Related Experiment Video
Updated: Apr 18, 2026
Analyzing Multifactorial RNA-Seq Experiments with DiCoExpress
Published on: July 29, 2022
Co-expression analysis of high-throughput transcriptome sequencing data with Poisson mixture models
Andrea Rau1, Cathy Maugis-Rabusseau2, Marie-Laure Martin-Magniette3
1INRA, UMR1313 Génétique animale et biologie intégrative, Jouy-en-Josas, France, AgroParisTech, UMR1313 Génétique animale et biologie intégrative, Paris 05, France, Institut de Mathématiques de Toulouse, INSA de Toulouse, Université de Toulouse, Toulouse, France, UMR AgroParisTech/INRA MIA 518, Paris, France, INRA, UMR 1165 URGV, Saclay Plant Sciences, Evry, France, UEVE, UMR URGV, Saclay Plant Sciences, Evry, France, CNRS, ERL 8196, URGV, Saclay Plant Sciences, Evry, France and Inria Saclay - Île-de-France, Orsay, France INRA, UMR1313 Génétique animale et biologie intégrative, Jouy-en-Josas, France, AgroParisTech, UMR1313 Génétique animale et biologie intégrative, Paris 05, France, Institut de Mathématiques de Toulouse, INSA de Toulouse, Université de Toulouse, Toulouse, France, UMR AgroParisTech/INRA MIA 518, Paris, France, INRA, UMR 1165 URGV, Saclay Plant Sciences, Evry, France, UEVE, UMR URGV, Saclay Plant Sciences, Evry, France, CNRS, ERL 8196, URGV, Saclay Plant Sciences, Evry, France and Inria Saclay - Île-de-France, Orsay, France.
Motivation:
In recent years, gene expression studies have increasingly made use of high-throughput sequencing technology. In turn, research concerning the appropriate statistical methods for the analysis of digital gene expression (DGE) has flourished, primarily in the context of normalization and differential analysis.
Results:
In this work, we focus on the question of clustering DGE profiles as a means to discover groups of co-expressed genes. We propose a Poisson mixture model using a rigorous framework for parameter estimation as well as the choice of the appropriate number of clusters. We illustrate co-expression analyses using our approach on two real RNA-seq datasets. A set of simulation studies also compares the performance of the proposed model with that of several related approaches developed to cluster RNA-seq or serial analysis of gene expression data.
Availability And And Implementation:
The proposed method is implemented in the open-source R package HTSCluster, available on CRAN.
Contact:
andrea.rau@jouy.inra.fr
Supplementary Information:
Supplementary data are available at Bioinformatics online.
Related Concept Videos
03:21RNA-seq
Before the discovery of RNA-seq, microarray-based methods and Sanger sequencing were used for transcriptome analysis. However, while...
01:09Poisson Probability Distribution
The...
02:24Ribosome Profiling
Applications of ribosome profiling
Ribosome profiling has many applications, including in vivo monitoring of translation inside a particular organ or tissue type and quantifying new protein synthesis levels.
The technique...
01:23Poisson's Ratio