A flexible protocol for targeted gene co-expression network analysis
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Author / Producer
Date
2014
Publication Type
Book Chapter
ETH Bibliography
yes
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Abstract
The inference of gene co-expression networks is a valuable resource for novel hypotheses in experimental research. Routine high-throughput microarray transcript profiling experiments and the rapid development of next-generation sequencing (NGS) technologies generate a large amount of publicly available data, enabling in silico reconstruction of regulatory networks. Analysis of the transcriptome under various experimental conditions proved that genes with an overall similar expression pattern often have similar functions. Consistently, genes involved in the same metabolic pathway are found in co-expressed modules. In this chapter, we describe a detailed workflow for analyzing gene co-expression networks using large-scale gene expression data and explain critical steps from design and data analysis to prediction of functionally related modules. This protocol is platform independent and can be used for data generated by ATH1 arrays, tiling arrays, or RNA sequencing for any organism. The most important feature of this workflow is that it can infer statistically significant gene co-expression networks for any number of genes and transcriptome data sets and it does not involve any particular hardware requirements.
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Publication status
published
Book title
Plant Isoprenoids
Journal / series
Volume
1153
Pages / Article No.
285 - 299
Publisher
Humana Press
Event
Edition / version
Methods
Software
Geographic location
Date collected
Date created
Subject
Co-expression; Isoprenoids; Circadian clock; Gene module; Network; Transcriptome
Organisational unit
03554 - Gruissem, Wilhelm (emeritus) / Gruissem, Wilhelm (emeritus)