is currently limited to a single tool. To close this gap, we have implemented an R package KeyPathwayMineR (KPM-R). The package extends the features and usability of existing versions of KeyPathwayMiner by leveraging the power, flexibility and versatility of R and by providing various novel functionalities for performing data preparation, visualization, and comparison. In addition, thanks to its interoperability with a plethora of existing R packages in e.g., Bioconductor, CRAN, and GitHub, KPM-R allows carrying out the initial preparation of the datasets and to meaningfully interpret the extracted subnetworks. To demonstrate the package’s potential, KPM-R was applied to bulk RNA-Seq data of nasopharyngeal swabs from SARS-CoV-2 infected individuals, and on single cell RNA-Seq data of aging mice tissue from the Tabula Muris Senis atlas.
    Keywords pathway enrichment ; network analysis ; data integration ; systems biology ; R package ; Genetics ; QH426-470
    Subject code 004
    Language English
    Publishing date 2022-01-01T00:00:00Z
    Publisher Frontiers Media S.A.
    Document type Article ; Online
    Database BASE - Bielefeld Academic Search Engine (life sciences selection)

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