Genome-wide analysis of gene expression

Genome-wide analysis of gene expression is the study of transcription at a genomic scale, also known as transcriptomics. Typically relying on data from microarrays or high throughput sequencing, it can determine what genes or transcript isoforms are enriched in a particular cell or tissue type, condition, disease or phenotype.

Latest Research and Reviews

  • Reviews |

    The functional interpretation of single-cell RNA sequencing (scRNA-seq) data can be enhanced by integrating additional data types beyond RNA-based gene expression. In this Review, Stuart and Satija discuss diverse approaches for integrative single-cell analysis, including experimental methods for profiling multiple omics types from the same cells, analytical approaches for extracting additional layers of information directly from scRNA-seq data and computational integration of omics data collected across different cell samples.

    • Tim Stuart
    •  & Rahul Satija
  • Reviews |

    Single-cell RNA sequencing (scRNA-seq) enables transcriptome-based characterization of the constituent cell types within a heterogeneous sample. However, reliable analysis and biological interpretation typically require optimal use of clustering algorithms. This Review discusses the multiple algorithmic options for clustering scRNA-seq data, including various technical, biological and computational considerations.

    • Vladimir Yu Kiselev
    • , Tallulah S. Andrews
    •  & Martin Hemberg
  • Research |

    A substantially improved genome assembly of Medicago truncatula generated using PacBio sequencing allows for the analyses about genome rearrangements, transposable elements, new players and candidate genomic regions involved in nodule development.

    • Yann Pecrix
    • , S. Evan Staton
    • , Erika Sallet
    • , Christine Lelandais-Brière
    • , Sandra Moreau
    • , Sébastien Carrère
    • , Thomas Blein
    • , Marie-Françoise Jardinaud
    • , David Latrasse
    • , Mohamed Zouine
    • , Margot Zahm
    • , Jonathan Kreplak
    • , Baptiste Mayjonade
    • , Carine Satgé
    • , Magali Perez
    • , Stéphane Cauet
    • , William Marande
    • , Céline Chantry-Darmon
    • , Céline Lopez-Roques
    • , Olivier Bouchez
    • , Aurélie Bérard
    • , Frédéric Debellé
    • , Stéphane Muños
    • , Abdelhafid Bendahmane
    • , Hélène Bergès
    • , Andreas Niebel
    • , Julia Buitink
    • , Florian Frugier
    • , Moussa Benhamed
    • , Martin Crespi
    • , Jérôme Gouzy
    •  & Pascal Gamas
    Nature Plants 4, 1017-1025
  • Reviews |

    Transcriptome profiling in different brain regions has revealed distinct patterns of gene and non-coding RNA expression, as well as alternative splicing, in autism spectrum disorder (ASD). The authors review these ASD-associated signatures and the resulting mechanistic insights into ASD.

    • Mathieu Quesnel-Vallières
    • , Robert J. Weatheritt
    • , Sabine P. Cordes
    •  & Benjamin J. Blencowe

News and Comment