Articles producció científica> Enginyeria Química

Variation-preserving normalization unveils blind spots in gene expression profiling

  • Dades identificatives

    Identificador: PC:2705
    Autors:
    Roca, C.P.Gomes, S.I.L.Amorim, M.J.B.Scott-Fordsmand, J.J.
    Resum:
    RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following the implicit assumption that most genes are not differentially expressed. Here, we present a mathematical approach to normalization that makes no assumption of this sort. We have found that variation in gene expression is much larger than currently believed, and that it can be measured with available assays. Our results also explain, at least partially, the reproducibility problems encountered in transcriptomics studies. We expect that this improvement in detection will help efforts to realize the full potential of gene expression profiling, especially in analyses of cellular processes involving complex modulations of gene expression.
  • Altres:

    Autor segons l'article: Roca, C.P.; Gomes, S.I.L.; Amorim, M.J.B.; Scott-Fordsmand, J.J.
    Departament: Enginyeria Química
    Autor/s de la URV: PEREZ ROCA, CARLOS; Gomes, S.I.L.; Amorim, M.J.B.; Scott-Fordsmand, J.J.
    Paraules clau: gene expression profiling reproducibility Gene expression regulation
    Resum: RNA-Seq and gene expression microarrays provide comprehensive profiles of gene activity, but lack of reproducibility has hindered their application. A key challenge in the data analysis is the normalization of gene expression levels, which is currently performed following the implicit assumption that most genes are not differentially expressed. Here, we present a mathematical approach to normalization that makes no assumption of this sort. We have found that variation in gene expression is much larger than currently believed, and that it can be measured with available assays. Our results also explain, at least partially, the reproducibility problems encountered in transcriptomics studies. We expect that this improvement in detection will help efforts to realize the full potential of gene expression profiling, especially in analyses of cellular processes involving complex modulations of gene expression.
    Àrees temàtiques: Enginyeria química Ingeniería química Chemical engineering
    Accès a la llicència d'ús: https://creativecommons.org/licenses/by/3.0/es/
    ISSN: 2045-2322
    Identificador de l'autor: ; n/a; n/a; 0000-0002-2260-1224
    Data d'alta del registre: 2017-03-28
    Volum de revista: 7
    Versió de l'article dipositat: info:eu-repo/semantics/publishedVersion
    Enllaç font original: https://www.nature.com/articles/srep42460
    URL Document de llicència: https://repositori.urv.cat/ca/proteccio-de-dades/
    DOI de l'article: 10.1038/srep42460
    Entitat: Universitat Rovira i Virgili
    Any de publicació de la revista: 2017
    Tipus de publicació: Article Artículo Article
  • Paraules clau:

    Expressió gènica -- Mètodes estadístics
    Microxips de DNA -- Mètodes estadístics
    gene expression profiling
    reproducibility
    Gene expression regulation
    Enginyeria química
    Ingeniería química
    Chemical engineering
    2045-2322
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