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Sánchez Laguna, Juan Antonio

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Sánchez Laguna, Juan Antonio
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Universidad de Murcia. Departamento de Ingeniería de la Informacióny las Comunicaciones
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    Modeling multifunctionality of genes with secondary gene co-expression networks in human brain provides novel disease insights
    (Oxford University Press, 2021-03-18) Sánchez Laguna, Juan Antonio; Gil Martínez, Ana Luisa; Cisterna, Alejandro; García Ruiz, Sonia; Gómez Pascual, Alicia; Reynolds, Regina H.; Botía Blaya, Juan Antonio; Nalls, Mike; Hardy, John; Ryten, Mina; Ingeniería de la Información y las Comunicaciones; Facultades de la UMU::Facultad de Informática
    Motivation Co-expression networks are a powerful gene expression analysis method to study how genes co-express together in clusters with functional coherence that usually resemble specific cell type behavior for the genes involved. They can be applied to bulk-tissue gene expression profiling and assign function, and usually cell type specificity, to a high percentage of the gene pool used to construct the network. One of the limitations of this method is that each gene is predicted to play a role in a specific set of coherent functions in a single cell type (i.e. at most we get a single for each gene). We present here GMSCA (Gene Multifunctionality Secondary Co-expression Analysis), a software tool that exploits the co-expression paradigm to increase the number of functions and cell types ascribed to a gene in bulk-tissue co-expression networks. Results We applied GMSCA to 27 co-expression networks derived from bulk-tissue gene expression profiling of a variety of brain tissues. Neurons and glial cells (microglia, astrocytes and oligodendrocytes) were considered the main cell types. Applying this approach, we increase the overall number of predicted triplets by 46.73%. Moreover, GMSCA predicts that the SNCA gene, traditionally associated to work mainly in neurons, also plays a relevant function in oligodendrocytes.
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