Transformation and model choice for RNA-seq co-expression analysis

Transformation and model choice for RNA-seq co-expression analysis.

Although a large number of clustering algorithms have been proposed to identify groups of co-expressed genes from microarray data, the question of if and how such methods may be applied to RNA sequencing (RNA-seq) data remains unaddressed. In this work, we investigate the use of data transformations in conjunction with Gaussian mixture models for RNA-seq co-expression analyses, as well as a pen...

Canonical correlation analysis for RNA-seq co-expression networks

Digital transcriptome analysis by next-generation sequencing discovers substantial mRNA variants. Variation in gene expression underlies many biological processes and holds a key to unravelling mechanism of common diseases. However, the current methods for construction of co-expression networks using overall gene expression are originally designed for microarray expression data, and they overlo...

Systematic analysis of RNA-seq-based gene co-expression

The complex cellular network was formed by the interacting gene modules. Building 10 the high-quality RNA-seq-based Gene Co-expression Network (GCN) is critical for 11 uncovering these modules and understanding the phenotypes of an organism. Here, 12 we established and analyzed the RNA-seq-based GCNs in two monocot species rice 13 and maize, and two eudicot species Arabidopsis and soybean, and ...

Differential Expression Analysis for RNA-Seq Data

RNA-Seq is increasingly being used for gene expression profiling. In this approach, next-generation sequencing (NGS) platforms are used for sequencing. Due to highly parallel nature, millions of reads are generated in a short time and at low cost. Therefore analysis of the data is a major challenge and development of statistical and computational methods is essential for drawing meaningful conc...

AuPairWise : a method to estimate RNA - seq 1 replicability through co - expression 2 3 RNA - seq replicability via co - expression