Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

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Guidance for RNA-seq co-expression network construction and analysis: safety in numbers

MOTIVATION RNA-seq co-expression analysis is in its infancy and reasonable practices remain poorly defined. We assessed a variety of RNA-seq expression data to determine factors affecting functional connectivity and topology in co-expression networks. RESULTS We examine RNA-seq co-expression data generated from 1970 RNA-seq samples using a Guilt-By-Association framework, in which genes are as...

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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...

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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...

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ژورنال

عنوان ژورنال: Bioinformatics

سال: 2015

ISSN: 1460-2059,1367-4803

DOI: 10.1093/bioinformatics/btv118